query
stringlengths 9
9.05k
| document
stringlengths 10
222k
| negatives
listlengths 19
20
| metadata
dict |
|---|---|---|---|
Get the interaction sites, which describe the position of interacting mutations in the genotypes. (type==list of lists, see self._build_interaction_sites)
|
def sites(self):
return self.data.sites.values
|
[
"def get_sites(self):\n st = self.site_text\n suffixes = [' residue', ' residues', ',', '/']\n for suffix in suffixes:\n if st.endswith(suffix):\n st = st[:-len(suffix)]\n assert(not st.endswith(','))\n\n # Strip parentheses\n st = st.replace('(', '')\n st = st.replace(')', '')\n st = st.replace(' or ', ' and ') # Treat end and or the same\n\n sites = []\n parts = st.split(' and ')\n for part in parts:\n if part.endswith(','):\n part = part[:-1]\n if len(part.strip()) > 0:\n sites.extend(ReachProcessor._parse_site_text(part.strip()))\n return sites",
"def genes(self) -> List[Gene]:\n return self.__genes",
"def locations(self):\n return self.__locations",
"def list_chemical_gene_interactions(self) -> List[ChemGeneIxn]:\n return self._list_model(ChemGeneIxn)",
"def reactant_species(self):\n return tuple([s.specie for s in self.reactants])",
"def get_unique_site_indices(structure: Structure | Molecule):\n spins = []\n oxi_states = []\n parsable_site_properties = {\n \"magmom\",\n \"oxi_state\",\n \"spin\",\n \"u_minus_j\",\n \"basis\",\n \"potential\",\n \"ghost\",\n \"aux_basis\",\n }\n\n for site in structure:\n for sp in site.species:\n oxi_states.append(getattr(sp, \"oxi_state\", 0))\n spins.append(getattr(sp, \"_properties\", {}).get(\"spin\", 0))\n\n structure.add_site_property(\"oxi_state\", oxi_states)\n structure.add_site_property(\"spin\", spins)\n structure.remove_oxidation_states()\n items = [\n (\n site.species_string,\n *[\n structure.site_properties[k][i]\n for k in structure.site_properties\n if k.lower() in parsable_site_properties\n ],\n )\n for i, site in enumerate(structure)\n ]\n unique_itms = list(set(items))\n _sites: dict[tuple, list] = {u: [] for u in unique_itms}\n for i, itm in enumerate(items):\n _sites[itm].append(i)\n sites = {}\n nums = {s: 1 for s in structure.symbol_set}\n for s in _sites:\n sites[f\"{s[0]}_{nums[s[0]]}\"] = _sites[s]\n nums[s[0]] += 1\n\n return sites",
"def get_sites(self):\n return self.sites.all()",
"def _all_pseudo_sites(self):\n def _all_restraint_sites():\n for r in self._all_restraints():\n if hasattr(r, 'cross_links'):\n for xl in r.cross_links:\n if xl.pseudo1:\n for x in xl.pseudo1:\n yield x.site\n if xl.pseudo2:\n for x in xl.pseudo2:\n yield x.site\n return itertools.chain(self.orphan_pseudo_sites,\n _all_restraint_sites(),\n (f.site for f in self._all_features()\n if hasattr(f, 'site') and f.site))",
"def extract_extra_sites(self):\n\n # weighting arrays for the virtual sites should not be changed\n w1o, w2o, w3o = 1.0, 0.0, 0.0 # SUM SHOULD BE 1\n w1x, w2x, w3x = -1.0, 1.0, 0.0 # SUM SHOULD BE 0\n w1y, w2y, w3y = -1.0, 0.0, 1.0 # SUM SHOULD BE 0\n\n with open('xyz_with_extra_point_charges.xyz') as xyz_sites:\n lines = xyz_sites.readlines()\n\n sites = OrderedDict()\n sites_no = 0\n for i, line in enumerate(lines[2:]):\n # get the current element\n element = str(line.split()[0])\n\n if element != 'X':\n # search the following entries for sites connected to this atom\n for pos_site in lines[i + 3:]:\n if str(pos_site.split()[0]) != 'X':\n # if there are no sites break and start the next loop\n break\n else:\n # get the virtual site coords\n v_pos = array([float(pos_site.split()[x]) for x in range(1, 4)])\n # get parent index number for the topology network\n parent = i + 1 - sites_no\n # get the two closest atoms to the parent\n closet_atoms = list(self.molecule.topology.neighbors(parent))\n if len(closet_atoms) < 2:\n # find another atom if we only have one\n # dont want to get the parent as a close atom\n closet_atoms.append(list(self.molecule.topology.neighbors(closet_atoms[0]))[-1])\n\n # Get the xyz coordinates of the reference atoms\n parent_pos = array(self.molecule.molecule['qm'][parent - 1][1:])\n close_a = array(self.molecule.molecule['qm'][closet_atoms[0] - 1][1:])\n close_b = array(self.molecule.molecule['qm'][closet_atoms[1] - 1][1:])\n\n # work out the local coordinates site using rules from the OpenMM guide\n orig = w1o * parent_pos + w2o * close_a + close_b * w3o\n ab = w1x * parent_pos + w2x * close_a + w3x * close_b # rb-ra\n ac = w1y * parent_pos + w2y * close_a + w3y * close_b # rb-ra\n # Get the axis unit vectors\n z_dir = cross(ab, ac)\n z_dir = z_dir / sqrt(dot(z_dir, z_dir.reshape(3, 1)))\n x_dir = ab / sqrt(dot(ab, ab.reshape(3, 1)))\n y_dir = cross(z_dir, x_dir)\n # Get the local coordinates positions\n p1 = dot((v_pos - orig), x_dir.reshape(3, 1))\n p2 = dot((v_pos - orig), y_dir.reshape(3, 1))\n p3 = dot((v_pos - orig), z_dir.reshape(3, 1))\n\n charge = float(pos_site.split()[4])\n\n # store the site info [(parent top no, a, b), (p1, p2, p3), charge]]\n sites[sites_no] = [(parent - 1, closet_atoms[0] - 1, closet_atoms[1] - 1), (p1 / 10, p2 / 10, p3 / 10), charge]\n sites_no += 1\n\n self.molecule.sites = sites\n\n # get the parent non bonded values\n for value in sites.values():\n charge, sigma, eps = self.non_bonded_force[value[0][0]]\n # Change the charge on the first entry\n charge = float(charge) - value[2]\n self.non_bonded_force[value[0][0]] = [str(charge), sigma, eps]",
"def positions(self):\n return get_positions(as_numpy=True).reshape((self.natom, 3))",
"def interactions(self):\n return self.__graph.labels()",
"def source_interactions(self, species):\n return self.__graph.parent_edges(species)",
"def interpretations(self):\n return self._interpretations",
"def interset(genotypes):\n\tsnplist = map(lambda x: getsnps(x), genotypes)\n\tprint len(snplist)\n\tineverything = reduce(lambda x,y: set(x) & set(y), snplist)\n\treturn ineverything",
"def structure_site_mappings(self):\n return [entry.data[\"site_mapping\"] for entry in self._entries]",
"def get_species(self, species):\n\n atoms = [site for site in self.sites\n if site.species_string == species]\n\n return atoms",
"def get_positions(self):\n return [package.position for package in self.active]",
"def known_solutions(self):\n return self._solver_instance.solutions_at_points",
"def get_locations(self) -> np.ndarray:\n return np.transpose(self.state[:, :, Boids.Attr.LOC])"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
List of site labels. Each site is represented as a list of labels returned by the `label_mapper` (see `get_label_mapper`).
|
def labels(self):
mapper = self.get_label_mapper()
labels = ['w.t.']
for term in self.sites[1:]:
labels.append([mapper[site] for site in term])
return labels
|
[
"def get_labels(self):\n return label_list",
"def list_labels(self):\n return list(self.repo.labels.list())",
"def getLabelsList(self):\n return HopperLowLevel.getLabelsList(self.__internal_segment_addr__)",
"def get_labels(self):\n return self.labels_list",
"def get_labels(self):\n if not self.labels:\n return []\n\n return [x.label for x in self.labels]",
"def get_labels(self):\n labels = []\n for g, graph in enumerate(self.graphs):\n for s in xrange(len(graph.sets)):\n label = \"G%dS%d\" % (g, s)\n labels.append(label)\n return labels",
"def get_labels(self):\n\t\tld = {}\n\t\tfor label in self.labels:\n\t\t\ttokens = label.split(\":\")\n\t\t\tld[tokens[0]] = tokens[1]\n\t\treturn ld",
"def labels_normalized(self):\n if self._db_searchinfo:\n labels = [\n rec[\"normalized_string\"]\n for rec in self._db_searchinfo\n if rec[\"category\"] == SEARCH_CATEGORY_LABEL\n ]\n else:\n labels = []\n return labels",
"def labels(self):\n return self._labels.copy()",
"def get_labels(self) -> list:\n # return [label[0] for label in self.indicators]\n labels = []\n for label, indicator in self.indicators:\n indicator_label = indicator.label\n if isinstance(indicator_label, list):\n labels.extend(indicator_label)\n else:\n labels.append(indicator_label)\n return labels",
"def getLabels(self):\n labels = []\n for category in self.totalForCategory:\n labels.append(category.name)\n return labels",
"def labels(data: CoNLLChunking) -> Set[str]:\n return {label for l_samples in data.label for label in l_samples}",
"def node_labels(self) -> pulumi.Output[Mapping[str, str]]:\n return pulumi.get(self, \"node_labels\")",
"def dimension_labels(self):\n return [dim.label for dim in self]",
"def get_labels(self):\n return {get_label_path(img) for img in self.imgs}",
"def app_labels(apps_list):\n return [get_app_label(app) for app in apps_list]",
"def label_map(self):\n return self._label_map",
"def sites(self):\n return self.data.sites.values",
"def list_sites(self):\n pass"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get epistasis of a given order.
|
def get_orders(self, *orders):
return EpistasisMapReference(self.data, orders)
|
[
"def get_ephemerides(hdr=None, return_eph=True, loc=None, epoch=None, target=None,\n cache=False, **kwargs):\n # Get info from FITS header\n if target is None:\n target = hdr['OBJECT'].casefold()\n target_dict = {\n 'io': 501,\n 'europa': 502,\n 'jupiter': 599,\n 'neptune': 899,\n }\n if target in target_dict:\n target = target_dict[target] # Correct names to unambiguous ID if necessary\n if epoch is None:\n epoch = hdr['MJD-OBS']\n if loc is None:\n loc = {'lon': hdr['ESO TEL GEOLON'],\n 'lat': hdr['ESO TEL GEOLAT'],\n 'elevation': hdr['ESO TEL GEOELEV']/1e3 # m -> km\n }\n SpaceTelescope_dict = {\n 'hst': '@hst',\n 'jwst': '@-170',\n }\n if loc in SpaceTelescope_dict:\n loc = SpaceTelescope_dict[loc]\n # Load ephemeris data\n conf.horizons_server = 'https://ssd.jpl.nasa.gov/horizons_batch.cgi'\n obj = Horizons(id=target, location=loc, id_type='majorbody', epochs=epoch)\n # Astroquery automatically caches query result locally, so should still work if no internet\n # connection is available and exact query has been performed before on the same machine.\n\n if cache:\n # Use cached results from previous runs etc. to avout bottleneck\n if cache is True:\n cache = 'rw'\n cache_path = tools.path.code('cache', 'ephemerides.pickle.gz')\n try:\n with gzip.open(cache_path, 'rb') as f:\n cache_db = pickle.load(f)\n except FileNotFoundError:\n cache_db = {}\n\n key = str(obj)\n if key in cache_db and 'r' in cache:\n eph = cache_db[key]\n else:\n eph = obj.ephemerides(**kwargs)\n\n if 'w' in cache and key not in cache_db:\n cache_db[key] = eph\n tools.file.check_path(cache_path)\n with gzip.open(cache_path, 'wb') as f:\n pickle.dump(cache_db, f)\n else:\n eph = obj.ephemerides(**kwargs)\n\n if return_eph:\n return eph\n # Return data relevant for mapping\n obs_long = -float(eph['PDObsLon'])\n obs_lat = float(eph['PDObsLat'])\n sun_long = -float(eph['PDSunLon'])\n sun_lat = float(eph['PDSunLat'])\n np_ang = float(eph['NPole_ang'])\n return obs_long, obs_lat, sun_long, sun_lat, np_ang",
"def find_eops(self):\n if self.is_eop:\n eops = [self]\n if self.special:\n for child in self.child_packages:\n eops.extend(child.find_eops())\n return eops\n else:\n l = []\n for child in self.child_packages:\n l.extend(child.find_eops())\n return l",
"def get_partition_ids_from_eids(self, eids: torch.Tensor,\n edge_type: Optional[EdgeType] = None):\n if self.meta[\"is_hetero\"]:\n assert edge_type is not None\n return self.edge_pb[edge_type][eids]\n return self.edge_pb[eids]",
"def get_all_orders(cls):\n return food_orders",
"def employee_offices(user, structure=None):\n if not user: return None\n oe = OrganizationalStructureOfficeEmployee.objects.filter(employee=user)\n if structure:\n oe = oe.filter(office__organizational_structure=structure)\n return oe",
"def get_result_ephemeris(self, run_number, force_update=False):\n\n ephemeris_text = self.get_result_raw_ephemeris(run_number, force_update)\n ephemeris = stk.io.ephemeris_file_data_to_dataframe(ephemeris_text.splitlines())\n return ephemeris",
"def all_edges(self, form='uv', order=None, etype=None):\n src, dst, eid = self._graph.edges(self.get_etype_id(etype), order)\n if form == 'all':\n return src, dst, eid\n elif form == 'uv':\n return src, dst\n elif form == 'eid':\n return eid\n else:\n raise DGLError('Invalid form: {}. Must be \"all\", \"uv\" or \"eid\".'.format(form))",
"def get_ehosts(self):\n return self.execution_host_manager.get_objects()",
"def get_all_open_orders(self):\n orders = self.client.get_open_orders()\n print(orders)\n for x in range(len(orders)):\n if orders[x]['side'] == 'BUY':\n print('Buy {} price {}'.format(orders[x]['symbol'] ,orders[x]['price']))\n\n else:\n print('Sell {} price {}'.format(orders[x]['symbol'] ,orders[x]['price']))\n\n if orders == []:\n print('there is NO open order!!')\n return orders",
"def get_energy_prices(self):\n prices = self._market_constraints_rhs_and_type['demand'].loc[:, ['region', 'price']]\n return prices",
"def __get_orders(self):\n orders = []\n\n # Get orders \n for l in self.GRISM_CONF:\n k = \"BEAM_\"\n if l[0:len(k)]==k:\n ws = l.split()\n order = ws[0].split(\"_\")[-1]\n orders.append(order)\n return orders",
"def solveSpeciesEqs(self, flag = 1):\n return _cantera.stflow_solveSpeciesEqs(self._hndl, _onoff[flag])",
"def resolved_ephemerals(self):\n return self.resolved_ephemerals_",
"def get_pxe_iso(env):\n name = env.config.require('ravello', 'pxe_iso')\n images = env.client.call('GET', '/diskImages')\n for image in images:\n if image['name'] == name:\n return image\n raise RuntimeError('PXE ISO `{}` not found.'.format(name))",
"async def futures_get_all_orders(self, **params):\r\n return await self.client_helper(\"futures_get_all_orders\", **params)",
"def get_equvalence_class(order, coords, P2F):\n for n in range(order):\n candidate = scalar_multiply(order, n, coords)\n if is_representative(candidate, P2F):\n return candidate\n assert False, \"couldn't get equivalence class\"",
"def get_order_history_by_market(self, ex, market):\n orders = []\n for ord in list(self.trader.order_history[ex].values()):\n if ord['market'] == market:\n orders.append(ord)\n return orders",
"def get_ephemeris_for(self, month: int, day: int) -> list:\n if month < 1 or month > 12:\n raise ValueError(f'Month {month} is invalid, expect a value between 1 and 12')\n if day < 1 or day > 31:\n raise ValueError(f'Day {day} is invalid, expect a value between 1 and 31')\n if day > 30 and month in [4, 6, 9, 11]:\n raise ValueError(f'Day {day} does not exist in month {self.id_to_string(month)}')\n if day > 29 and month == 2:\n raise ValueError(f'Day {day} does not exist in month {self.id_to_string(month)}')\n\n return self._json[self.id_to_string(month)][day-1]",
"def get_oem_inventory(self):\n for desc in self.get_oem_inventory_descriptions():\n yield (desc, self.get_inventory_of_component(desc))",
"def getEVs():\n vehTypes = getAllVehicleTypes()\n return [veh for veh in vehTypes if veh['vehType'] in [ER, C_ER]]"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Dictionary that maps attr1 to attr2.
|
def map(self, attr1, attr2):
return dict(zip(getattr(self, attr1), getattr(self, attr2)))
|
[
"def get_attr_map():\n custom_attributes = get_custom_attrs()\n standard_attributes = get_standard_attrs()\n mapping = {}\n for attr in custom_attributes.keys():\n mapping[f'custom:{attr}'] = attr\n mapping.update(standard_attributes)\n return mapping",
"def _get_edge_attributes(self, link, attributes):\n\n attribute_map = {link: dict()}\n\n # map each attribute to edge value\n for idx, row in self.frame.iterrows():\n\n attribute_map[link].update({\n\n # reverse tuple since it gets ordered???\n (row[link[1]], row[link[0]]): {attribute: row[attribute] for attribute in attributes}\n })\n\n return attribute_map",
"def get_attrs(self, node1, node2):\n return self._graph[node1][node2]",
"def createAttrDicts():\n ret = {}\n # lfw v1.1\n ret['lfw_v1.1'] = d = {}\n fields = getmodelfields('lfw_v1.1')\n for l in open('attrnames.txt'):\n num, name = l.strip().split('\\t', 1)\n if name not in fields: continue\n d[num] = d[int(num)] = d[name] = name\n return ret",
"def get_sequentialAttrDict(self,attr = None):\n\t#log.debug(\">>> %s.get_sequentialAttrDict(attr = '%s') >> \"%(self.p_nameShort,attr) + \"=\"*75) \t\t\n\tuserAttrs = self.getUserAttrsAsDict()\n\td_attrList = {}\n\tfor key in userAttrs.keys():\n\t if '_' in key:\n\t\t_split = key.split('_')\n\t\t_int_ = _split[-1]\n\t\t_str_ = ('_').join(_split[:-1])\n\t\tif \"%s\"%attr == _str_:\n\t\t try:\n\t\t\td_attrList[int(_int_)] = key\n\t\t\t#log.debug(\"match: '%s'\"%key)\n\t\t except:log.warning(\"%s failed to int | int: %s\"%(key,_int_))\n\t\t \n\t#log.debug(\"-\"*100) \t \t\n\treturn d_attrList",
"def separate_by_attribute(listInst, ixAttr):\n dictInst = {}\n for inst in listInst:\n cAttr = inst.listAttrs[ixAttr]\n if cAttr not in dictInst:\n dictInst[cAttr] = []\n dictInst[cAttr].append(inst)\n return dictInst",
"def __get_measurement_attr(self, attr):\n return dict([(key, self.measurements[key][attr]) for key in self.measurements.keys()])",
"def fattr2dict(obj):\n\n result = {}\n unpacker = FancyNFS4Unpacker(obj.attr_vals)\n list = bitmap2list(obj.attrmask)\n for bitnum in list:\n result[bitnum] = get_attrunpacker(unpacker)[bitnum]()\n unpacker.done()\n return result",
"def translate_attribs(attribs):\r\n return dict((_attribute_translate(k, k), v) for k, v in attribs.iteritems())",
"def map_attr(attr, iterable):\n return map(mattr(attr), iterable)",
"def attribs(self):\r\n for key, val in self.dict.items():\r\n yield (key, val)",
"def __compute_attrs(self):\n attributes = {}\n for attr in self.policy.typeattributes():\n attributes[str(attr)] = set(str(x) for x in attr.expand())\n return attributes",
"def populate_attributes_table(conn):\n log_info('. populating \"attributes\" table')\n curs = conn.cursor()\n attributes_map = {}\n for attribute in ATTRIBUTES:\n internal_id, internal_name, label, hidden = attribute\n attributes_map[internal_name] = internal_id\n log_verbose('Adding attribute', internal_name, ':', internal_id)\n curs.execute(\"\"\"\n insert into attrs_tab(attr_id, attr_hidden, attr_value)\n values (?, ?, ?);\n \"\"\", (internal_id, 1 if hidden else 0, label,))\n curs.close()\n conn.commit()\n return attributes_map",
"def _get_distances_map(self, distances):\n distances_map = {}\n for a, b, d in distances:\n distances_map[(a, b)] = d\n distances_map[(b, a)] = d\n distances_map[(a, a)] = 0.0\n distances_map[(b, b)] = 0.0\n return distances_map",
"def get_value_map_for_update(self):\n value_map = dict()\n for attr_name in self.__attribute_names_lookup.keys():\n value = getattr(self, attr_name)\n if not value is None:\n self.check_attribute_validity(attr_name, value)\n value_map[attr_name] = value\n\n return value_map",
"def get_line_dict(x_1, y_1, x_2, y_2):\n line_dict = {'p_1': (x_1, y_1),\n 'p_2': (x_2, y_2),\n 'x_1': x_1, \n 'y_1': y_1,\n 'x_2': x_2,\n 'y_2': y_2,\n 'a': y_2 - y_1,\n 'b': x_1 - x_2,\n 'c': (y_2 - y_1) * x_1 + (x_1 - x_2) * y_1}\n return line_dict",
"def relationship_resource(resource1, resource2, **kwargs):\n resource1 = {k:v for k,v in resource1.iteritems()}\n resource1[\"data\"].pop(\"attributes\", None)\n resource2 = {k:v for k,v in resource2.iteritems()}\n resource2[\"data\"].pop(\"attributes\", None)\n\n attributes = {\n resource1[\"data\"][\"type\"]: resource1,\n resource2[\"data\"][\"type\"]: resource2,\n }\n attributes.update(kwargs)\n attributes.update(deletable())\n attributes.update(timestamp())\n return attributes",
"def _format_data(self) -> Dict[str, Any]:\n set_data = dict()\n for attribute_name, _ in self._attribute_mapping.items():\n attribute_value = self._get_attribute_data(attribute_name)\n set_data[attribute_name] = attribute_value\n\n return set_data",
"def getattrs(obj, attr_names=[], alias={}):\n return dict((alias.get(attr, attr), getattr(obj, attr)) for attr in attr_names)",
"def get_attributes(self):\n retdict = {}\n if self.lane_id == None:\n raise ValueError('lane id is not set correctly.')\n retdict['id'] = str(self.lane_id)\n retdict['type'] = enum2str(self.lane_type)\n retdict['level'] = 'false'\n return retdict"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get the interaction sites, which describe the position of interacting mutations in the genotypes. (type==list of lists, see self._build_interaction_sites)
|
def sites(self):
return self.data.sites.values
|
[
"def get_sites(self):\n st = self.site_text\n suffixes = [' residue', ' residues', ',', '/']\n for suffix in suffixes:\n if st.endswith(suffix):\n st = st[:-len(suffix)]\n assert(not st.endswith(','))\n\n # Strip parentheses\n st = st.replace('(', '')\n st = st.replace(')', '')\n st = st.replace(' or ', ' and ') # Treat end and or the same\n\n sites = []\n parts = st.split(' and ')\n for part in parts:\n if part.endswith(','):\n part = part[:-1]\n if len(part.strip()) > 0:\n sites.extend(ReachProcessor._parse_site_text(part.strip()))\n return sites",
"def genes(self) -> List[Gene]:\n return self.__genes",
"def locations(self):\n return self.__locations",
"def list_chemical_gene_interactions(self) -> List[ChemGeneIxn]:\n return self._list_model(ChemGeneIxn)",
"def reactant_species(self):\n return tuple([s.specie for s in self.reactants])",
"def get_unique_site_indices(structure: Structure | Molecule):\n spins = []\n oxi_states = []\n parsable_site_properties = {\n \"magmom\",\n \"oxi_state\",\n \"spin\",\n \"u_minus_j\",\n \"basis\",\n \"potential\",\n \"ghost\",\n \"aux_basis\",\n }\n\n for site in structure:\n for sp in site.species:\n oxi_states.append(getattr(sp, \"oxi_state\", 0))\n spins.append(getattr(sp, \"_properties\", {}).get(\"spin\", 0))\n\n structure.add_site_property(\"oxi_state\", oxi_states)\n structure.add_site_property(\"spin\", spins)\n structure.remove_oxidation_states()\n items = [\n (\n site.species_string,\n *[\n structure.site_properties[k][i]\n for k in structure.site_properties\n if k.lower() in parsable_site_properties\n ],\n )\n for i, site in enumerate(structure)\n ]\n unique_itms = list(set(items))\n _sites: dict[tuple, list] = {u: [] for u in unique_itms}\n for i, itm in enumerate(items):\n _sites[itm].append(i)\n sites = {}\n nums = {s: 1 for s in structure.symbol_set}\n for s in _sites:\n sites[f\"{s[0]}_{nums[s[0]]}\"] = _sites[s]\n nums[s[0]] += 1\n\n return sites",
"def get_sites(self):\n return self.sites.all()",
"def _all_pseudo_sites(self):\n def _all_restraint_sites():\n for r in self._all_restraints():\n if hasattr(r, 'cross_links'):\n for xl in r.cross_links:\n if xl.pseudo1:\n for x in xl.pseudo1:\n yield x.site\n if xl.pseudo2:\n for x in xl.pseudo2:\n yield x.site\n return itertools.chain(self.orphan_pseudo_sites,\n _all_restraint_sites(),\n (f.site for f in self._all_features()\n if hasattr(f, 'site') and f.site))",
"def extract_extra_sites(self):\n\n # weighting arrays for the virtual sites should not be changed\n w1o, w2o, w3o = 1.0, 0.0, 0.0 # SUM SHOULD BE 1\n w1x, w2x, w3x = -1.0, 1.0, 0.0 # SUM SHOULD BE 0\n w1y, w2y, w3y = -1.0, 0.0, 1.0 # SUM SHOULD BE 0\n\n with open('xyz_with_extra_point_charges.xyz') as xyz_sites:\n lines = xyz_sites.readlines()\n\n sites = OrderedDict()\n sites_no = 0\n for i, line in enumerate(lines[2:]):\n # get the current element\n element = str(line.split()[0])\n\n if element != 'X':\n # search the following entries for sites connected to this atom\n for pos_site in lines[i + 3:]:\n if str(pos_site.split()[0]) != 'X':\n # if there are no sites break and start the next loop\n break\n else:\n # get the virtual site coords\n v_pos = array([float(pos_site.split()[x]) for x in range(1, 4)])\n # get parent index number for the topology network\n parent = i + 1 - sites_no\n # get the two closest atoms to the parent\n closet_atoms = list(self.molecule.topology.neighbors(parent))\n if len(closet_atoms) < 2:\n # find another atom if we only have one\n # dont want to get the parent as a close atom\n closet_atoms.append(list(self.molecule.topology.neighbors(closet_atoms[0]))[-1])\n\n # Get the xyz coordinates of the reference atoms\n parent_pos = array(self.molecule.molecule['qm'][parent - 1][1:])\n close_a = array(self.molecule.molecule['qm'][closet_atoms[0] - 1][1:])\n close_b = array(self.molecule.molecule['qm'][closet_atoms[1] - 1][1:])\n\n # work out the local coordinates site using rules from the OpenMM guide\n orig = w1o * parent_pos + w2o * close_a + close_b * w3o\n ab = w1x * parent_pos + w2x * close_a + w3x * close_b # rb-ra\n ac = w1y * parent_pos + w2y * close_a + w3y * close_b # rb-ra\n # Get the axis unit vectors\n z_dir = cross(ab, ac)\n z_dir = z_dir / sqrt(dot(z_dir, z_dir.reshape(3, 1)))\n x_dir = ab / sqrt(dot(ab, ab.reshape(3, 1)))\n y_dir = cross(z_dir, x_dir)\n # Get the local coordinates positions\n p1 = dot((v_pos - orig), x_dir.reshape(3, 1))\n p2 = dot((v_pos - orig), y_dir.reshape(3, 1))\n p3 = dot((v_pos - orig), z_dir.reshape(3, 1))\n\n charge = float(pos_site.split()[4])\n\n # store the site info [(parent top no, a, b), (p1, p2, p3), charge]]\n sites[sites_no] = [(parent - 1, closet_atoms[0] - 1, closet_atoms[1] - 1), (p1 / 10, p2 / 10, p3 / 10), charge]\n sites_no += 1\n\n self.molecule.sites = sites\n\n # get the parent non bonded values\n for value in sites.values():\n charge, sigma, eps = self.non_bonded_force[value[0][0]]\n # Change the charge on the first entry\n charge = float(charge) - value[2]\n self.non_bonded_force[value[0][0]] = [str(charge), sigma, eps]",
"def positions(self):\n return get_positions(as_numpy=True).reshape((self.natom, 3))",
"def interactions(self):\n return self.__graph.labels()",
"def source_interactions(self, species):\n return self.__graph.parent_edges(species)",
"def interpretations(self):\n return self._interpretations",
"def interset(genotypes):\n\tsnplist = map(lambda x: getsnps(x), genotypes)\n\tprint len(snplist)\n\tineverything = reduce(lambda x,y: set(x) & set(y), snplist)\n\treturn ineverything",
"def structure_site_mappings(self):\n return [entry.data[\"site_mapping\"] for entry in self._entries]",
"def get_species(self, species):\n\n atoms = [site for site in self.sites\n if site.species_string == species]\n\n return atoms",
"def get_positions(self):\n return [package.position for package in self.active]",
"def known_solutions(self):\n return self._solver_instance.solutions_at_points",
"def get_locations(self) -> np.ndarray:\n return np.transpose(self.state[:, :, Boids.Attr.LOC])"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
test task with NO chain does not call task.delay
|
def test_task_no_chain(self):
kwargs = {"a": 400, "b": 901}
worker = wiji.Worker(the_task=self.myTask, worker_id="myWorkerID1")
self.myTask.synchronous_delay(a=kwargs["a"], b=kwargs["b"])
with mock.patch("wiji.task.Task.delay", new=AsyncMock()) as mock_task_delay:
dequeued_item = self._run(worker.consume_tasks(TESTING=True))
self.assertEqual(dequeued_item["version"], 1)
self.assertFalse(mock_task_delay.mock.called)
|
[
"def test_task_with_chain(self):\n\n class DividerTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-DividerTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a):\n res = a / 3\n print(\"divider res: \", res)\n return res\n\n class AdderTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-AdderTaskQueue\".format(uuid.uuid4())\n chain = DividerTask\n\n async def run(self, a, b):\n res = a + b\n return res\n\n MYAdderTask = AdderTask()\n\n kwargs = {\"a\": 400, \"b\": 603}\n worker = wiji.Worker(the_task=MYAdderTask, worker_id=\"myWorkerID1\")\n MYAdderTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n\n with mock.patch.object(\n AdderTask, \"delay\", new=AsyncMock()\n ) as mock_adder_delay, mock.patch.object(\n DividerTask, \"delay\", new=AsyncMock()\n ) as mock_divider_delay:\n mock_adder_delay.mock.return_value = None\n mock_divider_delay.return_value = None\n\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n\n # adder task is not queued\n self.assertFalse(mock_adder_delay.mock.called)\n # but divider task(the chain) is queued\n self.assertTrue(mock_divider_delay.mock.called)\n self.assertEqual(mock_divider_delay.mock.call_args[0][1], kwargs[\"a\"] + kwargs[\"b\"])",
"def task_bypassed(self, task):\n pass",
"def test_no_chaining_if_retrying(self):\n\n class DividerTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-DividerTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a):\n res = a / 3\n print(\"divider res: \", res)\n return res\n\n class AdderTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-AdderTaskQueue\".format(uuid.uuid4())\n chain = DividerTask\n\n async def run(self, a, b):\n res = a + b\n await self.retry(a=221, b=555, task_options=wiji.task.TaskOptions(max_retries=2))\n return res\n\n MYAdderTask = AdderTask()\n\n kwargs = {\"a\": 400, \"b\": 603}\n worker = wiji.Worker(the_task=MYAdderTask, worker_id=\"myWorkerID1\")\n MYAdderTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n\n with mock.patch.object(\n AdderTask, \"delay\", new=AsyncMock()\n ) as mock_adder_delay, mock.patch.object(\n DividerTask, \"delay\", new=AsyncMock()\n ) as mock_divider_delay:\n mock_adder_delay.mock.return_value = None\n mock_divider_delay.return_value = None\n\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n\n # divider chain is not queued\n self.assertFalse(mock_divider_delay.mock.called)\n # but adder task is queued again\n self.assertTrue(mock_adder_delay.mock.called)",
"def test_start_no_more_task(self):\n self.fake_worker.task.fetch.side_effect = [None, 'fake_task']\n self.fake_worker.start()\n self.assertEqual(2, self.fake_worker.task.fetch.call_count)\n self.fake_worker.task.execute.assert_called_once()\n self.assertEqual(1, self.fake_worker.handled_tasks)",
"def test_no_chaining_if_exception(self):\n\n class DividerTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-DividerTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a):\n res = a / 3\n print(\"divider res: \", res)\n return res\n\n class AdderTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-AdderTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a, b):\n return await self.do_work(a, b)\n\n @staticmethod\n async def do_work(a, b):\n return a + b\n\n MYAdderTask = AdderTask()\n\n kwargs = {\"a\": 400, \"b\": 603}\n worker = wiji.Worker(the_task=MYAdderTask, worker_id=\"myWorkerID1\")\n MYAdderTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n\n with mock.patch(\n \"wiji.task.Task.delay\", new=AsyncMock()\n ) as mock_task_delay, mock.patch.object(\n AdderTask, \"do_work\", side_effect=Exception(\"test_no_chaining_if_exception\")\n ) as mock_do_work:\n mock_task_delay.mock.return_value = None\n _ = mock_do_work\n\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n # chain is not queued\n self.assertFalse(mock_task_delay.mock.called)",
"def test_no_task_call(self, fake_get, fake_sleep):\n fake_resp = MagicMock()\n fake_resp.ok = True\n fake_resp.status_code = 200\n fake_resp.json.return_value = {'json-body': True}\n fake_get.return_value = fake_resp\n\n vm._call_api('https://some-vlab-service', self.token, task_call=False)\n\n self.assertFalse(fake_sleep.called)",
"def test_check_pending_call_processing(self):\n result = pending_call_processing.delay(1)\n self.assertEqual(result.successful(), True)",
"def test_new_task_waiting_input(self):\n self.assertTrue(self.task.get_id(), 1)\n self.call(system.CmdTasks(), f\"/cancel {self.task.get_id()}\")\n self.task_handler.clock.advance(self.timedelay + 1)\n self.assertFalse(self.task.exists())\n self.task = self.task_handler.add(self.timedelay, func_test_cmd_tasks)\n self.assertTrue(self.task.get_id(), 1)\n self.char1.msg = Mock()\n self.char1.execute_cmd(\"y\")\n text = \"\"\n for _, _, kwargs in self.char1.msg.mock_calls:\n text += kwargs.get(\"text\", \"\")\n self.assertEqual(text, \"Task completed while waiting for input.\")",
"def test_run_once_file_upload(self, chain):\n task = mock.Mock()\n chain.return_value = task\n task.delay.return_value = mock.Mock(task_id='42')\n\n assert isinstance(\n tasks.validate(self.file_upload, listed=True), mock.Mock)\n assert task.delay.call_count == 1\n\n assert isinstance(\n tasks.validate(self.file_upload, listed=True), AsyncResult)\n assert task.delay.call_count == 1",
"def delayable(f):\n def delay(*args, **kwargs):\n queue_key = current_app.config.get('REDIS_QUEUE_KEY', 'default')\n task_id = '%s:result:%s' % (queue_key, str(uuid4()))\n s = dumps((f, task_id, args, kwargs))\n redis.set(task_id, '')\n redis.rpush(queue_key, s)\n return Task(task_id)\n def get_task(task_id):\n result = Task(task_id)\n return result if result.exists else None\n f.delay = delay\n f.get_task = get_task\n return f",
"def test_simple_task_pipeline(self):\n previous_task_result = None\n for i in range(5):\n task = SimpleTask(previous_task_result)\n previous_task_result = task()\n with self.subTest(i=i):\n self.assertEqual(previous_task_result.status, TaskStatus.SUCCESS)",
"def test_analysis_pipeline_task_skips_task_when_analysis_doesnt_exist(self):\n # Setup\n # delete the analysis before running the task\n analysis_id = self.analysis.id\n self.analysis.delete()\n\n @analysis_pipeline_task(Analysis.RUNNING)\n def my_func(self, analysis_id):\n return 'I did work'\n\n my_task = MockCeleryTask()\n\n # Act\n # no exception should be raised b/c the analysis doesn't exist\n result = my_func(my_task, analysis_id)\n\n # Assert\n # it should have returned None b/c the task wasn't run\n self.assertEqual(None, result)\n # it should have updated the celery task to stop the chain\n self.assertEqual(None, my_task.request.chain)\n self.assertEqual(None, my_task.request.callbacks)",
"def do_task(self, task):\n def _on_fail():\n raise self.TaskFailed(\"Task failed\")\n task.on_fail.append(_on_fail)\n taskset = Taskset([task])\n if not self.do_taskset(taskset, timeout=task.timeout):\n raise self.TaskFailed(\"Task timeout\")\n return task.result",
"def discard_task(self, task):\n self.tasks.discard(task)",
"def test_remove_dependencies_for_task(self):\n pass",
"def test_run_single_task_call_method(self):\n task = SimpleTask()\n result = task()\n self.assertTrue(result.status == TaskStatus.SUCCESS)",
"def test_create_subtask_for_task(self):\n pass",
"def test_duplicate_task(self):\n pass",
"def run_task_without_blocking_gui(self, task, *, msg: Optional[str] = None) -> Any:\n raise NotImplementedError()"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
test task with chain CALLS task.delay
|
def test_task_with_chain(self):
class DividerTask(wiji.task.Task):
the_broker = self.BROKER
queue_name = "{0}-DividerTaskQueue".format(uuid.uuid4())
async def run(self, a):
res = a / 3
print("divider res: ", res)
return res
class AdderTask(wiji.task.Task):
the_broker = self.BROKER
queue_name = "{0}-AdderTaskQueue".format(uuid.uuid4())
chain = DividerTask
async def run(self, a, b):
res = a + b
return res
MYAdderTask = AdderTask()
kwargs = {"a": 400, "b": 603}
worker = wiji.Worker(the_task=MYAdderTask, worker_id="myWorkerID1")
MYAdderTask.synchronous_delay(a=kwargs["a"], b=kwargs["b"])
with mock.patch.object(
AdderTask, "delay", new=AsyncMock()
) as mock_adder_delay, mock.patch.object(
DividerTask, "delay", new=AsyncMock()
) as mock_divider_delay:
mock_adder_delay.mock.return_value = None
mock_divider_delay.return_value = None
dequeued_item = self._run(worker.consume_tasks(TESTING=True))
self.assertEqual(dequeued_item["version"], 1)
# adder task is not queued
self.assertFalse(mock_adder_delay.mock.called)
# but divider task(the chain) is queued
self.assertTrue(mock_divider_delay.mock.called)
self.assertEqual(mock_divider_delay.mock.call_args[0][1], kwargs["a"] + kwargs["b"])
|
[
"def test_task_no_chain(self):\n kwargs = {\"a\": 400, \"b\": 901}\n\n worker = wiji.Worker(the_task=self.myTask, worker_id=\"myWorkerID1\")\n self.myTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n with mock.patch(\"wiji.task.Task.delay\", new=AsyncMock()) as mock_task_delay:\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n self.assertFalse(mock_task_delay.mock.called)",
"def test_no_chaining_if_retrying(self):\n\n class DividerTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-DividerTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a):\n res = a / 3\n print(\"divider res: \", res)\n return res\n\n class AdderTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-AdderTaskQueue\".format(uuid.uuid4())\n chain = DividerTask\n\n async def run(self, a, b):\n res = a + b\n await self.retry(a=221, b=555, task_options=wiji.task.TaskOptions(max_retries=2))\n return res\n\n MYAdderTask = AdderTask()\n\n kwargs = {\"a\": 400, \"b\": 603}\n worker = wiji.Worker(the_task=MYAdderTask, worker_id=\"myWorkerID1\")\n MYAdderTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n\n with mock.patch.object(\n AdderTask, \"delay\", new=AsyncMock()\n ) as mock_adder_delay, mock.patch.object(\n DividerTask, \"delay\", new=AsyncMock()\n ) as mock_divider_delay:\n mock_adder_delay.mock.return_value = None\n mock_divider_delay.return_value = None\n\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n\n # divider chain is not queued\n self.assertFalse(mock_divider_delay.mock.called)\n # but adder task is queued again\n self.assertTrue(mock_adder_delay.mock.called)",
"def task_bypassed(self, task):\n pass",
"def test_no_chaining_if_exception(self):\n\n class DividerTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-DividerTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a):\n res = a / 3\n print(\"divider res: \", res)\n return res\n\n class AdderTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-AdderTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a, b):\n return await self.do_work(a, b)\n\n @staticmethod\n async def do_work(a, b):\n return a + b\n\n MYAdderTask = AdderTask()\n\n kwargs = {\"a\": 400, \"b\": 603}\n worker = wiji.Worker(the_task=MYAdderTask, worker_id=\"myWorkerID1\")\n MYAdderTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n\n with mock.patch(\n \"wiji.task.Task.delay\", new=AsyncMock()\n ) as mock_task_delay, mock.patch.object(\n AdderTask, \"do_work\", side_effect=Exception(\"test_no_chaining_if_exception\")\n ) as mock_do_work:\n mock_task_delay.mock.return_value = None\n _ = mock_do_work\n\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n # chain is not queued\n self.assertFalse(mock_task_delay.mock.called)",
"def test_new_task_waiting_input(self):\n self.assertTrue(self.task.get_id(), 1)\n self.call(system.CmdTasks(), f\"/cancel {self.task.get_id()}\")\n self.task_handler.clock.advance(self.timedelay + 1)\n self.assertFalse(self.task.exists())\n self.task = self.task_handler.add(self.timedelay, func_test_cmd_tasks)\n self.assertTrue(self.task.get_id(), 1)\n self.char1.msg = Mock()\n self.char1.execute_cmd(\"y\")\n text = \"\"\n for _, _, kwargs in self.char1.msg.mock_calls:\n text += kwargs.get(\"text\", \"\")\n self.assertEqual(text, \"Task completed while waiting for input.\")",
"def sleepTask(self, delay=0):\r\n return self.timeKeeper.sleep(delay)",
"def delayable(f):\n def delay(*args, **kwargs):\n queue_key = current_app.config.get('REDIS_QUEUE_KEY', 'default')\n task_id = '%s:result:%s' % (queue_key, str(uuid4()))\n s = dumps((f, task_id, args, kwargs))\n redis.set(task_id, '')\n redis.rpush(queue_key, s)\n return Task(task_id)\n def get_task(task_id):\n result = Task(task_id)\n return result if result.exists else None\n f.delay = delay\n f.get_task = get_task\n return f",
"def test_run_once_file_upload(self, chain):\n task = mock.Mock()\n chain.return_value = task\n task.delay.return_value = mock.Mock(task_id='42')\n\n assert isinstance(\n tasks.validate(self.file_upload, listed=True), mock.Mock)\n assert task.delay.call_count == 1\n\n assert isinstance(\n tasks.validate(self.file_upload, listed=True), AsyncResult)\n assert task.delay.call_count == 1",
"def test_check_pending_call_processing(self):\n result = pending_call_processing.delay(1)\n self.assertEqual(result.successful(), True)",
"def do_task(self, task):\n def _on_fail():\n raise self.TaskFailed(\"Task failed\")\n task.on_fail.append(_on_fail)\n taskset = Taskset([task])\n if not self.do_taskset(taskset, timeout=task.timeout):\n raise self.TaskFailed(\"Task timeout\")\n return task.result",
"def test_task_call(self, fake_get, fake_sleep):\n fake_resp1 = MagicMock()\n fake_resp1.ok = True\n fake_resp1.links = {'status': {'url': 'https://some-url'}}\n fake_resp1.status_code = 202\n fake_resp2 = MagicMock()\n fake_resp2.ok = True\n fake_resp2.status_code = 200\n fake_resp2.json.return_value = {'json-body': True}\n fake_get.side_effect = [fake_resp1, fake_resp2]\n\n vm._call_api('https://some-vlab-service', self.token, task_call=True)\n\n self.assertTrue(fake_sleep.called)",
"def test_simple_task_pipeline(self):\n previous_task_result = None\n for i in range(5):\n task = SimpleTask(previous_task_result)\n previous_task_result = task()\n with self.subTest(i=i):\n self.assertEqual(previous_task_result.status, TaskStatus.SUCCESS)",
"def fire_task():\n # Choose a good task to compute\n key = state[\"ready\"].pop()\n state[\"running\"].add(key)\n for f in pretask_cbs:\n f(key, dsk, state)\n\n # Prep data to send\n data = {dep: state[\"cache\"][dep] for dep in get_dependencies(dsk, key)}\n # Submit\n apply_async(\n execute_task,\n args=(\n key,\n dumps((dsk[key], data)),\n dumps,\n loads,\n get_id,\n pack_exception,\n ),\n callback=queue.put,\n )",
"def testTaskLike(self):\n # Call with different parameters.\n parameters = (\n (logging.getLogger(\"task\"), {}),\n (logging.getLogger(\"task\"), None),\n (None, {}),\n (None, None),\n )\n\n duration = 0.1\n for log, metadata in parameters:\n with self.subTest(log=log, metadata=metadata):\n task = Example1(log=log, metadata=metadata)\n self.assertTimer(duration, task)",
"def sleep(delay=0):\r\n return _activeScheduler.sleepTask(delay)",
"def test_delayDelayedCall(self):\n reactor = TimeoutReportReactor()\n call = reactor.callLater(50, lambda: None)\n reactor.now += 10\n call.delay(20)\n timeout = self._checkIterationTimeout(reactor)\n self.assertEqual(timeout, 60)",
"def __call__(self, the_task):\n\n # Wrap the delay method\n self._original_delay = the_task.delay\n @wraps(self._original_delay)\n def new_delay(*args, **kwargs):\n \"\"\" Wrap the original .delay, including a timestamp kwarg \"\"\"\n if self.TIMESTAMP_KWARG not in kwargs:\n kwargs[self.TIMESTAMP_KWARG] = datetime.datetime.utcnow()\n self._original_delay(*args, **kwargs)\n the_task.delay = new_delay\n\n # Wrap the apply_async method\n self._original_apply_async = the_task.apply_async\n @wraps(self._original_apply_async)\n def new_apply_async(args=None, kwargs=None, **celery_options):\n \"\"\" Wrap the original .apply_async, including a timestamp kwarg \"\"\"\n kwargs = kwargs or {}\n if self.TIMESTAMP_KWARG not in kwargs:\n kwargs[self.TIMESTAMP_KWARG] = datetime.datetime.utcnow()\n self._original_apply_async(args, kwargs, **celery_options)\n the_task.apply_async = new_apply_async\n\n # Wrap the run method\n self._original_run = the_task.run\n @wraps(self._original_run)\n def new_run(*args, **kwargs):\n \"\"\"\n Wrap the original .run, extracting the timestamp kwarg that was\n inserted by our wrapped .delay or .apply_async method and call the\n hook with the elapsed time.\n\n We'll also remove the timestamp kwarg before allowing the original\n .run method to execute.\n \"\"\"\n if self.TIMESTAMP_KWARG in kwargs:\n time_delta = datetime.datetime.utcnow() - kwargs[self.TIMESTAMP_KWARG]\n del kwargs[self.TIMESTAMP_KWARG]\n self.hluq_run_hook(the_task, time_delta.total_seconds())\n self._original_run(*args, **kwargs)\n the_task.run = new_run\n\n return the_task",
"def simulated_blocking_io_task(self):\n seconds_to_run = randint(5, 10)\n sleep(seconds_to_run)\n self.task_queue.task_done()",
"def finish_delay(self):"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
test that if parent task raises exception, the chained task is not queued
|
def test_no_chaining_if_exception(self):
class DividerTask(wiji.task.Task):
the_broker = self.BROKER
queue_name = "{0}-DividerTaskQueue".format(uuid.uuid4())
async def run(self, a):
res = a / 3
print("divider res: ", res)
return res
class AdderTask(wiji.task.Task):
the_broker = self.BROKER
queue_name = "{0}-AdderTaskQueue".format(uuid.uuid4())
async def run(self, a, b):
return await self.do_work(a, b)
@staticmethod
async def do_work(a, b):
return a + b
MYAdderTask = AdderTask()
kwargs = {"a": 400, "b": 603}
worker = wiji.Worker(the_task=MYAdderTask, worker_id="myWorkerID1")
MYAdderTask.synchronous_delay(a=kwargs["a"], b=kwargs["b"])
with mock.patch(
"wiji.task.Task.delay", new=AsyncMock()
) as mock_task_delay, mock.patch.object(
AdderTask, "do_work", side_effect=Exception("test_no_chaining_if_exception")
) as mock_do_work:
mock_task_delay.mock.return_value = None
_ = mock_do_work
dequeued_item = self._run(worker.consume_tasks(TESTING=True))
self.assertEqual(dequeued_item["version"], 1)
# chain is not queued
self.assertFalse(mock_task_delay.mock.called)
|
[
"def test_task_no_chain(self):\n kwargs = {\"a\": 400, \"b\": 901}\n\n worker = wiji.Worker(the_task=self.myTask, worker_id=\"myWorkerID1\")\n self.myTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n with mock.patch(\"wiji.task.Task.delay\", new=AsyncMock()) as mock_task_delay:\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n self.assertFalse(mock_task_delay.mock.called)",
"def test_set_parent_for_task(self):\n pass",
"def test_no_chaining_if_retrying(self):\n\n class DividerTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-DividerTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a):\n res = a / 3\n print(\"divider res: \", res)\n return res\n\n class AdderTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-AdderTaskQueue\".format(uuid.uuid4())\n chain = DividerTask\n\n async def run(self, a, b):\n res = a + b\n await self.retry(a=221, b=555, task_options=wiji.task.TaskOptions(max_retries=2))\n return res\n\n MYAdderTask = AdderTask()\n\n kwargs = {\"a\": 400, \"b\": 603}\n worker = wiji.Worker(the_task=MYAdderTask, worker_id=\"myWorkerID1\")\n MYAdderTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n\n with mock.patch.object(\n AdderTask, \"delay\", new=AsyncMock()\n ) as mock_adder_delay, mock.patch.object(\n DividerTask, \"delay\", new=AsyncMock()\n ) as mock_divider_delay:\n mock_adder_delay.mock.return_value = None\n mock_divider_delay.return_value = None\n\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n\n # divider chain is not queued\n self.assertFalse(mock_divider_delay.mock.called)\n # but adder task is queued again\n self.assertTrue(mock_adder_delay.mock.called)",
"def task_bypassed(self, task):\n pass",
"def test_task_with_chain(self):\n\n class DividerTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-DividerTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a):\n res = a / 3\n print(\"divider res: \", res)\n return res\n\n class AdderTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-AdderTaskQueue\".format(uuid.uuid4())\n chain = DividerTask\n\n async def run(self, a, b):\n res = a + b\n return res\n\n MYAdderTask = AdderTask()\n\n kwargs = {\"a\": 400, \"b\": 603}\n worker = wiji.Worker(the_task=MYAdderTask, worker_id=\"myWorkerID1\")\n MYAdderTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n\n with mock.patch.object(\n AdderTask, \"delay\", new=AsyncMock()\n ) as mock_adder_delay, mock.patch.object(\n DividerTask, \"delay\", new=AsyncMock()\n ) as mock_divider_delay:\n mock_adder_delay.mock.return_value = None\n mock_divider_delay.return_value = None\n\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n\n # adder task is not queued\n self.assertFalse(mock_adder_delay.mock.called)\n # but divider task(the chain) is queued\n self.assertTrue(mock_divider_delay.mock.called)\n self.assertEqual(mock_divider_delay.mock.call_args[0][1], kwargs[\"a\"] + kwargs[\"b\"])",
"def test_sibling_cancels(sched):\n a = sched.add_node('a')\n b = sched.add_node('b')\n b2 = sched.add_node('b2')\n a.depends_on(b)\n a.depends_on(b2)\n\n sched.initialize()\n b.submit()\n assert b2.state == \"ready\"\n assert b.state == \"submitted\"\n b.cancel()\n assert a.state == \"cancelled\"\n assert b2.state == \"ready\"",
"def test_create_subtask_for_task(self):\n pass",
"def wrappertask(task):\r\n\r\n @functools.wraps(task)\r\n def wrapper(*args, **kwargs):\r\n parent = task(*args, **kwargs)\r\n\r\n subtask = next(parent)\r\n\r\n while True:\r\n try:\r\n if subtask is not None:\r\n subtask_running = True\r\n try:\r\n step = next(subtask)\r\n except StopIteration:\r\n subtask_running = False\r\n\r\n while subtask_running:\r\n try:\r\n yield step\r\n except GeneratorExit as ex:\r\n subtask.close()\r\n raise ex\r\n except:\r\n try:\r\n step = subtask.throw(*sys.exc_info())\r\n except StopIteration:\r\n subtask_running = False\r\n else:\r\n try:\r\n step = next(subtask)\r\n except StopIteration:\r\n subtask_running = False\r\n else:\r\n yield\r\n except GeneratorExit as ex:\r\n parent.close()\r\n raise ex\r\n except:\r\n subtask = parent.throw(*sys.exc_info())\r\n else:\r\n subtask = next(parent)\r\n\r\n return wrapper",
"def next_task(self):\n # print(self.stack)\n if self.stack == []:\n return False\n task = self.stack.pop()\n # Execute task and push back to stack if not completed\n if not task.execute_task():\n self.stack.append(task)\n return True",
"def test_duplicate_task(self):\n pass",
"def test_cant_call_while_running():\n\n def rerun(instance):\n \"\"\"\n call the transition again\n \"\"\"\n instance.do_thing(None)\n\n x = get_thing()\n\n with pytest.raises(TransitionNotAllowed):\n x.do_thing(rerun)\n\n # ensure the target transition is set when the process is done\n assert x.state == x.CHOICES.error",
"def test_failure(sched):\n a = sched.add_node('a')\n b = sched.add_node('b')\n b2 = sched.add_node('b2')\n a.depends_on(b)\n a.depends_on(b2)\n\n sched.initialize()\n b.submit()\n stat = sched.status()\n assert stat['submitted'] == [b]\n\n b.failed('timeout')\n assert a.state == 'waiting'\n assert b2.state == 'ready'\n assert b.state == 'ready'\n assert len(b.failures) == 1",
"def test_start_no_more_task(self):\n self.fake_worker.task.fetch.side_effect = [None, 'fake_task']\n self.fake_worker.start()\n self.assertEqual(2, self.fake_worker.task.fetch.call_count)\n self.fake_worker.task.execute.assert_called_once()\n self.assertEqual(1, self.fake_worker.handled_tasks)",
"def test_save_failed_class_task(self):\n cat = tasks.Cat(1, 'Felix')\n\n cat.raise_exception()\n with run_kuyruk(save_failed_tasks=True) as worker:\n worker.expect('raise Exception')\n worker.expect('Saving failed task')\n worker.expect('Saved')\n\n assert is_empty('kuyruk')\n r = redis.StrictRedis()\n assert r.hvals('failed_tasks')\n\n run_requeue()\n assert not r.hvals('failed_tasks')\n assert not is_empty('kuyruk')",
"def delay_if_needed(self, **kwargs):\n kwargs.setdefault('task_id', uuid4().hex)\n\n fn_kwargs = dict(\n (k, v) for k, v in kwargs.iteritems()\n if k not in ('task_id', 'parent_task_id')\n )\n\n task, created = get_or_create(Task, where={\n 'task_name': self.task_name,\n 'task_id': kwargs['task_id'],\n }, defaults={\n 'parent_id': kwargs.get('parent_task_id'),\n 'data': {\n 'kwargs': fn_kwargs,\n },\n 'status': Status.queued,\n })\n\n if created or self.needs_requeued(task):\n if not created:\n task.date_modified = datetime.utcnow()\n db.session.add(task)\n\n db.session.commit()\n\n queue.delay(\n self.task_name,\n kwargs=kwargs,\n )\n\n if created:\n self._report_created()",
"def task_failed(self, task, errors):\n pass",
"def ensure_current_task(self):\n\n if self.current_task is None:\n raise Exception(\"No current task\")",
"def test_get_subtasks_for_task(self):\n pass",
"def do(task, subtasks):\n raise Exception('TODO IMPLEMENT ME !')"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
test that if parent task is been retried, the chained task is not queued
|
def test_no_chaining_if_retrying(self):
class DividerTask(wiji.task.Task):
the_broker = self.BROKER
queue_name = "{0}-DividerTaskQueue".format(uuid.uuid4())
async def run(self, a):
res = a / 3
print("divider res: ", res)
return res
class AdderTask(wiji.task.Task):
the_broker = self.BROKER
queue_name = "{0}-AdderTaskQueue".format(uuid.uuid4())
chain = DividerTask
async def run(self, a, b):
res = a + b
await self.retry(a=221, b=555, task_options=wiji.task.TaskOptions(max_retries=2))
return res
MYAdderTask = AdderTask()
kwargs = {"a": 400, "b": 603}
worker = wiji.Worker(the_task=MYAdderTask, worker_id="myWorkerID1")
MYAdderTask.synchronous_delay(a=kwargs["a"], b=kwargs["b"])
with mock.patch.object(
AdderTask, "delay", new=AsyncMock()
) as mock_adder_delay, mock.patch.object(
DividerTask, "delay", new=AsyncMock()
) as mock_divider_delay:
mock_adder_delay.mock.return_value = None
mock_divider_delay.return_value = None
dequeued_item = self._run(worker.consume_tasks(TESTING=True))
self.assertEqual(dequeued_item["version"], 1)
# divider chain is not queued
self.assertFalse(mock_divider_delay.mock.called)
# but adder task is queued again
self.assertTrue(mock_adder_delay.mock.called)
|
[
"def task_bypassed(self, task):\n pass",
"def _retry(self):\n # TODO(dcramer): this needs to handle too-many-retries itself\n assert self.task_id\n\n task = Task.query.filter(\n Task.task_name == self.task_name,\n Task.task_id == self.task_id,\n Task.parent_id == self.parent_id,\n ).first()\n if task and self.max_retries and task.num_retries > self.max_retries:\n date_finished = datetime.utcnow()\n self._update({\n Task.date_finished: date_finished,\n Task.date_modified: date_finished,\n Task.status: Status.finished,\n Task.result: Result.failed,\n })\n db.session.commit()\n\n raise TooManyRetries('%s failed after %d retries' %\n (self.task_name, task.num_retries))\n\n self._update({\n Task.date_modified: datetime.utcnow(),\n Task.status: Status.in_progress,\n Task.num_retries: Task.num_retries + 1,\n })\n\n db.session.commit()\n\n kwargs = self.kwargs.copy()\n kwargs['task_id'] = self.task_id\n kwargs['parent_task_id'] = self.parent_id\n\n retry_number = db.session.query(Task.num_retries).filter(\n Task.task_name == self.task_name,\n Task.task_id == self.task_id,\n Task.parent_id == self.parent_id,\n ).scalar() or 0\n\n retry_countdown = min(BASE_RETRY_COUNTDOWN + (retry_number ** 2), 300)\n\n queue.delay(\n self.task_name,\n kwargs=kwargs,\n countdown=retry_countdown,\n )",
"def test_set_parent_for_task(self):\n pass",
"def task_retried(event: Event):\n logger.info(\"task_retried\", event)",
"def test_task_no_chain(self):\n kwargs = {\"a\": 400, \"b\": 901}\n\n worker = wiji.Worker(the_task=self.myTask, worker_id=\"myWorkerID1\")\n self.myTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n with mock.patch(\"wiji.task.Task.delay\", new=AsyncMock()) as mock_task_delay:\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n self.assertFalse(mock_task_delay.mock.called)",
"def delay_if_needed(self, **kwargs):\n kwargs.setdefault('task_id', uuid4().hex)\n\n fn_kwargs = dict(\n (k, v) for k, v in kwargs.iteritems()\n if k not in ('task_id', 'parent_task_id')\n )\n\n task, created = get_or_create(Task, where={\n 'task_name': self.task_name,\n 'task_id': kwargs['task_id'],\n }, defaults={\n 'parent_id': kwargs.get('parent_task_id'),\n 'data': {\n 'kwargs': fn_kwargs,\n },\n 'status': Status.queued,\n })\n\n if created or self.needs_requeued(task):\n if not created:\n task.date_modified = datetime.utcnow()\n db.session.add(task)\n\n db.session.commit()\n\n queue.delay(\n self.task_name,\n kwargs=kwargs,\n )\n\n if created:\n self._report_created()",
"def retry(self, task_id, force=False):\n return",
"def retry_notifier():\n if graph_copy.has_node(target.name):\n ready_nodes.append(target.name)\n produced_event.set()",
"def test_no_chaining_if_exception(self):\n\n class DividerTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-DividerTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a):\n res = a / 3\n print(\"divider res: \", res)\n return res\n\n class AdderTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-AdderTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a, b):\n return await self.do_work(a, b)\n\n @staticmethod\n async def do_work(a, b):\n return a + b\n\n MYAdderTask = AdderTask()\n\n kwargs = {\"a\": 400, \"b\": 603}\n worker = wiji.Worker(the_task=MYAdderTask, worker_id=\"myWorkerID1\")\n MYAdderTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n\n with mock.patch(\n \"wiji.task.Task.delay\", new=AsyncMock()\n ) as mock_task_delay, mock.patch.object(\n AdderTask, \"do_work\", side_effect=Exception(\"test_no_chaining_if_exception\")\n ) as mock_do_work:\n mock_task_delay.mock.return_value = None\n _ = mock_do_work\n\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n # chain is not queued\n self.assertFalse(mock_task_delay.mock.called)",
"def test_task_with_chain(self):\n\n class DividerTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-DividerTaskQueue\".format(uuid.uuid4())\n\n async def run(self, a):\n res = a / 3\n print(\"divider res: \", res)\n return res\n\n class AdderTask(wiji.task.Task):\n the_broker = self.BROKER\n queue_name = \"{0}-AdderTaskQueue\".format(uuid.uuid4())\n chain = DividerTask\n\n async def run(self, a, b):\n res = a + b\n return res\n\n MYAdderTask = AdderTask()\n\n kwargs = {\"a\": 400, \"b\": 603}\n worker = wiji.Worker(the_task=MYAdderTask, worker_id=\"myWorkerID1\")\n MYAdderTask.synchronous_delay(a=kwargs[\"a\"], b=kwargs[\"b\"])\n\n with mock.patch.object(\n AdderTask, \"delay\", new=AsyncMock()\n ) as mock_adder_delay, mock.patch.object(\n DividerTask, \"delay\", new=AsyncMock()\n ) as mock_divider_delay:\n mock_adder_delay.mock.return_value = None\n mock_divider_delay.return_value = None\n\n dequeued_item = self._run(worker.consume_tasks(TESTING=True))\n self.assertEqual(dequeued_item[\"version\"], 1)\n\n # adder task is not queued\n self.assertFalse(mock_adder_delay.mock.called)\n # but divider task(the chain) is queued\n self.assertTrue(mock_divider_delay.mock.called)\n self.assertEqual(mock_divider_delay.mock.call_args[0][1], kwargs[\"a\"] + kwargs[\"b\"])",
"def next_task(self):\n # print(self.stack)\n if self.stack == []:\n return False\n task = self.stack.pop()\n # Execute task and push back to stack if not completed\n if not task.execute_task():\n self.stack.append(task)\n return True",
"def test_disable_if_replied_noreply(self):\n job = self.create_job(only_if_noreply=True, state='checking')\n with mock_instance('sndlatr.gmail.Mailman') as mailman:\n mailman.get_thread.return_value = []\n job.disable_if_replied('token')\n self.assertEqual(job.state, 'scheduled')",
"def test_sibling_cancels(sched):\n a = sched.add_node('a')\n b = sched.add_node('b')\n b2 = sched.add_node('b2')\n a.depends_on(b)\n a.depends_on(b2)\n\n sched.initialize()\n b.submit()\n assert b2.state == \"ready\"\n assert b.state == \"submitted\"\n b.cancel()\n assert a.state == \"cancelled\"\n assert b2.state == \"ready\"",
"def _is_pending(self, taskid):\n raise NotImplementedError",
"def skip(self, chore, id):\n\n task = chore[\"tasks\"][id]\n\n # Pause if it isn't. \n\n if \"skipped\" not in task or not task[\"skipped\"]:\n\n task[\"skipped\"] = True\n\n task[\"end\"] = time.time()\n\n # If it hasn't been started, do so now\n\n if \"start\" not in task:\n task[\"start\"] = task[\"end\"]\n \n task[\"notified\"] = time.time()\n self.speak(chore, f\"you do not have to {task['text']}\")\n\n # Check to see if there's another one and set\n\n self.check(chore)\n self.set(chore)\n\n return True\n\n return False",
"def is_task_remaining(self):\n if self._task_list:\n return True\n else:\n return False",
"def test_duplicate_task(self):\n pass",
"def retryable(self):\n return self._retryable",
"def retry_never(attempt):\n return False"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
sleep for a few seconds so that some tasks can be consumed, then shutdown worker
|
async def call_worker_shutdown():
await asyncio.sleep(5)
await worker.shutdown()
|
[
"async def call_worker_shutdown():\n await asyncio.sleep(5)\n await worker.shutdown()",
"def cleanThreadTimeToWait() -> None:\n ...",
"def _sleep(self):\n self.kill()",
"def simulated_blocking_io_task(self):\n seconds_to_run = randint(5, 10)\n sleep(seconds_to_run)\n self.task_queue.task_done()",
"def sleepTask(self, delay=0):\r\n return self.timeKeeper.sleep(delay)",
"def stop_workers(self, delay=0):\n if delay > 0: time.sleep(delay)\n for w in self.all_workers:\n p = w[\"process\"]\n wid = w[\"wid\"]\n logger.debug(\"killing worker id(%s)\" % (wid))\n ept_utils.terminate_process(p)",
"def sleep(seconds=0):\n loop = evergreen.current.loop\n current = Fiber.current()\n assert loop.task is not current\n timer = loop.call_later(seconds, current.switch)\n try:\n loop.switch()\n finally:\n timer.cancel()",
"def _kill_after_delay() -> None:\n time.sleep(5)\n proc.kill()",
"def _thread_sleep(self) -> None:\n local_jm_interval = 2\n if isinstance(self._launcher, (LocalLauncher)):\n time.sleep(local_jm_interval)\n else:\n time.sleep(CONFIG.jm_interval)",
"def _wait_for_workers(self):\n while True:\n with self._lock:\n num_workers = len(self._worker_connections.keys())\n if num_workers < self._num_workers:\n time.sleep(5)\n else:\n break",
"def sleep(delay=0):\r\n return _activeScheduler.sleepTask(delay)",
"async def done():\n while True:\n if Framework.get_terminate_event().is_set():\n break\n await asyncio.sleep(0.5)",
"def sleep_asynchronously():\n time.sleep(20)",
"def _on_stop(self):\n self._pool.join()",
"def doSleep(self):\n if os.environ.get(\"TRAVIS\"):\n time.sleep(10)\n else:\n time.sleep(20)\n return",
"def wait(self):\n \n # Wait for some time\n time.sleep(10)\n\n count = 0\n while self.work_pending():\n time.sleep(5)\n \n # Every 2 minutes raise heartbeat event\n count += 5\n if count == 120:\n self.eventr.publish(self, 'heartbeat')\n count = 0 \n\n # Push empty values\n [w.stop() for w in self.workers]\n # [w.join() for w in self.workers]\n \n self.eventr.publish(self, 'crawl_ended') \n log.info('Crawl done.')\n\n # Wait a bit\n time.sleep(2)\n \n # print self.url_graph\n self.stats.publish_stats()\n log.info(\"Log file for this crawl can be found at\", os.path.abspath(self.task_logfile))",
"def wait_until_done(self):\n self.tasks.join()\n for worker in self.workers:\n worker.join()",
"def _stopwait(self,idx):\n while(psOnID(self.procs[idx].pid)):\n time.sleep(1)\n del self.procs[idx]",
"def stop(self):\n # Wait for all workers to finish\n for p in self.pool:\n p.terminate()"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
sleep for a few seconds so that some tasks can be consumed, then shutdown worker
|
async def call_worker_shutdown():
await asyncio.sleep(5)
await worker.shutdown()
|
[
"async def call_worker_shutdown():\n await asyncio.sleep(5)\n await worker.shutdown()",
"def cleanThreadTimeToWait() -> None:\n ...",
"def _sleep(self):\n self.kill()",
"def simulated_blocking_io_task(self):\n seconds_to_run = randint(5, 10)\n sleep(seconds_to_run)\n self.task_queue.task_done()",
"def sleepTask(self, delay=0):\r\n return self.timeKeeper.sleep(delay)",
"def stop_workers(self, delay=0):\n if delay > 0: time.sleep(delay)\n for w in self.all_workers:\n p = w[\"process\"]\n wid = w[\"wid\"]\n logger.debug(\"killing worker id(%s)\" % (wid))\n ept_utils.terminate_process(p)",
"def sleep(seconds=0):\n loop = evergreen.current.loop\n current = Fiber.current()\n assert loop.task is not current\n timer = loop.call_later(seconds, current.switch)\n try:\n loop.switch()\n finally:\n timer.cancel()",
"def _kill_after_delay() -> None:\n time.sleep(5)\n proc.kill()",
"def _thread_sleep(self) -> None:\n local_jm_interval = 2\n if isinstance(self._launcher, (LocalLauncher)):\n time.sleep(local_jm_interval)\n else:\n time.sleep(CONFIG.jm_interval)",
"def _wait_for_workers(self):\n while True:\n with self._lock:\n num_workers = len(self._worker_connections.keys())\n if num_workers < self._num_workers:\n time.sleep(5)\n else:\n break",
"def sleep(delay=0):\r\n return _activeScheduler.sleepTask(delay)",
"async def done():\n while True:\n if Framework.get_terminate_event().is_set():\n break\n await asyncio.sleep(0.5)",
"def sleep_asynchronously():\n time.sleep(20)",
"def _on_stop(self):\n self._pool.join()",
"def doSleep(self):\n if os.environ.get(\"TRAVIS\"):\n time.sleep(10)\n else:\n time.sleep(20)\n return",
"def wait(self):\n \n # Wait for some time\n time.sleep(10)\n\n count = 0\n while self.work_pending():\n time.sleep(5)\n \n # Every 2 minutes raise heartbeat event\n count += 5\n if count == 120:\n self.eventr.publish(self, 'heartbeat')\n count = 0 \n\n # Push empty values\n [w.stop() for w in self.workers]\n # [w.join() for w in self.workers]\n \n self.eventr.publish(self, 'crawl_ended') \n log.info('Crawl done.')\n\n # Wait a bit\n time.sleep(2)\n \n # print self.url_graph\n self.stats.publish_stats()\n log.info(\"Log file for this crawl can be found at\", os.path.abspath(self.task_logfile))",
"def wait_until_done(self):\n self.tasks.join()\n for worker in self.workers:\n worker.join()",
"def _stopwait(self,idx):\n while(psOnID(self.procs[idx].pid)):\n time.sleep(1)\n del self.procs[idx]",
"def stop(self):\n # Wait for all workers to finish\n for p in self.pool:\n p.terminate()"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Enqueues all kinds of messages.
|
def enqueue_all(self, requests=None, replies=None, routed=None):
fast = []
medium = []
slow = []
if requests is not None:
if SPEED_FAST in requests:
fast = requests[SPEED_FAST]
if SPEED_MEDIUM in requests:
medium = requests[SPEED_MEDIUM]
if SPEED_SLOW in requests:
slow = requests[SPEED_SLOW]
if replies is not None:
if SPEED_FAST in replies:
fast = fast + replies[SPEED_FAST]
if SPEED_MEDIUM in replies:
medium = medium + replies[SPEED_MEDIUM]
if SPEED_SLOW in replies:
slow = slow + replies[SPEED_SLOW]
if routed is not None:
fast = fast + routed
total = len(fast) + len(medium) + len(slow)
if len(fast) > 0:
assert Message.validate_messages_for_send(fast, self.app)
self.fast_queue.enqueue(fast)
if len(medium) > 0:
assert Message.validate_messages_for_send(medium, self.app)
self.medium_queue.enqueue(medium)
if len(slow) > 0:
assert Message.validate_messages_for_send(slow, self.app)
self.slow_queue.enqueue(slow)
if total > 0:
self.sleep.set()
|
[
"def send_messages(self, queues):\n for q in queues:\n queue = q['queue']\n try:\n m = queue.get(block=False)\n org, flow = q['dest_channel'].split('|')\n url = '{server}/flows/{org}/{flow}/messages'.format(\n server=self.server,\n org=org,\n flow=flow,\n )\n auth = (self.token, '')\n payload = {\n 'event': 'message',\n 'content': self.format_message(m),\n }\n headers = {\n 'Content-Type': 'application/json'\n }\n r = requests.post(url,\n data=json.dumps(payload),\n auth=auth,\n headers=headers)\n if not r.status_code == 201:\n raise Exception(r.text)\n sent_msg_counter.labels('flowdock', q['dest_channel']).inc()\n queue.task_done()\n except Queue.Empty:\n pass",
"def publish_message(self, message, queue):",
"async def queue(self, ctx):\n game = get_game(ctx)\n mode = get_channel_mode(ctx)\n await ctx.send(embed=Embed(color=0x00FF00,\n description=str(game.queues[mode])))",
"def send_msg(self, msg):\n if isinstance(msg, list):\n work = [m.jsonify() for m in msg]\n if len(work) == 0:\n # rpush requires at least one event, if msg is empty list then just return\n return\n self.redis.rpush(MANAGER_WORK_QUEUE, *work)\n self.increment_stats(MANAGER_WORK_QUEUE, tx=True, count=len(work))\n else:\n self.redis.rpush(MANAGER_WORK_QUEUE, msg.jsonify())\n self.increment_stats(MANAGER_WORK_QUEUE, tx=True)",
"def send_enqueue(self) -> None:\n self._set_state(\"QUEUED\")",
"def dump(self):\n if len(self.queue) < 1: \n return\n\n for level, messages in self.queue.items():\n if len(messages) < 1:\n continue\n\n joined = '\\n'.join(messages)\n if len(joined) >= 2000:\n joined = joined[:2000]\n\n channel = self.channels[level]\n\n send = getattr(channel, 'send', None)\n\n if send is None:\n print(f'[chdump] you sure this is a channel: {channel!r}')\n else:\n self.loop.create_task(channel.send(joined))\n\n # empty queue\n self.queue[level] = []",
"def message_listener(self):\n queue = self.chatty_server.message_queues[self.username]\n while self.socket:\n if not queue.empty():\n message, message_type = queue.get()\n self.write(message, message_type=message_type)\n gevent.sleep(self.tick)",
"def start_handling_messages(self):\n for amqp_consumer in self._amqp_consumers:\n amqp_consumer.start_handling_messages()",
"def sendmany(self, messages):\n with self.lock_many:\n for i in messages:\n self.send(i)",
"def handle_all_the_msgs(msg):\n\n # make the user Q date\n user = UserQueueData(\n user_id=msg.from_user.id,\n username=msg.from_user.username,\n chat_id=msg.chat.id,\n text=msg.text,\n )\n\n messsage_id.add_msg_id(user_id=msg.from_user.id, msg_id=msg.message_id)\n # add the user q data to the Q handler\n user_q_handler.add_user(user)",
"def produce(self, messages):\n raise NotImplementedError",
"def send_msgs(self):\n for publisher, msg in self.msgs_to_publish:\n self.bag.write(publisher.name, msg, self.get_current_ros_time())\n super(CarlaRosBridgeWithBag, self).send_msgs()",
"def submit_sqs_message(self, priority, msg):\n try:\n sqsconn = boto.connect_sqs(self.aws_accesskey,self.aws_secretkey)\n queues = sqsconn.get_all_queues()\n except:\n self.logger.error(\"Error while receiving all available queues.\")\n self.logger.error(\"Traceback:\\n%s\"%traceback.format_exc())\n return False\n for q in queues:\n if q.url.endswith(\"P%s\" % priority):\n # By default, the class boto.sqs.message.Message is used.\n # This does base64 encoding itself\n sqs_msg = q.new_message(body=msg)\n try:\n q.write(sqs_msg)\n except:\n self.logger.error(\"Error while writing message.\")\n self.logger.error(\"Traceback:\\n%s\"%traceback.format_exc())\n return False\n return True\n logger.info(\"No queue found for priority %s\" % priority)\n return False",
"def route_msgs(self):\n while not self.out_queue.empty():\n msg_type, msg_content = self.out_queue.get_nowait()\n # print(msg_type)\n self.out_queue.task_done()\n\n recipient_id = int(msg_content.get(MSGCONTENT.RECIPIENT_ID))\n if recipient_id is not None:\n msg = (msg_type, msg_content)\n if recipient_id == GAME.LOCAL_SERVER_ID:\n # In server mode, messages for the server should go to the server component\n if self.mode == NETWORK.MODE_SERVER:\n self.server_queue.put(msg, True)\n # In client mode, the server is remote, so direct its messages to the network outbox\n else:\n self.remote_queue.put(msg, True)\n elif recipient_id == GAME.LOCAL_CLIENT_ID:\n # \"Local\" is relative to the server, so if we're on a remote client, then local client messages\n # should go to the remote client\n if self.mode == NETWORK.MODE_SERVER:\n self.client_queue.put(msg, True)\n else:\n self.remote_queue.put(msg, True)\n elif recipient_id == GAME.REMOTE_CLIENT_ID:\n # Similarly, \"Remote\" is also relative\n if self.mode == NETWORK.MODE_SERVER:\n self.remote_queue.put(msg, True)\n else:\n self.client_queue.put(msg, True)\n else:\n self.log('Recipient ID %d is not registered.' % (recipient_id))\n else:\n self.log('No recipient ID specified. Message type: %s' % msg_type)",
"def requeue(self):\r\n self.log.error('Requeuing unprocessed messages.')\r\n update_count = 0\r\n delete_count = 0\r\n\r\n for update in self.actions['update']:\r\n if not update in self.processed_updates:\r\n self.queue.write('update:%s' % update)\r\n update_count += 1\r\n\r\n for delete in self.actions['delete']:\r\n if not delete in self.processed_deletes:\r\n self.queue.write('delete:%s' % delete)\r\n delete_count += 1\r\n\r\n self.log.error('Requeued %d updates and %d deletes.' % (update_count, delete_count))",
"async def send_pending(self, conn, queue):\n # TODO: pending queue and processing of another message calls send,\n # what happens first?\n # TODO: Send lock?\n while conn.can_send() and not queue.empty():\n msg, to_key, from_key = queue.get_nowait()\n\n if '~transport' not in msg:\n msg['~transport'] = {}\n\n msg['~transport']['pending_message_count'] = queue.qsize()\n\n wire_msg = await crypto.pack_message(\n self.wallet_handle,\n msg.serialize(),\n [to_key],\n from_key\n )\n\n await conn.send(wire_msg)",
"def message_all(self, message):\n self.log.debug('Sending message to {} clients'.format(len(self._clients)))\n for address, handler in self._clients.items():\n handler.message(message)",
"def dispatch(event, queue):\n for s in queue:\n s(event)",
"def flushOutboundQueues(self):\r\n\t\twhile 1:\r\n\t\t\tif len(self.__packet_queues[PRIORITY_HIGH]) == 0 and len(self.__packet_queues[PRIORITY_NORMAL]) == 0:\r\n\t\t\t\tbreak\r\n\t\t\t# check to make sure outbound socket is writable\r\n\t\t\tpacket = self.__generateNextOutboundPacket()\r\n\t\t\tif packet:\r\n\t\t\t\tself.__sendRawPacket(packet)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Adds one or more messages to internal slow queue to be send later.
|
def enqueue_slow(self, message):
assert Message.validate_messages_for_send(message, self.app)
self.slow_queue.enqueue(message)
self.sleep.set()
|
[
"def add_to_queue(self):\n self.manager.client.song_q.put(self.get_text(None))",
"def flushQueuedMessages(self):\n if self.queued_time is not None:\n self.getProxy(0).massDelayedActions(self.queued_time, \n self.queued_messages)\n self.queued_messages = []\n self.queued_time = None",
"def process_queued_msg(self):\n try:\n while not self.queue.empty():\n task_entry = self.queue.get()\n self.route_task_handler.update_entry(task_entry)\n except:\n pass",
"def requeue(self):\r\n self.log.error('Requeuing unprocessed messages.')\r\n update_count = 0\r\n delete_count = 0\r\n\r\n for update in self.actions['update']:\r\n if not update in self.processed_updates:\r\n self.queue.write('update:%s' % update)\r\n update_count += 1\r\n\r\n for delete in self.actions['delete']:\r\n if not delete in self.processed_deletes:\r\n self.queue.write('delete:%s' % delete)\r\n delete_count += 1\r\n\r\n self.log.error('Requeued %d updates and %d deletes.' % (update_count, delete_count))",
"def add_to_master(self):\n ordered_queue = self.queueorderer.get_queue()\n if (len(ordered_queue) == 0):\n pass\n else:\n for line in ordered_queue:\n self.master.write(line)",
"def addLogRecord(self, items):\n self.queue.put(items)",
"def post(self, message):\n with self.__lock:\n # Store the message\n timestamp = time.time()\n try:\n # Already got a message at the exact same time\n self.__messages[timestamp].append(message)\n\n except KeyError:\n # New message\n bisect.insort_right(self.__times, timestamp)\n self.__messages[timestamp] = [message]\n\n # Notify listeners\n if self._listeners:\n self.__pool.enqueue(self.__notify_message,\n self._listeners[:], timestamp)",
"def sendmany(self, messages):\n with self.lock_many:\n for i in messages:\n self.send(i)",
"def publish_message(self, message, queue):",
"def enqueue_all(self, requests=None, replies=None, routed=None):\n fast = []\n medium = []\n slow = []\n\n if requests is not None:\n if SPEED_FAST in requests:\n fast = requests[SPEED_FAST]\n if SPEED_MEDIUM in requests:\n medium = requests[SPEED_MEDIUM]\n if SPEED_SLOW in requests:\n slow = requests[SPEED_SLOW]\n\n if replies is not None:\n if SPEED_FAST in replies:\n fast = fast + replies[SPEED_FAST]\n if SPEED_MEDIUM in replies:\n medium = medium + replies[SPEED_MEDIUM]\n if SPEED_SLOW in replies:\n slow = slow + replies[SPEED_SLOW]\n\n if routed is not None:\n fast = fast + routed\n\n total = len(fast) + len(medium) + len(slow)\n\n if len(fast) > 0:\n assert Message.validate_messages_for_send(fast, self.app)\n self.fast_queue.enqueue(fast)\n if len(medium) > 0:\n assert Message.validate_messages_for_send(medium, self.app)\n self.medium_queue.enqueue(medium)\n if len(slow) > 0:\n assert Message.validate_messages_for_send(slow, self.app)\n self.slow_queue.enqueue(slow)\n\n if total > 0:\n self.sleep.set()",
"def _dispatch_delayed(self):\n for message in self._messages:\n if self._time >= message.dispatch_time:\n self.dispatch(message)\n self._messages.remove(message)",
"def add_to_queue(self, person, time):\n self.queue.append(person)\n if len(self.queue) == 1:\n person.start_serving(self, time)",
"def message_queue(to_write):\n global moveOffset\n MessagesTurtle.up()\n\n # reset the messages if it goes beyond the space height\n if moveOffset < -(BOARD_DIMENSION/4.5):\n moveOffset = SAVED_OFFSET\n MessagesTurtle.clear()\n\n moveOffset -= int(BOARD_DIMENSION/40) * 1.25\n MessagesTurtle._tracer(False)\n MessagesTurtle.color(\"grey\")\n\n MessagesTurtle.goto(BOARD_DIMENSION/2 - screen.window_width() * 0.08, moveOffset)\n MessagesTurtle.write(to_write, move=True, align=\"left\", font=(\"Ariel\", int(BOARD_DIMENSION/45)))\n moveOffset = MessagesTurtle.ycor()",
"def create_queue(self, queue):",
"def add_messages(self, messages, contacts=None):\n for sms in messages:\n self.add_message(sms, contacts)",
"def send_enqueue(self) -> None:\n self._set_state(\"QUEUED\")",
"def _add_unbuffered(self, qs, elem):\n qs.unbuffered_elements.append(elem)\n if len(qs.unbuffered_elements) == qs.buffer_size:\n qs.unbuffered_elements.sort(key=self._key, reverse=self._reverse)\n heapq.heappush(\n qs.buffers, _QuantileBuffer(elements=qs.unbuffered_elements))\n qs.unbuffered_elements = []\n self._collapse_if_needed(qs)",
"def _additem(self):\n\n self.queue.put(self._genitem())",
"def create_queue_entries():\n # FollowersQueueService().add_followers_to_be_updated()\n FollowersQueueService().add_last_downloaded_followers()"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get positions relative to unit cell i.e. fractional coordinates. If wrap is True, atoms outside the unit cell will be wrapped into the cell in those directions with periodic boundary conditions so that the scaled coordinates are between zero and one.
|
def get_scaled_positions(coords, cell, pbc, wrap=True):
fractional = np.linalg.solve(cell.T,
coords.T).T
if wrap:
for i, periodic in enumerate(pbc):
if periodic:
# Yes, we need to do it twice.
# See the scaled_positions.py test in ase library.
fractional[:, i] %= 1.0
fractional[:, i] %= 1.0
return fractional
|
[
"def transform(self):\n return self.cellx, 0.0, self.left, 0.0, -self.celly, self.top",
"def return_position(self, unit='volts'):\n if unit == 'volts':\n curr_x, curr_y = self.position['x'], self.position['y']\n else:\n curr_x, curr_y = self.volts_to_micron(self.position['x'],'x'), self.volts_to_micron(self.position['y'],'y')\n return curr_x, curr_y",
"def get_cell_coords(pt):\n\n return int(pt[0] // a), int(pt[1] // a), int(pt[2] // a)",
"def get_coords(self, cell):\n i, j = cell \n return (self.left_offset + i * self.cell_size, self.top_offset + j * self.cell_size)",
"def get_real_position(self, unit='volts'):\n with nidaqmx.Task() as fsm_task:\n fsm_task.ai_channels.add_ai_voltage_chan(self.ai_chan['x'], 'FSM x axis')\n fsm_task.ai_channels.add_ai_voltage_chan(self.ai_chan['y'], 'FSM y axis')\n target_x, target_y = fsm_task.read()\n\n curr_x = target_x\n curr_y = target_y\n self.go_to_position(self.volts_to_micron(curr_x,'x'),self.volts_to_micron(curr_y,'y'))\n \n threshold = 0.005 # volt\n \n # repeat at most 3 times\n for i in list(range(3)):\n \n with nidaqmx.Task() as fsm_task:\n fsm_task.ai_channels.add_ai_voltage_chan(self.ai_chan['x'], 'FSM x axis')\n fsm_task.ai_channels.add_ai_voltage_chan(self.ai_chan['y'], 'FSM y axis')\n curr_x2, curr_y2 = fsm_task.read()\n if max(abs(target_x - curr_x2),abs(target_y - curr_y2))< threshold:\n break\n\n curr_x += target_x - curr_x2\n curr_y += target_y - curr_y2\n self.go_to_position(self.volts_to_micron(curr_x,'x') ,self.volts_to_micron(curr_y,'y') )\n\n# self.go_to_position(self.volts_to_micron(curr_x,'x') +(curr_x-curr_x2)*self.conversion['x'] ,self.volts_to_micron(curr_y,'y')+(curr_y-curr_y2)*self.conversion['y'])\n\n return self.return_position(unit)",
"def moveWrap(self):\n\n for i in xrange(2):\n if not 0<self.realCenter[i]<self.worldSize[i]:\n newVal=self.realCenter[i]%self.worldSize[i]\n di = self.dest[i]-self.realCenter[i]+newVal\n self.realCenter[i]=newVal\n self.dest[i]=di\n \n self.rect.center = tuple(self.realCenter)",
"def to_positions(self):\n if self.coords_are_displacement:\n cumulative_displacements = np.cumsum(self.frac_coords, axis=0)\n positions = self.base_positions + cumulative_displacements\n self.frac_coords = positions\n self.coords_are_displacement = False",
"def rewrap(self) -> None:\n self.measured_widths = self.colwidth[:]\n for cell in self.cells:\n cell.wrap(width=self.cell_width(cell, self.colwidth))\n if not cell.wrapped:\n continue\n if cell.row is None or cell.col is None:\n msg = 'Cell co-ordinates have not been set'\n raise ValueError(msg)\n width = math.ceil(max(column_width(x) for x in cell.wrapped) / cell.colspan)\n for col in range(cell.col, cell.col + cell.colspan):\n self.measured_widths[col] = max(self.measured_widths[col], width)",
"def _get_pos(self):\r\n \r\n return (self.rect.midbottom[0]-(MAP_TILE_WIDTH/2))/MAP_TILE_WIDTH, (self.rect.midbottom[1]-(MAP_TILE_HEIGHT))/MAP_TILE_HEIGHT",
"def calc_snaptogrid_pos( posX, posY, gridX, gridY ):\n\toffGridX = posX % gridX\n\toffGridY = posY % gridY\n\tif offGridX > gridX/2:\n\t\txAdjust = gridX -offGridX\n\telse:\n\t\txAdjust = -offGridX\n\tif offGridY > gridY/2:\n\t\tyAdjust = gridY-offGridY\n\telse:\n\t\tyAdjust = -offGridY\n\treturn ( xAdjust, yAdjust )",
"def get_cell_coords(pt,a):\n\n return int(pt[0] // a), int(pt[1] // a)",
"def _get_move_positions(self, step, rep):\n\n # Get starting positions\n x, y = self.system.xy_stage.read_xy()\n z = self.system.inlet_z.read_z()\n xyz0 = [x, y, z]\n\n # Get Ending Positions, Special command for collection will override this\n x, y = self.template.wells[step.well_location[rep % len(step.well_location)]].xy\n x,y = x + self.offset[0], y + self.offset[1]\n z = step.inlet_height\n xyz1 = [x, y, z]\n\n # If xy0 and xy1 are the same location, we don't need to move z\n if abs(xyz0[0] - xyz1[0]) < 0.1 and abs(xyz0[1] - xyz1[1]) < 0.1:\n skip_z = True\n else:\n skip_z = False\n return xyz0, xyz1, step.well_location[rep % len(step.well_location)], skip_z",
"def sliced_coords(self, rows):\n if self.original:\n return rows\n else:\n rows = np.array(rows)\n row0 = rows - self.start\n if self.step != 1:\n correct_mod = np.mod(row0, self.step) == 0\n row0 = row0[correct_mod]\n if self.step > 0:\n ok = (row0 >= 0) & (row0 < self.stop - self.start)\n else:\n ok = (row0 <= 0) & (row0 > self.stop - self.start)\n return row0[ok] // self.step",
"def fold_to_unitcell(self, atoms_coords):\n atoms_coords = np.array(atoms_coords)\n if self.period_type == \"0D\":\n return atoms_coords\n relcoords, shifts = self.splitcoords(atoms_coords) \n relcoords_folded = relcoords % 1.0\n atoms_coords = shifts + np.dot(relcoords_folded, self.axis_cart) \n return atoms_coords",
"def get_object_position_on_grid(self, distance):\n #now we know the spatial resolution per grid spacing\n dx = distance[0] / self._dx\n dy = distance[1] / self._dy\n dz = distance[2] / self._dz\n #get the center loction\n cx = int(self.x_dim / 2)\n cy = int(self.y_dim / 2)\n cz = int(self.z_dim / 2)\n #return the x, y, z indicies to add at\n return cx + dx, cy + dy, cz + dz",
"def periodic_wrap(pos, boxsize, centre=None):\n\tif centre is None:\n\t\treturn np.mod(pos, boxsize)\n\telse:\n\t\treturn np.mod(pos-centre+0.5*boxsize, boxsize)+centre-0.5*boxsize",
"def _wrap_tick_range(x, wraprange):\n if wraprange is None:\n return x\n base = wraprange[0]\n modulus = wraprange[1] - wraprange[0]\n return (x - base) % modulus + base",
"def compute_position_center_of_mass(self):\n return self.position_collection[..., 0].copy()",
"def ir_grid_points(self):\n return self._ir_grid_points"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
fetch documents from egov by document id and save it to raw directory.
|
def do_fetchdoc(self, line):
if not line.strip():
print "usage: fetchdoc <document_id>\n"
key = line.strip()
url = self.base_doc_url % (key[:3], key)
print "fetchdoc: %s" % url
doc = lxml.html.parse(url).getroot()
content = lxml.html.tostring(doc, encoding='utf-8')
filedir = os.path.join(self.root_dir, "raw", key[:3])
if not os.path.exists(filedir):
os.makedirs(filedir)
filepath = os.path.join(filedir, "%s.html" % key)
f_out = open(filepath, 'w')
f_out.write(content)
f_out.close()
|
[
"def download_query_data(doc_id=\"16AZ9Po7h8Qa3ink55bZn4GaiS2pBPVQMMuDd2TBIByA\"):\n warn(\"We still have a dummy version of download_query_data !\")\n example_filepath = \"testdata/ex-query.csv\"\n return example_filepath",
"def retrieve_document(doc_id):\n\n db = config_db.get_db()\n success, output = db.get_documents_from_db([doc_id])\n if success:\n return jsonify({\n \"documents\" : output\n }), 200\n else:\n return jsonify(output), 400",
"def download_documents(query):\n\n # Modified Google search query for .doc files\n query += \" filetype:doc\"\n\n doc_count = 0\n for url in search(query, stop=50):\n\n # Cleaning the encoded URL for filename\n filename = urllib.unquote(url).split('/')[-1]\n\n print \"\\nDownloading: \\nFilename: %s\\nURL: %s\" % (filename, url)\n urllib.urlretrieve(url, filename)\n # print urllib.unquote(url)\n\n doc_count += 1\n # Hacky check to get desired number of docs\n global NUM_DOCS_DOWNLOAD\n if doc_count == NUM_DOCS_DOWNLOAD:\n break",
"def get_documents(credentials, google_id):\n\n log.info('get documents')\n auth_code = credentials.authorize(httplib2.Http())\n drive_service = build('drive', 'v2', http=auth_code)\n files_resource = drive_service.files()\n page_token = None\n while True:\n try:\n param = {}\n if page_token:\n param['pageToken'] = page_token\n files = files_resource.list(**param).execute()\n for file_ in files['items']:\n yield Document(\n owner=file_['owners'][0]['displayName'],\n creation_time=datetime_parser.parse_iso(\n file_['createdDate']),\n modification_time=datetime_parser.parse_iso(\n file_['modifiedDate']),\n header=file_['title'],\n link=file_.get('downloadUrl', '...'),\n last_modification_author=file_['lastModifyingUserName'],\n is_public_access=file_['shared'],\n type_access=u'1',\n permission_access=file_['userPermission']['role'],\n google_code_id=google_id\n )\n page_token = files.get('nextPageToken')\n if not page_token:\n break\n except errors.HttpError as error:\n print 'An error occurred: %s' % error\n break",
"def get_documents(file_type: str, args):\n\n # To debug if start and end of records works well in the loop for.\n # listTmp = [i for i in range(100)]\n # print(listTmp[start:end])\n\n # Getting valid page number and page length , by calling a function form utils.\n page, per_page, start, end = utils.get_valid_pagination_args(args)\n\n file_type = file_type.strip()\n\n mongo_documents = list(mongo.db.documents.find(\n {\"dataType\": file_type}).sort(\"name\", 1))\n total_records = len(mongo_documents)\n error = None\n documents = mongo_documents[start:end]\n for document in documents:\n link = None\n if document[\"format\"] == \"link\":\n\n link = document[\"link\"]\n\n clinicalCases = list(mongo.db.clinicalCases.find(\n {\"sourceId\": document[\"_id\"]}, {\"locationId\": 0}\n ))\n\n for case in clinicalCases:\n case.update({\"_id\": str(case[\"_id\"]),\n \"sourceId\": str(case[\"sourceId\"]),\n })\n try:\n for version in case[\"versions\"]:\n version.pop('locationId', None)\n except:\n pass\n\n document.update({\"_id\": str(document[\"_id\"]),\n \"link\": link,\n \"clinicalCases\": clinicalCases})\n\n data = {\n \"documents\": documents,\n \"totalRecords\": total_records,\n \"currentPage\": page,\n \"perPage\": per_page,\n \"error\": error,\n }\n\n return data",
"def task_download_data(dreem: Dreem, mongoid: str) -> str:\n dreem.download_file(mongoid)\n return mongoid",
"def query(id):\n\n row = HLOM_Record.get(HLOM_Record.id==id)\n\n # Execute the query.\n results = config.es.search('osp', 'document', timeout=30, body={\n 'fields': ['doc_id'],\n 'size': 100000,\n 'filter': {\n 'query': {\n 'match_phrase': {\n 'body': {\n 'query': row.query,\n 'slop': 50\n }\n }\n }\n }\n })\n\n if results['hits']['total'] > 0:\n\n citations = []\n for hit in results['hits']['hits']:\n citations.append({\n 'document': hit['fields']['doc_id'][0],\n 'record': row.id\n })\n\n # Write the citation links.\n HLOM_Citation.insert_many(citations).execute()",
"def get_documents_to_merge(connection, gdrive_id):\n sql = \"\"\"\n SELECT DISTINCT\n res.id,\n res.modified_by_id,\n res.title,\n res.link,\n res.description,\n res.context_id,\n res.kind,\n res.source_gdrive_id,\n res.gdrive_id,\n res.slug,\n res.status,\n res.recipients,\n res.send_by_default,\n rel_id,\n counterparty_id,\n counterparty_type\n FROM\n (SELECT\n d.id,\n d.modified_by_id,\n d.title,\n d.link,\n d.description,\n d.context_id,\n d.kind,\n d.source_gdrive_id,\n d.gdrive_id,\n d.slug,\n d.status,\n d.recipients,\n d.send_by_default,\n r.id AS rel_id,\n r.destination_id AS counterparty_id,\n r.destination_type AS counterparty_type\n FROM\n documents d\n LEFT OUTER JOIN relationships r\n ON r.source_id = d.id\n AND r.source_type = 'Document'\n UNION ALL\n SELECT\n d.id,\n d.modified_by_id,\n d.title,\n d.link,\n d.description,\n d.context_id,\n d.kind,\n d.source_gdrive_id,\n d.gdrive_id,\n d.slug,\n d.status,\n d.recipients,\n d.send_by_default,\n r.id AS rel_id,\n r.source_id AS counterparty_id,\n r.source_type AS counterparty_type\n FROM\n documents d\n LEFT OUTER JOIN relationships r\n ON r.destination_id = d.id\n AND r.destination_type = 'Document') AS res\n WHERE\n res.gdrive_id = :gdrive_id\n ORDER BY res.id\n \"\"\"\n return connection.execute(text(sql), gdrive_id=gdrive_id).fetchall()",
"def get_documents():\n\n DB_USER = app.config.get('DB_USER', 'postgres')\n DB_PASSWORD = app.config.get('DB_PASSWORD', 'dbpass')\n DB_NAME = app.config.get('DB_NAME', 'envirolens')\n\n DB.connect(\n database=DB_NAME,\n user=DB_USER,\n password=DB_PASSWORD\n )\n\n if DB.cursor is None:\n return jsonify({'Error' : 'The connection could not be established'})\n\n document_ids = request.json.get('document_ids', None)\n\n # If the \"document_ids\" parameter was not set:\n if document_ids is None:\n return jsonify(\n {'Message' : 'You need to provide json with \"document_ids\" : [list of documents ids] value'}\n )\n\n statement = \"\"\"SELECT * FROM documents WHERE document_id IN %s;\"\"\"\n DB.cursor.execute(statement, (tuple(document_ids), )) \n\n # Enumerating the fields\n num_fields = len(DB.cursor.description)\n field_names = [i[0] for i in DB.cursor.description]\n documents = [{ field_names[i]: row[i] for i in range(num_fields) } for row in DB.cursor.fetchall()]\n \n # Cleaning the ouput:\n # - removing fulltext field\n # - slicing down the fulltext_cleaned field to 500 chars\n # - we return only the first 10 results\n for i in range(len(documents)):\n if documents[i]['fulltext_cleaned'] is not None:\n documents[i]['fulltext_cleaned'] = documents[i]['fulltext_cleaned'][:500]\n documents[i].pop('fulltext')\n\n DB.disconnect()\n\n return jsonify(documents[:10])",
"def get_caltechdata_files(collection, production=True, full=False):\n # Delete existing collection\n if os.path.isdir(collection):\n shutil.rmtree(collection)\n if not dataset.init(collection):\n print(\"Dataset failed to init collection\")\n exit()\n\n if production == True:\n url = \"https://data.caltech.edu/api/records\"\n else:\n url = \"https://data.caltechlibrary.dev/api/records\"\n\n if full == True:\n query = \"?&sort=newest\"\n else:\n # Exclude HTE and tomograms for efficiency\n query = '?q=-metadata.related_identifiers.identifier%3A\"10.25989%2Fes8t-kswe\"-metadata.identifiers.scheme%3Atiltid&sort=newest'\n\n response = requests.get(f\"{url}{query}\")\n total = response.json()[\"hits\"][\"total\"]\n pages = math.ceil(int(total) / 1000)\n hits = []\n for c in progressbar(range(1, pages + 1)):\n chunkurl = f\"{url}{query}&size=1000&page={c}\"\n response = requests.get(chunkurl).json()\n hits += response[\"hits\"][\"hits\"]\n\n for h in progressbar(hits):\n rid = str(h[\"id\"])\n files = {\"files\": []}\n # Capture external files:\n metadata = h[\"metadata\"]\n doi = h[\"links\"][\"doi\"].split(\"doi.org/\")[1].lower()\n # Need lower because of dataset key limitations\n if \"additional_descriptions\" in metadata:\n for desc in metadata[\"additional_descriptions\"]:\n if \"type\" in desc and desc[\"type\"][\"id\"] == \"files\":\n description = desc[\"description\"]\n chunks = description.split('href=\"')[1:]\n for c in chunks:\n files[\"files\"].append({\"url\": c.split('\"')[0]})\n\n response = requests.get(f\"{url}/{rid}/files\")\n if response.status_code == 200:\n if \"entries\" in response.json():\n files[\"files\"] += response.json()[\"entries\"]\n\n if len(files[\"files\"]) > 0:\n if not dataset.create(collection, doi, files):\n err = dataset.error_message()\n print(err)",
"def get_doc_by_id(doc_id, cursor):\n return cursor.execute(f\"select * from documents where id='{doc_id}'\").fetchall()",
"def fetch(self):\n resp = self.r_session.get(self.document_url)\n resp.raise_for_status()\n self.clear()\n self.update(response_to_json_dict(resp))",
"def test_find_business_documents(self):\n query_string = [('offset', 100),\n ('limit', 200),\n ('query', 'query_example')]\n response = self.client.open(\n '/api_cas_fundscorner/v1//businesses/{businessId}/Files'.format(businessId='businessId_example'),\n method='GET',\n content_type='application/json',\n query_string=query_string)\n self.assert200(response,\n 'Response body is : ' + response.data.decode('utf-8'))",
"def get_pickle(self, document_id, filename):\n response = self.get_file(document_id, filename)\n data = io.BytesIO()\n data.write(response.read())\n data.seek(0)\n try:\n return pickle.load(data)\n except Exception as e:\n print e\n raise DataRetrievalException",
"def export_doc_single(request, *args, **kwargs):\n data_id = kwargs.get('pk', None)\n data = ExistingData.objects.filter(id=data_id).first()\n\n if not data:\n return HttpResponseRedirect(request)\n\n filename = '%s.docx' % slugify(data.source_title)\n\n document = Document()\n document.add_heading(\n 'Existing Data Search: %s' % data.source_title, level=1)\n\n document.add_heading('User Work Office/Lab', level=3)\n document.add_paragraph(data.work)\n document.add_heading('Email Address', level=3)\n document.add_paragraph(data.email)\n document.add_heading('Phone Number', level=3)\n document.add_paragraph(data.phone)\n document.add_heading('Search Phrase', level=3)\n document.add_paragraph(data.search)\n document.add_heading('Source', level=3)\n document.add_paragraph(data.source.name)\n document.add_heading('Source Title', level=3)\n document.add_paragraph(data.source_title)\n document.add_heading('Keywords', level=3)\n document.add_paragraph(data.keywords)\n document.add_heading('URL', level=3)\n document.add_paragraph(data.url)\n document.add_heading('Citation', level=3)\n document.add_paragraph(data.citation)\n document.add_heading('Date Accessed', level=3)\n document.add_paragraph(str(data.date_accessed))\n document.add_heading('Comments', level=3)\n document.add_paragraph(data.comments)\n document.add_heading('Created by', level=3)\n document.add_paragraph(str(data.created_by))\n\n teams = data.teams.all()\n if teams:\n document.add_heading('Shared With Teams', level=3)\n table = document.add_table(rows=len(teams), cols=1)\n row = 0\n for team in teams:\n table.rows[row].cells[0].text = team.name\n # List members?\n row += 1\n\n # Create a zip archive to return multiple files: Docx, n attachments.\n zip_mem = BytesIO()\n archive = ZipFile(zip_mem, 'w')\n\n attachments = data.attachments.all()\n if attachments:\n document.add_heading('Attachments', level=2)\n table = document.add_table(rows=len(attachments), cols=1)\n row = 0\n for attachment in attachments:\n table.rows[row].cells[0].text = attachment.name\n # List uploaded_by?\n # Make hyperlink to open included file?\n row += 1\n try:\n file = attachment.file.file\n archive.write(file.name, path.basename(file.name))\n except FileNotFoundError:\n print('AttachmentFileNotFound')\n\n # Write the finalized docx to zip file:\n content_type = 'application/vnd.openxmlformats-officedocument.' + \\\n 'wordprocessingml.document'\n fake_response = HttpResponse(content_type)\n fake_response['Content-Disposition'] = 'attachment; filename=%s' % filename\n document.save(fake_response)\n\n with tempfile.SpooledTemporaryFile():\n archive.writestr(filename, fake_response.content)\n\n archive.close()\n\n response = HttpResponse(zip_mem.getvalue(),\n content_type='application/force-download')\n response['Content-Disposition'] = 'attachment; filename=\"%s.zip\"' % \\\n filename\n response['Content-length'] = zip_mem.tell()\n response['filename'] = '%s.zip' % filename\n return response",
"def getDocs():\n docs = dict()\n double_transcripts=0\n for file in glob.glob(INPUT_FOLDER+\"*\"):\n # get RG number\n rg_number = file.split('/')[-1].split(\"_\")[0]\n\n # find last occurrence of '.' and replace it with '*' \n k = rg_number.rfind(\".\")\n mongo_rg = rg_number[:k] + \"*\" + rg_number[k+1:]\n\n\n # add it to dictionary\n\n if mongo_rg in docs.keys():\n docs[mongo_rg].append(file.split('/')[-1])\n else:\n docs[mongo_rg] = [file.split('/')[-1]]\n \n \n \n # return\n return docs",
"def _getfileids(self, documents, subcorpus):\n ...",
"def get_documents_by_ids(es_client, app, ids):\n return es_client.mget(\n index=app.es_model.get_read_alias(),\n body={\n 'ids': ids,\n },\n )",
"def documents_get(self,\r\n document_id):\r\n\r\n # Validate required parameters\r\n self.validate_parameters(document_id=document_id)\r\n\r\n # Prepare query URL\r\n _query_builder = Configuration.get_base_uri()\r\n _query_builder += '/signature/documents/{documentId}'\r\n _query_builder = APIHelper.append_url_with_template_parameters(_query_builder, { \r\n 'documentId': document_id\r\n })\r\n _query_url = APIHelper.clean_url(_query_builder)\r\n\r\n # Prepare headers\r\n _headers = {\r\n 'accept': 'application/json'\r\n }\r\n\r\n # Prepare and execute request\r\n _request = self.http_client.get(_query_url, headers=_headers)\r\n OAuth2.apply(_request)\r\n _context = self.execute_request(_request)\r\n self.validate_response(_context)\r\n\r\n # Return appropriate type\r\n return APIHelper.json_deserialize(_context.response.raw_body, CreateDocumentResponse.from_dictionary)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
show a list of categories and their keys
|
def _show_categories(self):
for (key, val) in self.categories:
separator = key % 5 == 0 and "\n" or ' ' * (15 - len(val) * 2)
print ('%02s: %s%s' % (key, val, separator)).encode('utf-8'),
|
[
"def categories_show(self):\n\n cursor = DatabaseManager.connection_to_database(self)\n\n cursor.execute(\"SELECT * FROM category\")\n\n my_results = cursor.fetchall()\n\n i = 1\n cat_list = []\n for cat_tuples in my_results:\n for cat_str in cat_tuples:\n cat_list2 = []\n cat_list2.append(i)\n cat_list2.append(cat_str)\n i += 1\n cat_list.append(cat_list2)\n\n for cat_list2 in cat_list:\n print(cat_list2)",
"def display_categories(self):\n self.get()",
"def show_categories():\n categories = service.get_categories()\n latest_items = service.get_latest_items()\n\n return render_template(\"categories.html\", categories=categories,\n items=latest_items)",
"def dumpCategories(self):\n categs = []\n for key_card in self.library:\n categs += [ca for ca in self.library[key_card].categ if ca not in categs]\n # categs_card = self.library[key_card].categ\n # for categ in categs_card:\n # if categ not in dict_categs.values():\n # dict_categs[key_counter] = categ\n # key_counter += 1\n # now we have list of categories, put this in a numbered fashion in a dictionary\n dict_categs = {i+1:categs[i] for i in range(len(categs))}# dictionary with structure {1: 'categoryA', 2:'categoryB',... }\n # print it\n print(\"\")\n for num_ca in dict_categs:\n print(\"{0}) {1}\".format(num_ca, dict_categs[num_ca]))\n # return it\n return dict_categs",
"def show_categories(self):\n self.__clean_box()\n\n categories_list = CategoryJSONManager.get_categories()\n\n for _category in categories_list:\n self.box_categories.insert(\"end\", _category.name)",
"def showCatalog():\n state = generateState(login_session, 'state')\n categories = session.query(Category).all()\n return render_template('allCategories.html', categories=categories,\n STATE=state, session=login_session)",
"def get_categories():\r\n return VIDEOS.iterkeys()",
"def print_categories():\n category_list = ['60fps', 'amateur', 'anal', 'arab', 'asian', 'bbw(big busty women)', 'babe', 'babysitter',\n 'btscenes(behind the scenes)',\n 'bigass', 'bigdick', 'titslg(big tits)', 'bimale', 'blonde', 'bj(blowjob)', 'bondage', 'brazilian',\n 'british', 'brunette',\n 'bukkake', 'cartoon', 'casting', 'celeb', 'cc', 'college', 'comp(compilation)', 'cosplay',\n 'creampie', 'cuckold',\n 'cumshot', 'czech', 'described', 'dp', 'ebony', 'euro', 'exclusive', 'feet',\n 'femaleorgy(female orgasm)',\n 'fetish', 'fisting', 'french', 'funny', 'gangbang', 'gay', 'german', 'hd', 'handjob', 'hardcore',\n 'hentai',\n 'indian', 'interactive', 'interracial', 'italian', 'japanese', 'korean', 'latina', 'lesbian',\n 'milf', 'massage',\n 'masturbate', 'mature', 'musclemen', 'music', 'oldyoung', 'orgy', 'pov', 'parody', 'party', 'piss',\n 'popww(popular with women)', 'pornstar', 'public', 'pussylick', 'reality', 'redhead',\n 'rp(roleplay)',\n 'romantic', 'rough', 'russian', 'sfw(safe for work)', 'school', 'titssm(small tits)', 'smoking', 'solofemale',\n 'solomale',\n 'squirt', 'step(step fantasy)', 'strip(striptease)', 'tatwomen(tatooed women)', 'teen', '3some',\n 'toys',\n 'tmale(transmale)', 'twgirl(trans with girl)', 'twguy(trans with guy)', 'trans(transgender)',\n 'veramateurs(verified amateurs)', 'vercouples(verified couples)', 'vermodels(verified models)',\n 'vintage', 'vr(virtual reality)', 'webcam']\n print(category_list)",
"def get_categories():\n return VIDEOS.keys()",
"def categories_dict():\n items = db_helper.get_categories()\n return [item.serialize for item in items]",
"def list_category(category):\n print(dedent(f'''\n {category}\n {'-' * len(category)}'''))\n for menue in MENUE:\n item = menue['item']\n price = \"%.2f\" % round(float(menue['price']),2)\n space = (' ' * (WIDTH - (len(item) + len(str(price)) + 2)))\n if category == menue['category']:\n print(dedent(f'''{item + space + ' $' + str(price)}'''))",
"def show_category_items(category_id):\r\n categories = session.query(Category).order_by(desc(Category.name))\r\n items = session.query(Item).filter_by(category_id=category_id)\r\n items = items.order_by(desc(Item.id))\r\n return render_template('content.html',\r\n categories=categories,\r\n items=items,\r\n client_id=gAuth.CLIENT_ID,\r\n state=login_session['state'],\r\n user=get_user())",
"def show_categories_json():\n categories = service.get_categories()\n return jsonify(categories=[category.serialize for category in categories])",
"def format_search_categories(book_categories: list):\n formatted_categories = \"\\n\"\n categories_dict = list(enumerate(book_categories))\n for key, category in categories_dict:\n formatted_categories += f\"\\t{key} : {category}\\n\"\n return formatted_categories",
"def show_categories_check(show_category_list):\n if show_category_list:\n print_categories()",
"def __send_get_categories(self):\n self.__send_command(CommandsBytes.GET_CATEGORIES)",
"def category(self, categories) -> dict:\n\n questions = [\n Checkbox(\n name=\"id\",\n message=\"CHOOSE CATEGORY:\",\n choices=[\n f\"{row['id']} - {row['name']}\"\n for row in categories])\n ]\n\n return prompt(questions)",
"def getCategoryDisplayList(self, ):\n\n return DisplayList([(normalizeString(x.decode(self.getCharset())), x) for x in self.getCategories()])",
"def get_category_label(category_key):\n for key, value in Listing.CATEGORY_CHOICES:\n if key == category_key:\n return value"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Extract the standard_id (standard citation key) for a csl_item and modify the csl_item inplace to set its "id" field. The standard_id is extracted from a "standard_citation" field, the "note" field, or the "id" field. If extracting the citation from the "id" field, uses the infer_citekey_prefix function to set the prefix.
|
def csl_item_set_standard_id(csl_item):
if not isinstance(csl_item, dict):
raise ValueError(
"csl_item must be a CSL Data Item represented as a Python dictionary")
from manubot.cite.citeproc import (
append_to_csl_item_note,
parse_csl_item_note,
)
note_dict = parse_csl_item_note(csl_item.get('note', ''))
original_id = None
original_standard_id = None
if 'id' in csl_item:
original_id = csl_item['id']
original_standard_id = infer_citekey_prefix(original_id)
if 'standard_id' in note_dict:
original_standard_id = note_dict['standard_id']
if 'standard_citation' in csl_item:
original_standard_id = csl_item.pop('standard_citation')
if original_standard_id is None:
raise ValueError(
'csl_item_set_standard_id could not detect a field with a citation / standard_citation. '
'Consider setting the CSL Item "id" field.')
assert is_valid_citekey(original_standard_id, allow_raw=True)
standard_id = standardize_citekey(
original_standard_id, warn_if_changed=False)
add_to_note = {}
if original_id and original_id != standard_id:
if original_id != note_dict.get('original_id'):
add_to_note['original_id'] = original_id
if original_standard_id and original_standard_id != standard_id:
if original_standard_id != note_dict.get('original_standard_id'):
add_to_note['original_standard_id'] = original_standard_id
if standard_id != note_dict.get('standard_id'):
add_to_note['standard_id'] = standard_id
append_to_csl_item_note(csl_item, dictionary=add_to_note)
csl_item['id'] = standard_id
return csl_item
|
[
"def id_replace(self):\n aws_lookup = self.lookup()\n var_lookup_list = pcf_util.find_nested_vars(self.desired_state_definition, var_list=[])\n for (nested_key, id_var) in var_lookup_list:\n if id_var[0] == \"lookup\":\n resource = id_var[1]\n names = id_var[2].split(':')\n var = aws_lookup.get_id(resource, names)\n pcf_util.replace_value_nested_dict(curr_dict=self.desired_state_definition,\n list_nested_keys=nested_key.split('.'), new_value=var)",
"def preprocess_paper_2(item: Tuple[str, Paper, List[MiniPaper]]) -> Tuple[str, Paper]:\n key, paper, reference_papers = item\n\n titles = \" \".join(filter(None, [paper.title for paper in reference_papers]))\n venues = \" \".join(filter(None, [paper.venue for paper in reference_papers]))\n journals = \" \".join(filter(None, [paper.journal_name for paper in reference_papers]))\n\n authors: List[str] = list(\n filter(\n None,\n [author.strip() for paper in reference_papers for author in paper.authors],\n )\n )\n blocks = [compute_block(author) for author in authors]\n names = \" \".join(authors)\n reference_details = (\n get_text_ngrams(names.strip(), use_bigrams=True, stopwords=None),\n get_text_ngrams(titles, use_bigrams=True),\n get_text_ngrams(\n venues + \" \" + journals if venues != journals else venues, stopwords=VENUE_STOP_WORDS, use_bigrams=True\n ),\n Counter(blocks),\n )\n paper = paper._replace(reference_details=reference_details)\n\n return (key, paper)",
"def fix_id(item_id):\n item_id = unquote_plus(item_id)\n item_id = safe_unicode(item_id)\n item_id = item_id.encode('ascii', 'ignore')\n return item_id",
"def regenerate_items_ids(items: List[Item]) -> None:\n id_map: Dict[ItemId, ItemId] = {item.id: generate_item_id() for item in items}\n\n for item in items:\n item.id = id_map[item.id]\n\n if item.parent_id in id_map:\n item.parent_id = id_map[item.parent_id]",
"def ConvertCiteKeys(line):\n line = re.sub(r'([A-Z][a-z]+:\\d{4}[a-z]{2})\\}\\{([A-Z][a-z]+:\\d{4}[a-z]{2})', r'\\1\\2', line)\n \n \"\"\"This regex will add \\citep in front of Papers citekeys (It will fail if suffixes or \n prefixes are included. I need to add functionality for this)\"\"\"\n line = re.sub(r'(\\\\cite)?(\\{(([A-Z][a-z]+:\\d{4}[a-z]{2},? ?)+)\\})', r'\\citep\\2', line)\n\n \"\"\"This regex is to deal with author suppression (ie OBrien et al. (2012) showed that...\n It will fail if the citekey has multiple papers, though I can't imagine a situation where\n this would happen\n \n \\citet would be a better way to handle this situation because it will handle things like \n formatting et al for the correct style automaticaly, but it would be harder to implement\"\"\"\n line = re.sub(r'(\\{\\*)([A-Z][a-z]+:\\d{4}[a-z]{2}\\})', r'\\citeyear{\\2', line)\n \n \"\"\"This regex will handle year suppression. See above for limitations\"\"\"\n line = re.sub(r'(\\{[A-Z][a-z]+:\\d{4}[a-z]{2})(\\*\\})', r'\\citeauthor\\1}', line)\n return line",
"def _fill_in_sample_ids(samples: List[dict], lims_map: dict, id_key: str = \"internal_id\"):\n for sample in samples:\n LOG.debug(f\"{sample['name']}: link sample to LIMS\")\n if not sample.get(id_key):\n internal_id = lims_map[sample[\"name\"]]\n LOG.info(f\"{sample['name']} -> {internal_id}: connect sample to LIMS\")\n sample[id_key] = internal_id",
"def post_process(self) -> None:\n if self.item.url:\n self.item.url = urljoin(self.base_url, self.item.url)\n\n # ID is the same as URL in this case.\n self.item.id = self.item.url\n\n # Titles and summaries are sometimes followed by a colon (usually when\n # they are followed by language-specific links). If so, drop it.\n self.item.title = self.item.title.strip().strip(':')\n if not self.item.title:\n raise FormatError(f'No title content found for {self.start_node}')\n\n if self.item.summary:\n self.item.summary = self.item.summary.strip().strip(':')",
"def get_pmc_csl_item(pmcid: str) -> Mapping[str, Any]:\n if not pmcid.startswith(\"PMC\"):\n raise ValueError(f\"not a valid pmd id: {pmcid}\")\n\n from manubot.cite.pubmed import get_pmc_csl_item\n\n csl_item = get_pmc_csl_item(pmcid)\n if \"URL\" not in csl_item:\n csl_item[\"URL\"] = f\"https://www.ncbi.nlm.nih.gov/pmc/articles/{csl_item.get('PMCID', pmcid)}/\"\n return csl_item",
"def _process_biblio_ref(self, item):\n a_ref = nodes.Reference()\n logger = logging.getLogger(self.__class__.__name__)\n\n a_ref.set_name(item[\"name\"])\n a_ref.set_title(item.get(\"title\", \"\"))\n a_ref.set_organization(item.get(\"organization\", \"\"))\n a_ref.set_category(item.get(\"category\", \"\"))\n a_ref.set_date(item.get(\"date\", \"\"))\n\n logger.debug(\"Processing Bibliography Reference: \\\"{}\\\"\".format(a_ref.get_name()))\n\n if \"hyperlink\" in item:\n if isinstance(item[\"hyperlink\"], list):\n for hyperlink_item in item[\"hyperlink\"]:\n a_ref.add_hyperlink(hyperlink_item)\n logger.debug(\"- Adding Hyperlink: \\\"{}\\\"\".format(hyperlink_item))\n else:\n a_ref.add_hyperlink(item[\"hyperlink\"])\n logger.debug(\"- Adding Hyperlink: \\\"{}\\\"\".format(item[\"hyperlink\"]))\n\n return a_ref",
"def update_item(self, id_, item):\n if id_ not in self.items:\n raise KeyError(\"Cannot update item with ID '%s': \"\n \"ID does not exist\")\n self.items[id_] = item\n return item",
"def addSoccerwayId(repo='', item='', lang='', soccerway_id='', confirm='', import_from=''):\n\n\t# item_1 = base.WdPage(wd_value='Q4115189')\n\t# item_1.printWdContents()\n\tif checkDuplicate(soccerway_id):\n\t\tprint('ID is already in use in another page. Skipping...')\n\t\treturn 1\n\n\tif import_from == 'enwiki':\n\t\titem.addIdentifiers(prop_id=prop_id, prop_value=soccerway_id, lang=lang, confirm=confirm)\n\telse:\n\t\titem.addIdentifiers(prop_id=prop_id, prop_value=soccerway_id, confirm=confirm)\n\treturn 0",
"def new_identifier(self, item_type):\n _DEPRECATION_ERROR_METHOD(\n self,\n \" new_identifier\",\n \"Use 'new_identifier' method of 'constructs' attribute instead.\",\n version=\"3.0.0\",\n removed_at=\"4.0.0\",\n ) # pragma: no cover",
"def i_product_item_id(self, i_product_item_id: int):\n\n self._i_product_item_id = i_product_item_id",
"def fix(\n self,\n items,\n apply_filters,\n apply_transforms,\n delete_fields,\n to_process_item,\n dry_run=True,\n ):\n for item in items:\n # If the number of keys is zero, it was a deleted entry, or\n # otherwise uninteresting.\n if len(item[\"meta\"].keys()) and to_process_item(item):\n data = item[\"data\"]\n self.apply_filters(data, apply_filters)\n self.apply_transforms(data, apply_transforms)\n self.delete_fields(data, delete_fields)\n if not dry_run:\n item[\"meta\"][\"fixed\"] = 1\n try:\n self.update_item(item)\n except zotero_errors.UnsupportedParams as e:\n print(item, e)\n if dry_run:\n print(\"WARNING: just a dry run\")",
"def replace_one(self, filter, replacement, upsert=False):\n self._assert_open()\n if len(filter) == 1 and self._primary_key in filter:\n _id = filter[self._primary_key]\n if upsert or _id in self:\n self[_id] = replacement\n return _id\n else:\n for _id in self._find(filter):\n self[_id] = replacement\n return _id\n else:\n if upsert:\n return self.insert_one(replacement)",
"def save_item(self, item):\n data = {\n 'item_id': item.item_id,\n 'name': item.name,\n }\n # 'aisle': item.aisle,\n # 'category': item.category,\n # 'description': item.description,\n # 'image_url': item.image_url\n # }\n new_row_id = self._save(item.DB_TABLE_NAME, data, item.id)\n if new_row_id:\n item.id = new_row_id\n return new_row_id",
"def enrich_item(self, item):\n\n try:\n identifier = strip_scheme(item.identifier_url)\n except AttributeError:\n raise Exception('No identifier_url for item: %s', item)\n\n try:\n date_modified = item.date_modified\n except AttributeError:\n date_modified = None\n\n item.url = '%s/%s' % (RESOLVER_BASE_URL, parse.quote(identifier))\n\n ori_enriched = GCSCachingMixin.factory('ori-enriched')\n if ori_enriched.exists(identifier):\n resource = ori_enriched.download_cache(identifier)\n try:\n item.text = json.load(resource.media_file)['data']\n\n # Adding the same text again for Elastic nesting\n item.text_pages = [\n {'text': text, 'page_number': i}\n for i, text in enumerate(item.text, start=1)\n if text\n ]\n except (ValueError, KeyError):\n # No json could be decoded or data not found, pass and parse again\n pass\n\n if not hasattr(item, 'text') or not item.text:\n try:\n resource = GCSCachingMixin.factory('ori-static').fetch(\n item.original_url,\n identifier,\n date_modified,\n )\n except requests.HTTPError as e:\n raise SkipEnrichment(e)\n\n item.content_type = resource.content_type\n item.size_in_bytes = resource.file_size\n\n # Make sure file_object is actually on the disk for pdf parsing\n temporary_file = NamedTemporaryFile(delete=True)\n temporary_file.write(resource.read())\n temporary_file.seek(0, 0)\n\n if os.path.exists(temporary_file.name):\n path = os.path.realpath(temporary_file.name)\n item.text = file_parser(path, max_pages=100)\n\n temporary_file.close()\n\n if hasattr(item, 'text') and item.text:\n # Adding the same text again for Elastic nesting\n item.text_pages = [\n {'text': text, 'page_number': i}\n for i, text in enumerate(item.text, start=1)\n if text\n ]\n\n # Save the enriched version to the ori-enriched bucket\n data = json.dumps({\n 'data': item.text,\n 'pages': len(item.text),\n })\n ori_enriched.upload(identifier, data, content_type='application/json')\n\n enrich_tasks = item.enricher_task\n if isinstance(enrich_tasks, str):\n enrich_tasks = [item.enricher_task]\n\n # The enricher tasks will executed in specified order\n for task in enrich_tasks:\n self.available_tasks[task](self.source_definition).enrich_item(item)\n\n item.db.save(item)",
"def update_item(self, xblock, user_id, allow_not_found=False, force=False, **kwargs):\n pass # lint-amnesty, pylint: disable=unnecessary-pass",
"def insert_ref(self, item, key=None, axes=None, copy=True, replace=True):\n _DEPRECATION_ERROR_METHOD(\n self,\n \"insert_ref\",\n \"Use method 'set_construct' or 'set_coordinate_reference' \"\n \"instead.\",\n version=\"3.0.0\",\n removed_at=\"4.0.0\",\n ) # pragma: no cover"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
generator that builds the list of logo filenames
|
def logos():
for n in range(12):
yield "eh_logo_%d.tiff" % (n + 1)
|
[
"def make_image_list(image_dir):",
"def logo():",
"def create_logo(self, seqs=[]):\n # seperate headers\n headers, instances = [list(x) for x in zip(*seqs)]\n\n if self.options.sequence_type is 'rna':\n alphabet = Alphabet('ACGU')\n elif self.options.sequence_type is 'protein':\n alphabet = Alphabet('ACDEFGHIKLMNPQRSTVWY')\n else:\n alphabet = Alphabet('ACGT')\n motif_corebio = SeqList(alist=instances, alphabet=alphabet)\n data = wbl.LogoData().from_seqs(motif_corebio)\n\n format = wbl.LogoFormat(data, self.options)\n\n if self.output_format == 'png':\n return wbl.png_formatter(data, format)\n elif self.output_format == 'png_print':\n return wbl.png_print_formatter(data, format)\n elif self.output_format == 'jpeg':\n return wbl.jpeg_formatter(data, format)\n else:\n return wbl.eps_formatter(data, format)",
"def imGenerator(LoTitles):\n\tLoImg = []\n\tfor i in LoTitles: \n\t\tLoImg += [cv2.imread(i,0)]\n\treturn LoImg",
"def create_weblogo(seq_list,out_file,alphabet=\"amino\"):\n\n # Alphabet and color scheme\n if alphabet == \"amino\":\n wl_alphabet = weblogo.seq.unambiguous_protein_alphabet\n wl_color_scheme = weblogo.colorscheme.hydrophobicity\n elif alphabet == \"dna\":\n wl_alphabet = weblogo.seq.unambiguous_dna_alphabet \n wl_color_scheme = weblogo.colorscheme.nucleotide\n \n # load data and create a logo\n logo_sequences = weblogo.seq.SeqList(seq_list,alphabet=wl_alphabet)\n logo_data = weblogo.LogoData.from_seqs(logo_sequences)\n\n # create format\n logo_format = weblogo.LogoFormat(logo_data)\n logo_format.color_scheme = wl_color_scheme\n\n # dump out as a pdf. \n logo = weblogo.pdf_formatter(logo_data, logo_format)\n f = open(out_file,'w')\n f.buffer.write(logo)\n f.close()",
"def _generate_examples(self, images_dir_path):\n for fname, fobj in images_dir_path:\n if fname.endswith(\".jpg\"):\n image_dir, image_file = os.path.split(fname)\n d = os.path.basename(image_dir)\n record = {\"image\": fobj, \"label\": d.lower()}\n yield \"%s/%s\" % (d, image_file), record",
"def make_fake():\n print(\"\\nFake images created:\\n\")\n for i in range(1,31):\n fake_name = rename.random_name_maker()\n fake_name += rename.random_name_maker()\n fake_name += file_ending[random.randint(1,3)]\n print(fake_name)\n with open(\"./{0}\".format(fake_name), \"w\") as my_file:\n my_file.write('')\n print(\"\")",
"def build_image_objects(result_dict):\n\n for file in os.listdir(IMG_DIR):\n print(\"Current image -> \", file)\n image_obj = construct_image_object(IMG_DIR + file)\n meta_obj = construct_meta_object(IMG_DIR + file)\n\n image_obj.file_path = IMG_DIR + \"/\" + file\n image_obj.metadata = meta_obj\n\n # add image object to the object list for later iteration\n IMG_OBJS.append(image_obj)\n IMG_PATHS.append(image_obj.file_path)\n result_dict[os.path.splitext(file)[0]] = [] # file name to be replace with shared guid\n\n return result_dict\n # show_obj_prop_debug()",
"def print_logo(self):\n\n pkg = importlib_resources.files(\"siena3d\")\n pkg_logo_file = pkg / \"data\" / \"logo.txt\"\n with pkg_logo_file.open() as f:\n logo = f.readlines()\n\n terminalsize = os.get_terminal_size()\n logosize = (len(logo[0]), len(logo)) # (x,y) assume rectangular shape\n\n for i in logo:\n line = i.rsplit('\\n')[0]\n string = (\"%s\".center((terminalsize[0] - logosize[0] // 2) // 2) % line)[:terminalsize[0]]\n print(string)",
"def get_all_logos() -> None:\n base_url = 'http://web2.ncaa.org/ncaa_style/img/All_Logos/{size}/{school_id}.gif'\n sizes = ['sm', 'lg'] # some schools have both sizes, some only have one or neither\n \n school_id_dict = data_utils.get_school_id_dict()\n \n logo_list = []\n logo_count = 0\n \n for school in school_id_dict:\n for size in sizes:\n url = base_url.format(size=size, school_id=school_id_dict[school])\n \n response = requests.get(url)\n\n # 200 means it got the page for that url which should include the logo\n if response.status_code == 200:\n print('Logo found: {school} {size}'.format(school=school, size=size))\n logo_file_name = '{logos_path}{school_name}_{size}.gif'.format(\n logos_path=file_utils.get_logos_directory(), school_name=school, size=size)\n \n # write the logo to file\n with open(logo_file_name, 'wb') as logo_file:\n logo_file.write(response.content)\n logo_list.append([school, size, True])\n logo_count += 1\n\n else:\n print('Logo not found: {school} {size}'.format(school=school, size=size))\n logo_list.append([school, size, False])\n \n # keeps track of whether schools have a logo or not\n logo_csv_name = file_utils.get_logos_csv_name()\n header = ['school_name', 'size', 'logo']\n with open(logo_csv_name, 'wb') as logo_csv:\n writer = unicodecsv.writer(logo_csv)\n writer.writerow(header)\n writer.writerows(logo_list)\n \n print('{} logos found out of {}'.format(logo_count, len(logo_list)))",
"def bicorpora_filenames():\n import common.hyperparameters, hyperparameters\n HYPERPARAMETERS = common.hyperparameters.read(\"language-model\")\n \n for (l1, l2) in HYPERPARAMETERS[\"W2W BICORPORA\"]:\n d = join(HYPERPARAMETERS[\"DATA_DIR\"], \"%s-%s\" % (l1, l2))\n assert isdir(d)\n l1re = re.compile(\"%s$\" % l1)\n alignre = re.compile(\"align.*-%s$\" % l1)\n for f1 in os.listdir(d):\n f1 = join(d, f1)\n if not l1re.search(f1) or alignre.search(f1): continue\n f2 = l1re.sub(l2, f1)\n assert exists(f2)\n falign = l1re.sub(\"align.%s-%s\" % (l1, l2), f1)\n assert exists(falign)\n yield l1, l2, f1, f2, falign",
"def generate_image(self) -> None:",
"def _generate_file_names():\n name_base = str(uuid.uuid4())[:6]\n return (name_base + '.out', name_base + '.err')",
"def gen_name_stamp_with_job_title(self, n_images):\n for i in range(n_images):\n # Select text from list at random and process text \n title, name = random.choice(self.texts)\n title = self.process_text(title, self.title_uppercase_prob)\n name = self.process_text(name, self.name_uppercase_prob)\n\n # Select font directory from list at random\n name_fontdir = random.choice(self.name_font_subdirs)\n if len(self.title_font_subdirs) > 0:\n title_fontdir = random.choice(self.title_font_subdirs)\n else:\n title_fontdir = name_fontdir\n\n # Get font size and line spacing\n name_font_size = self.get_size(self.name_font_size)\n title_font_size = self.get_size(self.title_font_size)\n line_spacing = self.get_size(self.line_spacing)\n\n # Generate image for job title and name\n title_image = gen_image_from_text(title, title_font_size, fontdir=title_fontdir,\n text_color=self.text_color, transparent_bg=self.transparent_bg)\n name_image = gen_image_from_text(name, name_font_size, fontdir=name_fontdir, \n text_color=self.text_color, transparent_bg=self.transparent_bg)\n\n # Get the size of generated images\n w_name, h_name = name_image.size[:2]\n w_title, h_title = title_image.size[:2]\n\n # Resize job title image using max width and height ratio if given\n max_w_title = int(w_name * self.max_width_ratio) if self.max_width_ratio else w_title\n max_h_title = int(h_name * self.max_height_ratio) if self.max_height_ratio else h_title\n w_title = min(w_title, max_w_title)\n h_title = min(h_title, max_h_title)\n title_image = title_image.resize([w_title, h_title], Image.ANTIALIAS)\n\n # Create a new image\n width = max(w_title, w_name)\n height = h_title + line_spacing + h_name\n alpha = 0 if self.transparent_bg else 255\n image = Image.new('RGBA', (width, height), color=(255, 255, 255, alpha))\n\n # Paste all generated images into the new image\n if random.random() < self.title_first_prob:\n image.paste(title_image, ((width - w_title) // 2, 0), title_image)\n image.paste(name_image, ((width - w_name) // 2, h_title + line_spacing), name_image)\n else:\n image.paste(name_image, ((width - w_name) // 2, 0), name_image)\n image.paste(title_image, ((width - w_title) // 2, h_name + line_spacing), title_image)\n\n # Save generated image\n filename = datetime.now().strftime(f\"%Y_%m_%d_%H_%M_%S_%f_{i}.png\")\n image.save(os.path.join(self.outdir, filename))",
"def gamelogo():\n cls()\n for i in value.logo.split(\"\\n\"):\n fancyPrint(i, speed=0.00001)\n print(\" \", end=\"\")\n time.sleep(0.75)\n fancyPrint(\"RPGame studios (C)\", speed=0.3)\n time.sleep(5)\n cls()",
"def generator(images, labels):\n\n def _gen():\n for image, label in zip(images, labels):\n yield image, label\n\n return _gen",
"def populate_files():\n image_list_html = \"<ul>\"\n\n for frame in CameraHandler.image_queue:\n image_list_html += \"<li>frame: <a href=\\\"/{}\\\">{}</a></li>\".format(\n frame,\n frame\n )\n\n for stream in CameraHandler.stream_queue:\n image_list_html += \"<li>stream: <a href=\\\"/{}\\\">{}</a></li>\".format(\n stream,\n stream\n )\n\n image_list_html += \"</ul>\"\n\n return image_list_html",
"def testGetImageItemList(self):\n image_list = self.oogranulator.getImageItemList()\n self.assertEquals([('10000000000000C80000009C38276C51.jpg', ''),\n ('10000201000000C80000004E7B947D46.png', 'TioLive Logo'),\n ('10000201000000C80000004E7B947D46.png', ''),\n # XXX The svg image are stored into odf as svm\n ('2000004F00004233000013707E7DE37A.svm', 'Python Logo'),\n ('10000201000000C80000004E7B947D46.png',\n 'Again TioLive Logo')], image_list)",
"def images(name):\n\n return static_file(name, root='images/')"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
build plaques structure from CSV file
|
def load_csv(filename):
plaques = []
plqs = csv.reader(open(filename, 'rb'))
for row in plqs:
image_url = row[1]
text = row[2]
# ignore id (0) and plaque url (3) for now
last_slash = image_url.rfind('/')
filename = image_url[last_slash+1:]
filename_base = os.path.splitext(filename)[0] # turn 'abc.jpg' into 'abc'
filename = filename_base + '.tif'
root_url = image_url[:last_slash+1]
plaque = [root_url, filename, text]
plaques.append(plaque)
return plaques
|
[
"def import_from_csv(self, csv_file):\n reader = csv.reader(csv_file)\n\n self.variable_labels = next(reader, None)[1:]\n self.element_labels = []\n self.data = []\n\n data_mode = True\n for row in reader:\n if not any(row):\n if data_mode:\n data_mode = False\n continue\n else:\n if data_mode:\n self.element_labels.append(row[0])\n self.data.append([int(i) for i in row[1:]])\n else:\n self.weights = [int(i) for i in row[1:]]\n self.neg_min = [int(i) for i in next(reader, None)[1:]]\n self.pos_max = [int(i) for i in next(reader, None)[1:]]\n break",
"def __init__(self, path_to_csv):\n with open(path_to_csv) as csvfile:\n reader = csv.reader(csvfile)\n t = BSTree()\n for row in reader:\n traffic = row[0]\n protocol = row[1]\n ip = row[3]\n ports = row[2]\n if '-' in ports:\n nports = ports.split('-')\n port1 = int(nports[0])\n portn = int(nports[1])\n for p in range(port1, portn):\n n = Node(p, traffic, protocol, ip)\n t.insert(n)\n else:\n n = Node(int(ports), traffic, protocol, ip)\n t.insert(n)\n self.tree = t",
"def read_kg_data(csv_file):\n print(f\"Started a model builder for data from: {csv_file}\")\n df = pd.read_csv(csv_file)\n df.columns = [\"h\", \"r\", \"t\"]\n entities = list(set(df[\"h\"].tolist() + df[\"t\"].tolist()))\n relations = list(set(df[\"r\"].tolist()))\n return entities, relations",
"def csvparser(cfile):\r\n\r\n csvreader = csv.reader(cfile, delimiter = ',')\r\n tile = []\r\n count = 0\r\n for row in csvreader:\r\n if count == 0:\r\n count += 1\r\n continue\r\n else:\r\n tile.append(row[1:])\r\n return tile",
"def import_from_csv(self, csv_file):\n data = []\n\n reader = csv.reader(csv_file)\n self.x_labels = next(reader, None)[1:]\n\n for row in reader:\n self.y_labels.append(row[0])\n d = []\n for cell in row[1:]:\n try:\n d.append(float(cell))\n except ValueError:\n d.append(0.0)\n data.append(d)\n self.data = numpy.array(data)\n self.fill()",
"def parse(input):\n with open(input) as file:\n input_reader = csv.DictReader(file)\n\n # make seperate lists for data to put in data dictionary\n countries = []\n regions = []\n population_density = []\n infant_mortality = []\n gdp_dollars = []\n # make list for central tendency and five number summary\n gdp_freq = []\n infant_five = []\n\n # make dictionary for data storage\n data_dict = {}\n\n # read in csv file per row\n for row in input_reader:\n # get data from csv file per row\n country = row['Country'].strip()\n region = row['Region'].strip()\n pop_den = row['Pop. Density (per sq. mi.)'].strip().replace(',', '.')\n infant = row['Infant mortality (per 1000 births)'].strip().replace(',', '.')\n gdp = row['GDP ($ per capita) dollars'].strip(' dollars')\n\n # missing or invalid values\n if pop_den == 'unknown' or pop_den == '':\n pop_den = None\n if infant == 'unknown' or infant == '':\n infant = None\n # gdp of Surinama is invalid\n if gdp == 'unknown' or gdp == '' or gdp == '400000':\n gdp = None\n\n # make floats\n if gdp != None:\n gdp = int(gdp)\n # make list without None values for histogram\n gdp_freq.append(gdp)\n if infant != None:\n infant = float(infant)\n infant_five.append(infant)\n if pop_den != None:\n pop_den = float(pop_den)\n\n # add data to all lists\n countries.append(country)\n regions.append(region)\n population_density.append(pop_den)\n infant_mortality.append(infant)\n gdp_dollars.append(gdp)\n\n\n # add data to data_dict\n data_dict['Country'] = countries\n data_dict['Region'] = regions\n data_dict['Pop. Density (per sq. mi.)'] = population_density\n data_dict['Infant mortality (per 1000 births)'] = infant_mortality\n data_dict['GDP ($ per capita) dollars'] = gdp_dollars\n\n # make dataframe with all data\n df = pd.DataFrame(data_dict)\n \n\n return df, gdp_freq, infant_five, data_dict",
"def parse_categories(path):\n\n conn = _sqlite3.connect(db_path + path)\n cursor = conn.cursor()\n with open(categories_path) as infile:\n reader = csv.reader(infile)\n first_line = True\n for category in reader:\n if first_line:\n first_line = False\n continue\n print(category)\n record = [category[0], category[2], category[1]]\n q.categories_insert(cursor, tuple(record))\n conn.commit()",
"def process_data_csv(file_path):\n df = pd.read_csv(file_path)\n # filter rows to finished projects, i.e. success or failure\n df = df.loc[df['state'].isin(['successful', 'failed'])]\n ## now load some categories that are stored as jsons\n # add some features\n df = df.assign(\n usd_goal = lambda x: x[\"goal\"] * x[\"fx_rate\"],\n available_time = lambda x: x[\"deadline\"] - x[\"launched_at\"], # figure out how time is encoded?\n blurb_len = lambda x: x[\"blurb\"].str.len()\n )\n # 1. project category\n cat_cols_to_keep = [\"id\", \"position\", \"parent_id\", \"color\"]\n tmp = df[\"category\"].apply(json.loads).apply(pd.Series)[cat_cols_to_keep]\n tmp.columns = \"cat_\" + tmp.columns\n cat_cols_to_keep = [\"cat_\" + w for w in cat_cols_to_keep]\n df = pd.concat((df, tmp), axis = 1)\n\n # 2. project location\n loc_cols_to_keep = [\"id\", \"type\", \"state\"]\n tmp = df['location'].fillna('{}').apply(json.loads).apply(pd.Series)[loc_cols_to_keep]\n tmp.columns = \"loc_\" + tmp.columns\n loc_cols_to_keep = [\"loc_\" + w for w in loc_cols_to_keep]\n df = pd.concat((df, tmp), axis=1)\n # 3. ??\n\n # specify cols to keep\n df_cols_to_keep = [\n \"state\", \"usd_goal\", \"available_time\", \"blurb_len\", \"launched_at\", \"deadline\", \"blurb\",\n \"name\", \"currency\", \"country\", \"is_starred\", \"is_starrable\", \"spotlight\", \"staff_pick\", \"photo\", \"urls\"\n ]\n return df[ df_cols_to_keep + cat_cols_to_keep + loc_cols_to_keep ]",
"def loadfile(name):\n\treader = csv.DictReader(open(name, \"r\"))\n\n\tfactories = []\n\n\tfactory = None\n\tfor row in reader:\n\t\tif len(row['Factory Name']) > 0:\n\t\t\tif factory is None or factory.name != row['Factory Name']:\n\t\t\t\tfactory = Factory(row['Factory Name'], row['Description'], row['Maximum'])\n\t\t\t\tfactories.append(factory)\n\n\t\trequirement = split(row['Requirement'])\t\n\t\tproduce = split(row['Produce'])\t\n\n\t\tfactory.add(requirement, produce)\n\n\treturn factories",
"def parser_file(file_in, need_mapping, header=False):\n mapping = {} # dict for the mappings of IDs \n last_id = 0 \n with open(file_in) as in_file:\n reader = csv.reader(in_file, delimiter=SEPARATOR)\n\n iter_reader = iter(reader)\n if header:\n next(iter_reader)\n F = {}\n layers = {}\n dim = 0 # no. of nonzero entries\n l = 0 # no. of layers\n for row in iter_reader:\n if row:\n source, target = map(int, row[:2])\n layer = row[2:3][0]\n if need_mapping:\n if source not in mapping:\n mapping[source] = last_id\n last_id += 1\n\n if target not in mapping:\n mapping[target] = last_id\n last_id += 1\n\n source = mapping[source]\n target = mapping[target]\n dim = max(dim, source, target)\n if layer not in layers:\n layers[layer] = l\n F[layers[layer]] = dok_matrix((DIM_MAX, DIM_MAX))\n l += 1\n\n if len(row) > 3:\n print(row)\n weight = float(row[3])\n F[layers[layer]][source, target] = weight\n else:\n F[layers[layer]][source, target] = 1\n\n\n dim += 1\n P = {}\n for i in F:\n P[i] = F[i].tocsr()[:dim, :dim]\n size = (len(P), len(mapping))\n\n return P, mapping, size",
"def parse_facilities_csv():\n # Parse CSV files\n facilities = []\n for fname in os.listdir(cwd):\n if not fname.endswith('.csv'):\n continue\n\n file_path = os.path.join(cwd, fname) \n with open(file_path, 'rb') as f:\n logging.debug('Parsing: ' + f.name)\n\n reader = csv.reader(f, delimiter=',', quotechar='\"')\n headers = [h.strip('\"') for h in reader.next()]\n\n for row in reader:\n facility = {}\n for header, col in zip(headers, row):\n facility[header.lower()] = col\n facilities.append(facility)\n \n # Build output data structure\n lgas = {}\n for fac in facilities:\n lga_id = fac['unique_lga']\n fac_id = fac['uid']\n fac_name = fac['name']\n\n lga = lgas.setdefault(lga_id, [])\n lga.append({\n 'id': fac_id,\n 'name': fac_name\n })\n return lgas",
"def constraints_from_csv(filename, power_spectrum, boxlen):\n f = open(filename)\n table = csvreader(f)\n # Skip header:\n table.next()\n return constraints_from_table(table, power_spectrum, boxlen)",
"def initDataStructs():\n\n with open(source) as csvfile:\n reader = csv.DictReader(csvfile)\n for row in reader:\n table_LoD[int(row['Index'])] = row\n for k in row.keys():\n table_DoL[k][int(row['Index'])] = row[k]",
"def csv2yaml(csvfile):\n statements = list_statements(csvreader(csvfile))\n shapes = list_shapes(statements)\n return shapes2yaml(shapes)",
"def parse_csv( fileLocation, Unique_Features=None ):\r\n\r\n print 'Parsing CSV: ', fileLocation\r\n\r\n headers = []\r\n\r\n # Change directory to the folder\r\n os.chdir( os.path.dirname( fileLocation) )\r\n\r\n # grab all the rows in the csv file\r\n coordFileToList = [ line for line in csv.reader(open( fileLocation, 'r')) ]\r\n\r\n # grabs the csv column headers \r\n headers = coordFileToList[0]\r\n\r\n # deletes list item, because it will get in the way later on if we don't\r\n del coordFileToList[0]\r\n\r\n # file name without the extension and minus the path\r\n rootFileName = os.path.splitext( os.path.basename( fileLocation ))[0]\r\n\r\n # If parsing csv for polylines or polygons\r\n if Unique_Features == True:\r\n\r\n # For kml_to_line and kml_to_polygon. Not used for kml_to_point. List \r\n # of names of the unique spatial feataures in csv file\r\n Unique_Features = list(set( [each[0] for each in coordFileToList ] ))\r\n\r\n return coordFileToList, rootFileName, headers, Unique_Features\r\n\r\n else:\r\n \r\n return coordFileToList, rootFileName, headers",
"def from_csv(cls, filepath_or_buffer): \n records = pd.read_csv(filepath_or_buffer)\n\n return cls(records)\n\n # ------------------------------------------------------------------\n # Old implementation kept for future use:\n\n # # Read the data from the csv file, assuming the third column of the\n # # file represents timestamp and parsing it as a datetime.\n # records = pd.read_csv(\n # filepath,\n # index_col=[0, 1],\n # header=[0, 1], \n # parse_dates=[2]\n # )\n\n # # Convert the index's 'offset' level to TimedeltaIndex.\n # records.index = records.index.set_levels(\n # pd.TimedeltaIndex(data.index.get_level_values('offset')),\n # level='offset')\n\n # # Fix column level values, an artifact of blank level values in a\n # # .csv file.\n # fields = data.columns.get_level_values('field')\n\n # #srcs = data.columns.get_level_values('source').str.replace('Un.*', 'device')\n # srcs = data.columns.get_level_values('elev_source').str.replace('Un.*', 'device')\n \n # col_tups = [(field, src) for field, src in zip(fields, srcs)]\n # data.columns = pandas.MultiIndex.from_tuples(col_tups,\n # names=['field', 'source'])\n # data['time', 'device'] = \\\n # (data['timestamp', 'device'] \\\n # - data['timestamp', 'device'].iloc[0]).dt.total_seconds()\n\n # ------------------------------------------------------------------",
"def _process_csv(filename):\n import csv\n\n node_dict, neighbor_dict = {}, {}\n\n with open(filename, \"r\") as csv_file:\n for row in csv.DictReader(csv_file):\n node = EuclideanNode(\n node_type=row['NodeType'],\n name=row['Name'],\n floor=row['Floor'],\n coord=eval(row['Coordinates'])\n )\n node_dict[row['Name']] = node\n neighbor_dict[row['Name']] = eval(row['Neighbors'])\n return node_dict, neighbor_dict",
"def __post_init__(self) -> None:\n verboseprint = verbose_print(self.verbose)\n with Path(self.fpath).open(\"r\", newline=\"\") as file:\n sample_data = file.read(1024) # Read a sample of the CSV data\n dialect = typing.cast(csv.Dialect, csv.Sniffer().sniff(sample_data))\n self._note = pd.read_csv(self.fpath, dialect=dialect)\n self.wells: list[str] = np.array(self._note)[:, 0].tolist()\n verboseprint(f\"Wells {self.wells[:2]}...{self.wells[-2:]} generated.\")",
"def csv_to_lst_build_sub(filename):\n lst = []\n with open(filename) as csv_file:\n reader = csv.reader(csv_file)\n for row in reader:\n first = tuple(row[:-1])\n if row[-1] == \"True\":\n second = True\n elif row[-1] == \"False\":\n second = False\n else:\n second = int(row[-1])\n lst.append((first, second))\n\n return lst",
"def parse_csv_line(csv_line):"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Calculates the value of Gamma and phi given the input site and the input parameters.
|
def Gamma_phi_fn(site,p):
if site.pos[0] <= p.left[-1]: #
Gamma = p.GammaL; phi = p.phiL
elif p.middle[0] <= site.pos[0] <= p.middle[-1]:
Gamma = 0; phi = 0
elif p.right[0] <= site.pos[0] <= p.right[-1]:
Gamma = p.GammaR; phi = p.phiR
else:
raise ValueError("In Gamma_phi_fn: site.pos[0] was in neither parts of the system. Cannot assign Gamma- and phi-values.")
return [Gamma,phi]
|
[
"def get_gamma_distribution_params(mean, std):\n # mean = k * theta\n # var = std**2 = k * theta**2\n k = std**2 / mean\n theta = mean / k\n return k, theta",
"def gamma(c, g):\n\n pass",
"def invgamma(x, a, b):\n return stats.gamma.pdf(1 / x, a, scale=(1 / b)) / x ** 2",
"def gamma(x):\n return 1.0",
"def calculate_g32(params):\n gamma32 = params[\"gamma32\"]\n Delta = calculate_Delta(params)\n\n return 1 - 1j*gamma32/2/Delta",
"def gammaPhe(alpha=1,beta=1):\r\n while 1: # an iterator for a random phenotype\r\n dat = random.gammavariate(float(alpha),float(beta))\r\n yield '%e' % dat",
"def get_phi(x, y, xa, ya):\n return np.exp(-alpha*(x - xa)**2 - alpha*(y - ya)**2)",
"def rhoe(pres):\n\n global gamma\n rhoe = pres/(gamma - 1.0)\n\n return rhoe",
"def _get_pd_gamma(data, params, var_elta_2_cast, sub_x_mean, dtype,\n cast_dtype):\n xl_mul = te.lang.cce.vmul(var_elta_2_cast, sub_x_mean)\n pdga_mul = te.lang.cce.vmul(data.get(\"data_dy\"), xl_mul)\n\n if params.get(\"param_axis\"):\n pd_gamma_ub = te.lang.cce.sum(pdga_mul, params.get(\"param_axis\"),\n keepdims=True)\n if dtype == \"float16\" and cast_dtype == \"float32\":\n pd_gamma = te.lang.cce.cast_to(pd_gamma_ub, dtype)\n else:\n return pd_gamma_ub\n else:\n if dtype == \"float16\" and cast_dtype == \"float32\":\n pd_gamma = te.lang.cce.cast_to(pdga_mul, dtype)\n else:\n return pdga_mul\n\n return pd_gamma",
"def haei_with_gamma(x, gamma):\n\n return 1 - (gamma/np.sqrt(gamma**2 + x))",
"def _gamma_ratio( xs, match_param, nonmatch_param, exp_param ):\n num = sp.stats.gamma.pdf( xs, *match_param )\n denom = sp.stats.gamma.pdf( xs, *nonmatch_param)\n val = num / (num+denom) * ( 1-exp_param[0] * np.exp(-xs/exp_param[1]))\n return np.log2(val) - np.log2(1.0-val)",
"def gammanu_to_tthphi(gamma, nu):\n ttheta = math.acos(math.cos(gamma)*math.cos(nu))\n phi = math.atan2(math.sin(nu), math.cos(nu)*math.sin(gamma))\n return ttheta, phi",
"def gamma(_df):\n return 1.e-6*CP*_df['p_a']/(0.622*(2.501-0.00236*_df['t_a']))",
"def gamma(F, F_grid, G_grid):\n zero_index = F.size//2\n F_step = abs(F_grid[1] - F_grid[0])\n\n G0_indices = np.floor(-np.log(np.tanh(G_grid/2)) / F_step)\n G0_indices = np.clip(G0_indices, 0, zero_index - 1).astype(int)\n G0 = 1 - F.take(G0_indices + zero_index)\n\n G1_indices = np.floor(np.log(np.tanh(G_grid/2)) / F_step)\n G1_indices = np.clip(G1_indices, -zero_index, -1).astype(int)\n G1 = F.take(G1_indices + zero_index)\n\n return np.stack((G0, G1))",
"def calculate_g21(params):\n delta1 = params[\"delta1\"]\n gamma21 = params[\"gamma21\"]\n\n return 1 - 1j*gamma21/2/delta1",
"def gOfPhi(p):\r\n return 1 / math.sqrt(1 + 3 * p **2 / math.pi **2)",
"def phi(x1, x2):\n return np.array([x1, x2, x1**2.0 + x2**2.0])",
"def hoppingx(site0,site1,p):\n\t # print(\"%s: in hoppingx()\" %str(misc.round_time(datetime.datetime.now(),round_to=60)))\n\treturn -p.tx*tau_z + 1j*p.alphahbar/(2.*p.ax)*sigma_ytau_z",
"def gamma(self) -> float:\n return self.angles[2]"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Hopping energy of onedimensional semiconductor, whose Hamiltonian is given as in onsite_1D_semiconductor.
|
def hoppingy_1D_semiconductor(site0,site1,p):
#print("%s: in hoppingy_1D_semiconductor()" %str(misc.round_time(datetime.datetime.now(),round_to=60)))
return -p.t_N*tau_z + 1j*p.alphahbar/(2*p.ay)*sigma_ytau_z
|
[
"def energy(params,circuit):\n # setup circuit (resolve parameters to numerical values)\n resolver = cirq.ParamResolver({'theta'+str(j):params[j] for j in range(n_var_params)})\n resolved_circuit = cirq.resolve_parameters(circuit, resolver) \n u = resolved_circuit.unitary(qubit_order = qp+qb)\n unitary = u.reshape([2**nphys,2**nbond,2**nphys,2**nbond])\n # Convert to MPS and compute <H> \n # change the order of indices to [p, vL, vR] = [p_out, b_in, b_out] \n # (with p_in = 0 to go from unitary to isometry)\n B = np.swapaxes(unitary[:,:,0,:],1,2)\n psi = MPS.from_Bflat([site], [B], bc='infinite', dtype=complex, form=None)\n psi.canonical_form()\n psi.convert_form(psi.form)\n holo_E = (H.expectation_value(psi)).real\n \n return holo_E",
"def HenonHeiles_Hamiltonian(t, u):\n points_positions = u.T[:2]\n points_momenta = u.T[2:4]\n x, y = points_positions\n p_x, p_y = points_momenta\n # Potential energy function\n H = 0.5*(x**2 + y**2) + (y * x**2) - (1/3)*y**3 + 0.5*(p_x**2 + p_y**2)\n return H",
"def onsite_1D_superconductor_pincher(site,p):\n\tEz_eff = p.Ez\n\treturn (2*p.ty_SC_pincher - p.mu_SC_pincher)*tau_z + Ez_eff*sigma_y/2. + p.Delta_pincher*tau_x",
"def opt_energy_env(isos_012,\n h_op_1site,\n h_mpo_2site,\n states_1site_above):\n if len(isos_012) == 1: # top of tree\n h_mpo_2site = add_mpos_2site(h_mpo_2site, reflect_mpo_2site(h_mpo_2site))\n env = opt_energy_env_1site(isos_012[0], h_op_1site, h_mpo_2site,\n states_1site_above[0])\n else:\n env1 = opt_energy_env_1site(isos_012[0], h_op_1site, h_mpo_2site,\n states_1site_above[0])\n env2 = opt_energy_env_2site(isos_012, h_mpo_2site, states_1site_above[1:])\n env = env1 + env2\n\n return env",
"def thermodynamics(pyom):\n advect_temperature(pyom)\n advect_salinity(pyom)\n\n if pyom.enable_conserve_energy:\n \"\"\"\n advection of dynamic enthalpy\n \"\"\"\n if pyom.enable_superbee_advection:\n advection.adv_flux_superbee(pyom,pyom.flux_east,pyom.flux_north,pyom.flux_top,pyom.Hd[:,:,:,pyom.tau])\n else:\n advection.adv_flux_2nd(pyom,pyom.flux_east,pyom.flux_north,pyom.flux_top,pyom.Hd[:,:,:,pyom.tau])\n\n pyom.dHd[2:-2, 2:-2, :, pyom.tau] = pyom.maskT[2:-2, 2:-2, :] * (-(pyom.flux_east[2:-2, 2:-2, :] - pyom.flux_east[1:-3, 2:-2, :]) \\\n / (pyom.cost[np.newaxis, 2:-2, np.newaxis] * pyom.dxt[2:-2, np.newaxis, np.newaxis]) \\\n - (pyom.flux_north[2:-2, 2:-2,:] - pyom.flux_north[2:-2, 1:-3, :]) \\\n / (pyom.cost[np.newaxis, 2:-2, np.newaxis] * pyom.dyt[np.newaxis, 2:-2, np.newaxis]))\n pyom.dHd[:,:,0,pyom.tau] += -pyom.maskT[:,:,0] * pyom.flux_top[:,:,0] / pyom.dzt[0]\n pyom.dHd[:,:,1:,pyom.tau] += -pyom.maskT[:,:,1:] * (pyom.flux_top[:,:,1:] - pyom.flux_top[:,:,:-1]) / pyom.dzt[np.newaxis, np.newaxis, 1:]\n\n \"\"\"\n changes in dyn. Enthalpy due to advection\n \"\"\"\n aloc = np.zeros((pyom.nx+4, pyom.ny+4, pyom.nz))\n aloc[2:-2, 2:-2, :] = pyom.grav / pyom.rho_0 * (-pyom.int_drhodT[2:-2, 2:-2, :, pyom.tau] * pyom.dtemp[2:-2, 2:-2, :, pyom.tau] \\\n - pyom.int_drhodS[2:-2, 2:-2, :, pyom.tau] * pyom.dsalt[2:-2, 2:-2, :, pyom.tau]) \\\n - pyom.dHd[2:-2, 2:-2, :, pyom.tau]\n\n \"\"\"\n contribution by vertical advection is - g rho w / rho0, substract this also\n \"\"\"\n aloc[:, :, :-1] += -0.25 * pyom.grav / pyom.rho_0 * pyom.w[:, :, :-1, pyom.tau] \\\n * (pyom.rho[:, :, :-1, pyom.tau] + pyom.rho[:, :, 1:, pyom.tau]) \\\n * pyom.dzw[np.newaxis, np.newaxis, :-1] / pyom.dzt[np.newaxis, np.newaxis, :-1]\n aloc[:, :, 1:] += -0.25 * pyom.grav / pyom.rho_0 * pyom.w[:, :, :-1, pyom.tau] \\\n * (pyom.rho[:, :, 1:, pyom.tau] + pyom.rho[:, :, :-1, pyom.tau]) \\\n * pyom.dzw[np.newaxis, np.newaxis, :-1] / pyom.dzt[np.newaxis, np.newaxis, 1:]\n\n if pyom.enable_conserve_energy and pyom.enable_tke:\n \"\"\"\n dissipation by advection interpolated on W-grid\n \"\"\"\n pyom.P_diss_adv[...] = 0.\n diffusion.dissipation_on_wgrid(pyom, pyom.P_diss_adv, aloc=aloc)\n\n \"\"\"\n distribute pyom.P_diss_adv over domain, prevent draining of TKE\n \"\"\"\n fxa = np.sum(pyom.area_t[2:-2, 2:-2, np.newaxis] * pyom.P_diss_adv[2:-2, 2:-2, :-1] \\\n * pyom.dzw[np.newaxis, np.newaxis, :-1] * pyom.maskW[2:-2, 2:-2, :-1]) \\\n + np.sum(0.5 * pyom.area_t[2:-2, 2:-2] * pyom.P_diss_adv[2:-2, 2:-2, -1] \\\n * pyom.dzw[-1] * pyom.maskW[2:-2, 2:-2, -1])\n tke_mask = pyom.tke[2:-2, 2:-2, :-1, pyom.tau] > 0.\n fxb = np.sum(pyom.area_t[2:-2, 2:-2, np.newaxis] * pyom.dzw[np.newaxis, np.newaxis, :-1] * pyom.maskW[2:-2, 2:-2, :-1] * tke_mask) \\\n + np.sum(0.5 * pyom.area_t[2:-2, 2:-2] * pyom.dzw[-1] * pyom.maskW[2:-2, 2:-2, -1])\n pyom.P_diss_adv[...] = 0.\n pyom.P_diss_adv[2:-2, 2:-2, :-1] = fxa / fxb * tke_mask\n pyom.P_diss_adv[2:-2, 2:-2, -1] = fxa / fxb\n\n \"\"\"\n Adam Bashforth time stepping for advection\n \"\"\"\n pyom.temp[:,:,:,pyom.taup1] = pyom.temp[:,:,:,pyom.tau] + pyom.dt_tracer * \\\n ((1.5+pyom.AB_eps)*pyom.dtemp[:,:,:,pyom.tau] - (0.5+pyom.AB_eps)*pyom.dtemp[:,:,:,pyom.taum1]) * pyom.maskT\n pyom.salt[:,:,:,pyom.taup1] = pyom.salt[:,:,:,pyom.tau] + pyom.dt_tracer * \\\n ((1.5+pyom.AB_eps)*pyom.dsalt[:,:,:,pyom.tau] - (0.5+pyom.AB_eps)*pyom.dsalt[:,:,:,pyom.taum1]) * pyom.maskT\n\n \"\"\"\n horizontal diffusion\n \"\"\"\n with pyom.timers[\"isoneutral\"]:\n if pyom.enable_hor_diffusion:\n diffusion.tempsalt_diffusion(pyom)\n if pyom.enable_biharmonic_mixing:\n diffusion.tempsalt_biharmonic(pyom)\n\n \"\"\"\n sources like restoring zones, etc\n \"\"\"\n if pyom.enable_tempsalt_sources:\n diffusion.tempsalt_sources(pyom)\n\n \"\"\"\n isopycnal diffusion\n \"\"\"\n if pyom.enable_neutral_diffusion:\n pyom.P_diss_iso[...] = 0.0\n pyom.dtemp_iso[...] = 0.0\n pyom.dsalt_iso[...] = 0.0\n isoneutral.isoneutral_diffusion_pre(pyom)\n isoneutral.isoneutral_diffusion(pyom,pyom.temp,True)\n isoneutral.isoneutral_diffusion(pyom,pyom.salt,False)\n if pyom.enable_skew_diffusion:\n pyom.P_diss_skew[...] = 0.0\n isoneutral.isoneutral_skew_diffusion(pyom,pyom.temp,True)\n isoneutral.isoneutral_skew_diffusion(pyom,pyom.salt,False)\n\n with pyom.timers[\"vmix\"]:\n \"\"\"\n vertical mixing of temperature and salinity\n \"\"\"\n pyom.dtemp_vmix[...] = pyom.temp[:,:,:,pyom.taup1]\n pyom.dsalt_vmix[...] = pyom.salt[:,:,:,pyom.taup1]\n\n a_tri = np.zeros((pyom.nx, pyom.ny, pyom.nz))\n b_tri = np.zeros((pyom.nx, pyom.ny, pyom.nz))\n c_tri = np.zeros((pyom.nx, pyom.ny, pyom.nz))\n d_tri = np.zeros((pyom.nx, pyom.ny, pyom.nz))\n delta = np.zeros((pyom.nx, pyom.ny, pyom.nz))\n\n ks = pyom.kbot[2:-2, 2:-2] - 1\n delta[:, :, :-1] = pyom.dt_tracer / pyom.dzw[np.newaxis, np.newaxis, :-1] * pyom.kappaH[2:-2, 2:-2, :-1]\n delta[:, :, -1] = 0.\n a_tri[:, :, 1:] = -delta[:,:,:-1] / pyom.dzt[np.newaxis, np.newaxis, 1:]\n b_tri[:, :, 1:] = 1 + (delta[:, :, 1:] + delta[:, :, :-1]) / pyom.dzt[np.newaxis, np.newaxis, 1:]\n b_tri_edge = 1 + delta / pyom.dzt[np.newaxis, np.newaxis, :]\n c_tri[:, :, :-1] = -delta[:, :, :-1] / pyom.dzt[np.newaxis, np.newaxis, :-1]\n d_tri[...] = pyom.temp[2:-2, 2:-2, :, pyom.taup1]\n d_tri[:, :, -1] += pyom.dt_tracer * pyom.forc_temp_surface[2:-2, 2:-2] / pyom.dzt[-1]\n sol, mask = utilities.solve_implicit(pyom, ks, a_tri, b_tri, c_tri, d_tri, b_edge=b_tri_edge)\n pyom.temp[2:-2, 2:-2, :, pyom.taup1] = np.where(mask, sol, pyom.temp[2:-2, 2:-2, :, pyom.taup1])\n d_tri[...] = pyom.salt[2:-2, 2:-2, :, pyom.taup1]\n d_tri[:, :, -1] += pyom.dt_tracer * pyom.forc_salt_surface[2:-2, 2:-2] / pyom.dzt[-1]\n sol, mask = utilities.solve_implicit(pyom, ks, a_tri, b_tri, c_tri, d_tri, b_edge=b_tri_edge)\n pyom.salt[2:-2, 2:-2, :, pyom.taup1] = np.where(mask, sol, pyom.salt[2:-2, 2:-2, :, pyom.taup1])\n\n pyom.dtemp_vmix[...] = (pyom.temp[:,:,:,pyom.taup1] - pyom.dtemp_vmix) / pyom.dt_tracer\n pyom.dsalt_vmix[...] = (pyom.salt[:,:,:,pyom.taup1] - pyom.dsalt_vmix) / pyom.dt_tracer\n\n \"\"\"\n boundary exchange\n \"\"\"\n if pyom.enable_cyclic_x:\n cyclic.setcyclic_x(pyom.temp[..., pyom.taup1])\n cyclic.setcyclic_x(pyom.salt[..., pyom.taup1])\n\n with pyom.timers[\"eq_of_state\"]:\n calc_eq_of_state(pyom, pyom.taup1)\n\n \"\"\"\n surface density flux\n \"\"\"\n pyom.forc_rho_surface[...] = (\n density.get_drhodT(pyom,pyom.salt[:,:,-1,pyom.taup1],pyom.temp[:,:,-1,pyom.taup1],np.abs(pyom.zt[-1])) * pyom.forc_temp_surface \\\n + density.get_drhodS(pyom,pyom.salt[:,:,-1,pyom.taup1],pyom.temp[:,:,-1,pyom.taup1],np.abs(pyom.zt[-1])) * pyom.forc_salt_surface \\\n ) * pyom.maskT[:,:,-1]\n\n with pyom.timers[\"vmix\"]:\n pyom.P_diss_v[...] = 0.0\n if pyom.enable_conserve_energy:\n \"\"\"\n diagnose dissipation of dynamic enthalpy by vertical mixing\n \"\"\"\n fxa = (-pyom.int_drhodT[2:-2, 2:-2, 1:, pyom.taup1] + pyom.int_drhodT[2:-2, 2:-2, :-1,pyom.taup1]) / pyom.dzw[np.newaxis, np.newaxis, :-1]\n pyom.P_diss_v[2:-2, 2:-2, :-1] += -pyom.grav / pyom.rho_0 * fxa * pyom.kappaH[2:-2, 2:-2, :-1] \\\n * (pyom.temp[2:-2, 2:-2, 1:, pyom.taup1] - pyom.temp[2:-2, 2:-2, :-1,pyom.taup1]) \\\n / pyom.dzw[np.newaxis, np.newaxis, :-1] * pyom.maskW[2:-2, 2:-2, :-1]\n fxa = (-pyom.int_drhodS[2:-2, 2:-2, 1:, pyom.taup1] + pyom.int_drhodS[2:-2, 2:-2, :-1,pyom.taup1]) / pyom.dzw[np.newaxis, np.newaxis, :-1]\n pyom.P_diss_v[2:-2, 2:-2, :-1] += -pyom.grav / pyom.rho_0 * fxa * pyom.kappaH[2:-2, 2:-2, :-1] \\\n * (pyom.salt[2:-2, 2:-2, 1:, pyom.taup1] - pyom.salt[2:-2, 2:-2, :-1,pyom.taup1]) \\\n / pyom.dzw[np.newaxis, np.newaxis, :-1] * pyom.maskW[2:-2, 2:-2, :-1]\n\n fxa = 2 * pyom.int_drhodT[2:-2, 2:-2, -1, pyom.taup1] / pyom.dzw[-1]\n pyom.P_diss_v[2:-2, 2:-2, -1] += - pyom.grav / pyom.rho_0 * fxa * pyom.forc_temp_surface[2:-2 ,2:-2] * pyom.maskW[2:-2, 2:-2, -1]\n fxa = 2 * pyom.int_drhodS[2:-2, 2:-2, -1, pyom.taup1] / pyom.dzw[-1]\n pyom.P_diss_v[2:-2, 2:-2, -1] += - pyom.grav / pyom.rho_0 * fxa * pyom.forc_salt_surface[2:-2 ,2:-2] * pyom.maskW[2:-2, 2:-2, -1]\n\n if pyom.enable_conserve_energy:\n \"\"\"\n determine effect due to nonlinear equation of state\n \"\"\"\n aloc[:,:,:-1] = pyom.kappaH[:,:,:-1] * pyom.Nsqr[:,:,:-1,pyom.taup1]\n pyom.P_diss_nonlin[:,:,:-1] = pyom.P_diss_v[:,:,:-1] - aloc[:,:,:-1]\n pyom.P_diss_v[:,:,:-1] = aloc[:,:,:-1]\n else:\n \"\"\"\n diagnose N^2 pyom.kappaH, i.e. exchange of pot. energy with TKE\n \"\"\"\n pyom.P_diss_v[:,:,:-1] = pyom.kappaH[:,:,:-1] * pyom.Nsqr[:,:,:-1,pyom.taup1]\n pyom.P_diss_v[:,:,-1] = -pyom.forc_rho_surface * pyom.maskT[:,:,-1] * pyom.grav / pyom.rho_0",
"def simulate_HH_neuron(I_e, simulation_time):\n\n # neuron parameters\n El = -59. * b2.mV\n EK = -82. * b2.mV\n ENa = 45. * b2.mV\n gl = 0.3 * b2.msiemens\n gK = 36. * b2.msiemens\n gNa = 120. * b2.msiemens\n C = 1. * b2.ufarad\n\n # forming HH model with differential equations\n eqs = \"\"\"\n membrane_Im = I_e + gNa*m**3*h*(ENa-vm) + \\\n gl*(El-vm) + gK*n**4*(EK-vm) : amp\n \n alphan = 0.01/mV * (-60.0*mV - vm) / (exp((-60.0*mV - vm) / (10.0*mV)) - 1.0)/ms: Hz\n alpham = (vm + 45.0*mV) / (10.0*mV) / (1.0 - exp(-(vm + 45.0*mV) / (10.0*mV)))/ms : Hz\n alphah = 0.07*exp(-(vm + 70.*mV)/(20.*mV))/ms : Hz\n \n betan = 0.125 * exp(-(vm + 70.0*mV) / (80.0*mV))/ms: Hz\n betam = 4.0 * exp(-(vm + 70.0*mV) / (18.0*mV))/ms: Hz\n betah = 1. / (exp(-(vm + 40.0*mV) / (10.0*mV)) + 1.0)/ms : Hz\n \n dn/dt = alphan*(1-n)-betan*n : 1\n dm/dt = alpham*(1-m)-betam*m : 1\n dh/dt = alphah*(1-h)-betah*h : 1\n \n dvm/dt = membrane_Im/C : volt\n \"\"\"\n \n neuron = b2.NeuronGroup(1, eqs, method=\"exponential_euler\")\n\n # parameter initialization [come from x_inf(v) {x:m,n,h}]\n neuron.vm = -70.*b2.mV\n neuron.m = 0.05\n neuron.h = 0.60\n neuron.n = 0.32\n\n # tracking parameters\n st_mon = b2.StateMonitor(neuron, \"vm\", record=True)\n\n # running the simulation\n hh_net = b2.Network(neuron)\n hh_net.add(st_mon)\n hh_net.run(simulation_time)\n\n return st_mon",
"def configuration_interaction(R,Z):\n\n # Hartree Fock computations yield a set of MOs\n C, Hcore, nuclear_energy, two_electron = hartree_fock(R, Z, CI=True)\n\n # number of configurations considered in the calculation\n ND = 2\n\n P = np.zeros(Hcore.shape)\n\n K = Hcore.shape[0]\n print('number of MOs = ', K)\n\n # density matrix\n for mu in range(K):\n for v in range(K):\n P[mu,v] = 2*C[mu,1]*C[v,1]\n\n\n\n coulomb = np.zeros(Hcore.shape)\n exchange = np.zeros(Hcore.shape)\n\n for i in range(K):\n for j in range(K):\n\n for mu in range(K):\n for v in range(K):\n for lamb in range(K):\n for sigma in range(K):\n coulomb[i,j] += two_electron[mu, v, sigma, lamb]\\\n * C[mu,i] *\\\n C[v,i] * C[sigma,j] * C[lamb,j]\n exchange[i,j] += two_electron[mu, v, sigma, lamb] \\\n * C[mu,i] *\\\n C[v,j] * C[sigma,j] * C[lamb,i]\n\n F = np.matmul(C.T, np.matmul(Hcore, C))\n\n electronic_energy = F[0,0]*2 + coulomb[0,0]\n electronic_energy1 = F[1,1]*2 + coulomb[1,1]\n\n H = np.zeros((ND,ND))\n # construct the Hamiltonian\n# for i in range(1, ND):\n# for j in range(i,ND):\n# H[i,j] =\n\n H[0,0] = electronic_energy\n H[1,1] = electronic_energy1\n H[0,1] = H[1,0] = exchange[0,1]\n\n # diagonalizing the matrix\n eigvals, U = scipy.linalg.eigh(H)\n\n # density matrix represented in terms of Slater Determinants\n Temp = 50000. # K\n # transfer to Hartree\n Temp *= 3.1667909e-6\n print('Temperature = {} au.'.format(Temp))\n\n energy_SD = np.array([electronic_energy, electronic_energy1])\n Z = sum(np.exp(-energy_SD/Temp))\n naive_rho = np.diagflat(np.exp(-energy_SD/Temp))\n print('naive density matrix = \\n',naive_rho/Z)\n\n # density matrix represented in terms of Slater Determinants\n Z = sum(np.exp(- eigvals/Temp))\n D = np.diagflat(np.exp(- eigvals/Temp))/Z\n rho = np.matmul(U, np.matmul(D, U.T))\n\n print('full density matrix = \\n', rho)\n\n total_energy = eigvals + nuclear_energy\n print('nuclear energy = {} \\n'.format(nuclear_energy))\n print('total energy = ', total_energy)\n return total_energy",
"def RunHydrogenCalculation(self,problemManager):\n \n if(self.type == \"NPV\" or self.type == \"HydrogenNPV\" ):\n rv = self.RunHydrogenNPVcalculation(problemManager)\n #elif(self.type == \"employment\"):\n # rv = self.RunEmploymentCalculation(problemManager)\n else:\n raise BluecapError(\"Error: Unrecognized regional hydrogen calculation: \" + self.type)\n \n return rv",
"def theta_h(self):\n if self._theta_h is not None:\n return self._S\n theta_h = 0.0\n n = self.n_hap\n nnm1 = n*(n-1.)/2.\n for i,site in enumerate(self.sfs):\n pi += site * i * i",
"def compute_harmonics(self) :\n\n Ye = np.zeros((self.L_max+1,self.L_max+1,self.n_dir))\n Yo = np.zeros((self.L_max+1,self.L_max+1,self.n_dir))\n\n phi = np.zeros((self.n_dir,1))\n for i in xrange(0,self.n_dir) :\n phi[i] = np.arctan(self.omega[i,1]/self.omega[i,0])\n if self.omega[i,0] < 0. :\n phi[i] = phi[i] + np.pi\n\n for l in xrange(0,self.L_max+1) :\n for m in xrange(0,l+1) :\n P_ml = scipy.special.lpmv(m,l,self.omega[:,2])\n# Normalization of the associated Legendre polynomials\n if m == 0 :\n norm_P = P_ml\n else :\n norm_P = (-1.0)**m*np.sqrt(2*sci.factorial(l-m)/sci.factorial(l+m))\\\n *P_ml\n size = norm_P.shape\n for i in xrange(0,size[0]) :\n Ye[l,m,i] = norm_P[i]*np.cos(m*phi[i])\n Yo[l,m,i] = norm_P[i]*np.sin(m*phi[i])\n\n# Build the matrix M \n self.sphr = np.zeros((self.n_dir,self.n_mom))\n self.M = np.zeros((self.n_dir,self.n_mom))\n if self.galerkin == True :\n for i in xrange(0,self.n_dir) :\n pos = 0\n for l in xrange(0,self.L_max+1) :\n fact = 2*l+1\n for m in xrange(l,-1,-1) :\n# do not use the EVEN when m+l is odd for L<sn of L=sn and m=0\n if l<self.sn and np.fmod(m+l,2)==0 :\n self.sphr[i,pos] = Ye[l,m,i]\n self.M[i,pos] = fact*self.sphr[i,pos]\n pos += 1\n for m in xrange(1,l+1) :\n# do not ise the ODD when m+l is odd for l<=sn\n if l<=self.sn and np.fmod(m+l,2)==0 :\n self.sphr[i,pos] = Yo[l,m,i]\n self.M[i,pos] = fact*self.sphr[i,pos]\n pos += 1\n else :\n for i in xrange(0,self.n_dir) :\n pos = 0\n for l in xrange(0,self.L_max+1) :\n fact = 2*l+1\n for m in xrange(l,-1,-1) :\n# do not use the EVEN when m+l is odd \n if np.fmod(m+l,2)==0 :\n self.sphr[i,pos] = Ye[l,m,i]\n self.M[i,pos] = fact*self.sphr[i,pos]\n pos += 1\n for m in xrange(1,l+1) :\n# do not ise the ODD when m+l is odd \n if np.fmod(m+l,2)==0 :\n self.sphr[i,pos] = Yo[l,m,i]\n self.M[i,pos] = fact*self.sphr[i,pos]\n pos += 1",
"def opt_energy_env_2site(isos_012, h_mpo_2site, states_1site_above):\n def _ascend_op_2site_to_2site_many(mpo_2site, isos):\n ops = []\n for l in range(len(isos)):\n mpo_2site = ascend_op_2site_to_2site(mpo_2site, *isos[l])\n ops.append(mpo_2site)\n return ops\n\n def _mpo_with_state(iso_012, iso_021, h_mpo_2site, state_1site):\n \"\"\"Contract a 2-site MPO with a 1-site descended state. O(D^4)\"\"\"\n h2L, h2R = h_mpo_2site\n\n envL = [\n backend.ncon(\n [state_1site, iso_021, h, backend.conj(iso_012)],\n [(1, 3), (1, -1, 2), (4, 2), (3, 4, -2)]) # one transpose required\n for h in h2L\n ]\n\n envR = [\n backend.ncon(\n [state_1site, iso_012, h, backend.conj(iso_021)],\n [(1, 3), (1, -1, 2), (4, 2), (3, 4, -2)]) # one transpose required\n for h in h2R\n ]\n\n return envL, envR\n\n def _descend_energy_env_L(env, iso_021):\n return [descend_state_1site_L(e, iso_021) for e in env]\n\n def _descend_energy_env_R(env, iso_012):\n return [descend_state_1site_R(e, iso_012) for e in env]\n\n isos_wt = isos_with_transposes(isos_012)\n iso_012, iso_021 = isos_wt[0]\n isos_wt_above = isos_wt[1:]\n levels_above = len(isos_wt_above)\n\n # Ascend two-site Hamiltonian terms to the bottom of the final isometry\n h2s_above = _ascend_op_2site_to_2site_many(h_mpo_2site, isos_wt)\n\n # hamiltonian with isometry opposite the gap\n h2L, h2R = h_mpo_2site\n iso_h2R_012 = [\n backend.ncon([iso_021, h], [(-1, -3, 1), (-2, 1)]) for h in h2R\n ] # transpose to 012\n iso_h2L_012 = [\n backend.ncon([iso_012, h], [(-1, -2, 1), (-3, 1)]) for h in h2L\n ]\n\n def _compute_env(lvl, reflect=False):\n # TODO: Could shorten this a bit by doing only left or right at one time\n h2 = h2s_above[lvl]\n if reflect:\n h2 = reflect_mpo_2site(h2)\n\n envL, envR = _mpo_with_state(*isos_wt_above[lvl], h2,\n states_1site_above[lvl])\n\n # descend envs back down to the level of the gap\n for lvl2 in reversed(range(lvl)):\n iso_012_l2, iso_021_l2 = isos_wt_above[lvl2]\n if reflect:\n envR = _descend_energy_env_L(envR, iso_021_l2)\n envL = _descend_energy_env_R(envL, iso_012_l2)\n else:\n envL = _descend_energy_env_L(envL, iso_021_l2)\n envR = _descend_energy_env_R(envR, iso_012_l2)\n\n if reflect:\n iso_h2_L, iso_h2_R = iso_h2R_012, iso_h2L_012\n else:\n iso_h2_L, iso_h2_R = iso_h2L_012, iso_h2R_012\n\n # contract with the hamiltonian + isometry opposite the gap\n envL = sum(\n backend.ncon([eL, ihR], [(1, -1), (1, -2, -3)])\n for eL, ihR in zip(envL, iso_h2_R))\n\n envR = sum(\n backend.ncon([eR, ihL], [(1, -1), (1, -2, -3)])\n for eR, ihL in zip(envR, iso_h2_L))\n\n # weight each term according to the number of occurrences\n # in the translation-invariant tree\n weight = 1 / 2.0**(lvl + 1)\n return (envL + envR) * weight, weight\n\n weightsum = 0.0\n env_total = []\n for lvl in range(levels_above):\n env, weight = _compute_env(lvl)\n weightsum += weight\n env_total.append(env)\n\n # Now compute the boundary term\n env, weight = _compute_env(levels_above - 1, reflect=True)\n weightsum += weight\n env_total.append(env)\n\n env_total = sum(env_total)\n\n assert weightsum == 1.0\n\n return env_total",
"def _fluid_mass_conservation(self):\n dx = self.grid.dx\n dy = self.grid.dy\n dt = self.dt_local\n\n wet_pwet_nodes = self.wet_pwet_nodes\n east_link_at_node = self.east_link_at_node\n west_link_at_node = self.west_link_at_node\n north_link_at_node = self.north_link_at_node\n south_link_at_node = self.south_link_at_node\n\n # mass conservation\n self.div[wet_pwet_nodes] = (\n self.u_temp[east_link_at_node[wet_pwet_nodes]]\n - self.u_temp[west_link_at_node[wet_pwet_nodes]]\n ) / (dx) + (\n self.v_temp[north_link_at_node[wet_pwet_nodes]]\n - self.v_temp[south_link_at_node[wet_pwet_nodes]]\n ) / (\n dy\n )\n\n # remove negative values\n self._remove_abnormal_values()\n\n self.h_temp[self.wet_pwet_nodes] /= 1 + self.div[wet_pwet_nodes] * dt\n self.Ch_i_temp[:, self.wet_pwet_nodes] /= 1 + \\\n self.div[wet_pwet_nodes] * dt\n\n # calculate flow expansion by water entrainment\n if self.water_entrainment is True:\n self.h_temp[self.wet_nodes] += (\n self.ew_node[self.wet_nodes]\n * self.U_node[self.wet_nodes]\n * self.dt_local\n )\n\n # map nodes to links\n map_nodes_to_links(\n self,\n h=self.h_temp,\n dhdx=self.dhdx_temp,\n dhdy=self.dhdy_temp,\n Ch_i=self.Ch_i_temp,\n dChdx_i=self.dChdx_i_temp,\n dChdy_i=self.dChdy_i_temp,\n Ch=self.Ch_temp,\n eta=self.eta_temp,\n h_link=self.h_link_temp,\n Ch_link_i=self.Ch_link_i_temp,\n Ch_link=self.Ch_link_temp,\n )\n\n # update boundary conditions\n self.update_boundary_conditions(\n h=self.h_temp,\n Ch=self.Ch_temp,\n h_link=self.h_link_temp,\n Ch_link=self.Ch_link_temp,\n eta=self.eta_temp,\n )",
"def ham_ising():\n E = np.array([[1, 0], [0, 1]])\n X = np.array([[0, 1], [1, 0]])\n Z = np.array([[1, 0], [0, -1]])\n # hmat = np.kron(X, np.kron(Z, X))\n hmat -= 0.5 * (np.kron(np.kron(X, X), E) + np.kron(E, np.kron(X, X)))\n return np.reshape(hmat, [2] * 6)",
"def energy(self,mu):\r\n\t\t\r\n\t\treturn -sum(sum(self.weight[i,j]*self.x[i]*self.x[j] for j in range(self.N)) for i in range(self.N))",
"def H(N, W1, c1, phi1, J1=1, W2=0, c2=0, phi2=0, J2=0, nleg=1, mode='open'):\n\n # try to load Sx, Sy, Sz from the Globals dictionary if they have been\n # generated\n try:\n Sx, Sy, Sz = G['sigmas']\n except KeyError:\n Sx, Sy, Sz = c.sigmax(), c.sigmay(), c.sigmaz()\n G['sigmas'] = [Sx, Sy, Sz]\n\n # try to load the full Hilbert space operators from the Globals\n # dictionary if they have been generated\n if not G.__contains__('full_S'):\n G['full_S'] = {}\n try:\n full_S = G['full_S'][N]\n except KeyError:\n full_S = [[half.full_matrix(S, k, N) for k in range(N)]\n for S in [Sx, Sy, Sz]]\n G['full_S'][N] = full_S\n\n # The following section describes a hamiltonian of a 2-D latice that\n # we label the following way\n # 0 l2 2*l2 ... (l1-1)*l2\n # 1 l2+1 2*l2+1 ... (l1-1)*l2+1\n # 2 l2+2 2*l2+2 ... (l1-1)*l2+2\n # ...\n # l2-1 2*l2-1 3*l2-1 ... l1*l2-1\n l1 = N // nleg # number of sites along the \"horizontal\"\n l2 = nleg # number of sites along the \"vertical\" (number of legs)\n # Nearest neighbor contributions along the horizontal direction (along\n # which J1 is the coupling constant)\n if nleg == N:\n J1 = 0 # interaction=0 if there's only 1 site along direction\n # mode == 'periodic' is self-explanatory. l1==2 and lb1=0 would imply\n # adjacent sites along adjacent legs interact with each other twice,\n # not exactly what we are looking for.\n lb1 = 0 if (mode == 'periodic' and not l1 == 2) else l2\n inter_terms1 = J1 * sum(full_S[i][j - l2] * full_S[i][j]\n for j in range(lb1, N) for i in range(3))\n\n # Nearest neighbor contributions along the vertical direction (along\n # which J2 is the coupling constant)\n if nleg == 1:\n J2 = 0 # interaction=0 if there's only 1 site along direction\n # mode == 'periodic' is self-explanatory. l2==2 and js looping over\n # every index would imply adjacent sites interact with each other\n # twice, not exactly what we are looking for.\n if (mode == 'periodic' and not l2 == 2):\n # if periodic BC, loop over every site\n js = range(0, l2)\n else:\n # if open BC, skip indices that are at the start of a column\n js = range(1, l2)\n # \"vert_os\" is the offset -- \"distance\" in our indices between\n # adjacent sites along the same rung. It is in general the number\n # of legs of the lattice.\n inter_terms2 = J2 * sum(full_S[i][vert_os: vert_os + l2][j - 1] *\n full_S[i][vert_os: vert_os + l2][j]\n for j in js for vert_os in range(0, N, l2)\n for i in range(3))\n\n inter_terms = inter_terms1 + inter_terms2\n\n # Contributions from the disorder field\n # --- along horizontal direction ---\n if l1 == 1: # field contrib=0 if length of leg=1 aka 1D\n field1 = np.zeros([1])\n else:\n field1 = W1 * np.cos(2 * np.pi * c1 * np.arange(1, l1 + 1) + phi1)\n # --- along vertical direction ---\n if l2 == 1: # field contrib=0 if length of leg=1 aka 1D\n field2 = np.zeros([1])\n else:\n field2 = W2 * np.cos(2 * np.pi * c2 * np.arange(1, l2 + 1) + phi2)\n\n field = field1.repeat(l2) + field2.repeat(l1).reshape(l2, l1).T.flatten()\n field_terms = sum(field * full_S[2])\n\n # Total\n H = inter_terms + field_terms\n return H.real",
"def sodiumHydrogenExchanger(Na_i, H_i, enable_I_NaH):\n if (enable_I_NaH == True):\n n_H = params_dict[\"n_H\"]; K_H_i_mod = params_dict[\"K_H_i_mod\"]; I_NaH_scale = params_dict[\"I_NaH_scale\"]\n k1_p = params_dict[\"k1_p\"]; k1_m = params_dict[\"k1_m\"]; k2_p = params_dict[\"k2_p\"]; k2_m = params_dict[\"k2_m\"]\n Na_o = params_dict[\"Na_o\"]; H_o = params_dict[\"H_o\"]; N_NaH_channel = params_dict[\"N_NaH_channel\"]\n K_Na_o = params_dict[\"K_Na_o\"]; K_H_o = params_dict[\"K_H_o\"];K_Na_i = params_dict[\"K_Na_i\"]; K_H_i = params_dict[\"K_H_i\"]\n\n I_NaH_mod = 1/(1 + (K_H_i_mod**(n_H)/H_i**(n_H)))\n t1 = k1_p*Na_o/K_Na_o / (1 + Na_o/K_Na_o + H_o/K_H_o)\n t2 = k2_p*H_i/K_H_i / (1 + Na_i/K_Na_i + H_i/K_H_i)\n t3 = k1_m*Na_i/K_Na_i / (1 + Na_i/K_Na_i + H_i/K_H_i)\n t4 = k2_m*H_o/K_H_o / (1 + Na_o/K_Na_o + H_o/K_H_o)\n I_NaH_exch = (t1*t2 - t3*t4) / (t1 + t2 + t3 + t4)\n I_NaH = I_NaH_scale*N_NaH_channel*I_NaH_mod*I_NaH_exch\n else:\n I_NaH = 0.0\n \n return I_NaH",
"def test_nose_hoover_integrator():\n temperature = 298*unit.kelvin\n testsystem = testsystems.WaterBox()\n num_dof = 3*testsystem.system.getNumParticles() - testsystem.system.getNumConstraints()\n integrator = NoseHooverChainVelocityVerletIntegrator(testsystem.system, temperature)\n # Create Context and initialize positions.\n context = openmm.Context(testsystem.system, integrator)\n context.setPositions(testsystem.positions)\n context.setVelocitiesToTemperature(temperature)\n integrator.step(200) # Short equilibration\n energies = []\n temperatures = []\n for n in range(100):\n integrator.step(1)\n state = context.getState(getEnergy=True)\n # temperature\n kinE = state.getKineticEnergy()\n temp = (2.0 * kinE / (num_dof * unit.MOLAR_GAS_CONSTANT_R)).value_in_unit(unit.kelvin)\n temperatures.append(temp)\n # total energy\n KE = kinE.value_in_unit(unit.kilojoules_per_mole)\n PE = state.getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole)\n bathKE = integrator.getGlobalVariableByName('bathKE')\n bathPE = integrator.getGlobalVariableByName('bathPE')\n conserved = KE + PE + bathKE + bathPE\n energies.append(conserved)\n\n # Compute maximum deviation from the mean for conserved energies\n meanenergies = np.mean(energies)\n maxdeviation = np.amax(np.abs(energies - meanenergies)/meanenergies)\n assert maxdeviation < 1e-3\n\n # Coarse check for target temperature\n mean_temperature = np.mean(temperatures)\n assert abs(mean_temperature - temperature.value_in_unit(unit.kelvin)) < 10.0, mean_temperature",
"def Hsp_element(state,omega):\n res= 0.0\n for i in range(len(state)):\n e = 1+i*(1-omega)\n res=res+state[i]*e\n return res",
"def displayHamiltonian(self):\r\n return self.displayE_kin() + self.displayE_pot()"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Onsite energy of 2D superconductor, e.g. used for same purpose as hoppingy_2D_superconductor_pincher.
|
def onsite_2D_superconductor_pincher(site,p):
return (2*(p.tx_SC_pincher+p.ty_SC_pincher) - p.mu_SC_pincher)*tau_z + p.Ez_2D_S*sigma_y/2. + p.Delta_pincher*tau_x
|
[
"def onsite_1D_superconductor_pincher(site,p):\n\tEz_eff = p.Ez\n\treturn (2*p.ty_SC_pincher - p.mu_SC_pincher)*tau_z + Ez_eff*sigma_y/2. + p.Delta_pincher*tau_x",
"def onsite_2D_superconductor_lead(site,p):\n\n\n\treturn (2*(p.tx_SC_lead+p.ty_SC_lead) - p.mu_SC_lead)*tau_z + p.Ez_2D_S_lead*sigma_y/2. + p.Delta_SC_lead*tau_x",
"def getEnergy(self) -> float:\n ...",
"def energy(self):\n return self.kinetic() + self.potential()",
"def __nn_energy2D(self, grid, J):\n N = np.shape(grid)[0]\n Energy = 0\n # going to the right and down in the grid\n # each spin has two neigbhours to the left\n # and above\n for i in range(N):\n for j in range(N):\n up = i-1 # neighbour above\n if i == 0: # periodic BC\n up = N-1\n left = j-1 # neibour left\n if j == 0: # periodic BC\n left = N-1\n Energy += -J*grid[i, j]*(grid[up, j] + grid[i, left])\n return Energy",
"def dual_gradient_energy(img):\n R = img[:, :, 0]\n G = img[:, :, 1]\n B = img[:, :, 2]\n\n horizontal_red = filters.sobel_h(R)\n horizontal_green = filters.sobel_h(G)\n horizontal_blue = filters.sobel_h(B)\n\n vertical_red = filters.sobel_v(R)\n vertical_green = filters.sobel_v(G)\n vertical_blue = filters.sobel_v(B)\n\n horizontal_square_sum = add_squares(horizontal_red,\n horizontal_green, horizontal_blue)\n\n vertical_square_sum = add_squares(vertical_red,\n vertical_green, vertical_blue)\n\n energy = numpy.add(horizontal_square_sum, vertical_square_sum)\n\n return energy",
"def _compute_kinetic_energy_cell(self):\n b_cell_sq = torch.matmul(\n self.b_velocities_cell.transpose(2, 3), self.b_velocities_cell\n )\n # Einsum computes the trace\n return (\n self.b_masses_cell * torch.einsum(\"abii->ab\", b_cell_sq)[:, :, None, None]\n )",
"def specific_energy_func(self):\n return self.P.val - self.inl[2].m.val_SI * self.e.val",
"def energyMultiplier(self) -> float:\n return self._getMultiplier('energy')",
"def Energy(spins):\n center = spins\n sides = np.roll(spins, 1, 0) + np.roll(spins, 1, 1) + np.roll(spins, -1, 0) + np.roll(spins, -1, 1)\n return -J*np.sum(center*sides)/2",
"def generationEnergy(self):\n return self.energy + BULLETKEFACTOR * self.energy * self.relativevelocity ** 2",
"def get_specific_energy(self):\n raise NotImplementedError",
"def energy(self,mu):\r\n\t\t\r\n\t\treturn -sum(sum(self.weight[i,j]*self.x[i]*self.x[j] for j in range(self.N)) for i in range(self.N))",
"def get_emb_energy(self):\n\n #Add all the components together to get an energy summary.\n energy_tot = 0\n for i in range(len(self.supersystems) - 1):\n sup = self.supersystems[i]\n sup_e = sup.get_supersystem_energy()\n sup.get_env_energy()\n sub_e = sup.subsystems[-1].env_energy\n print(f\"Supersystem {i + 1} Energy: {sup_e}\")\n print(f\"Higher level subsystem Energy: {sub_e}\")\n energy_tot += sup_e - sub_e\n\n sup = self.supersystems[-1]\n sup_e = sup.get_supersystem_energy()\n sup.get_env_in_env_energy()\n sup.get_hl_energy()\n sup.get_env_energy()\n energy_tot += sup_e\n for sub in sup.subsystems:\n #THIS IS VERY HACKY. NEED TO COME UP WITH A BETTER WAY TO GET SUBSYSTEM STUFF.\n if 'hl_energy' in vars(sub):\n energy_tot -= sub.env_energy\n energy_tot += sub.hl_energy\n\n print(\"\".center(80, '*'))\n print(f\"Total Embedding Energy: {energy_tot}\")\n print(\"\".center(80, '*'))\n return energy_tot",
"def elastic_energy(c1, c2, R, D):\n\n import numpy as np\n\n rho = R*R / D*D # Volume density of BZO. ** For further calculations, assume rho << 1. **\n\n lambda_1 = (c_1[(1,1)] + c_1[(1,2)]) / c_1[(1,3)]\n lambda_2 = (c_2[(1,1)] + c_2[(1,2)]) / c_2[(1,3)]\n\n # TODO: Does f_3 == f_z?? #####\n f_3 = (C2 - C1) / C1\n f_theta = np.sqrt(2)*f_x\n\n a_0 = (f_3(1+f_theta)+lambda_2*f_theta*(1+f3))/(c_1[(1,3)]*(lambda_1*(1+f_theta) - lambda_2*(1+f_3)))\n # b_0 = # DNE\n\n a_1 = a_0 / (np.ln(D) - np.ln(R))\n b_1 = ( f3 + lambda_1*f_theta ) / (c_2[(1,3)] * ( lambda_1*(1+f_theta)-lambda_2*(1+f_3) ))\n\n\n v_1 = 0.5 * ( c1[(1,1)] + c1[(1,2)] ) - ( 1/c1[(3,3)] ) * ( c1[(1,3)] * c1[(1,3)] )\n v_2 = 0.5 * ( c2[(1,2)] + c2[(1,2)] ) - ( 1/c2[(3,3)] ) * ( c2[(1,3)] * c2[(1,3)] )\n\n E = (c1[(1,1)] + c1[(1,2)])*c[(3,3)]*v_1*((2*(1-rho)+rho*np.ln(rho*(2-np.ln(rho))))/(np.ln(rho)*np.ln(rho)))*a_0*a_0 + (c_2[(1,1)]+c_2[(1,2)])*c_2[(3,3)]*v_2*b_1*b_1*rho",
"def SecondaryElectrons(self, E):\n EnergyMeV = 0.001*np.copy(np.asarray(E, dtype=float))\n\n Rcut = self.AvGeomagCutOff\n\n if Rcut >= 10.3872 and Rcut <= 12.4706:\n Flux = self.MizunoBrokenpl(0.3, 2.2, 3000, 4.0, EnergyMeV)\n elif Rcut >= 5.7857 and Rcut <= 10.3872:\n Flux = self.MizunoPl(0.3, 2.7, EnergyMeV)\n elif Rcut >= 2.9375 and Rcut <= 5.7857:\n Flux = self.MizunoPlhump(0.3, 3.3, 2/10000, 1.5, 2.3, EnergyMeV)\n elif Rcut >= 1.8613 and Rcut <= 2.9375:\n Flux = self.MizunoPlhump(0.3, 3.5, 1.6/1000, 2.0, 1.6, EnergyMeV)\n elif Rcut >= 1.0623 and Rcut <= 1.8613:\n Flux = self.MizunoPl(0.3, 2.5, EnergyMeV)\n\n return Flux/10**7",
"def SecondaryPositrons(self, E):\n EnergyMeV = 0.001*np.copy(np.asarray(E, dtype=float))\n\n Rcut = self.AvGeomagCutOff\n\n if Rcut >= 10.3872 and Rcut <= 12.4706:\n Flux = self.MizunoBrokenpl(0.3, 2.2, 3000, 4.0, EnergyMeV)\n ratio = 3.3\n elif Rcut >= 5.7857 and Rcut <= 10.3872:\n Flux = self.MizunoPl(0.3, 2.7, EnergyMeV)\n ratio = 1.66\n elif Rcut >= 2.9375 and Rcut <= 5.7857:\n Flux = self.MizunoPlhump(0.3, 3.3, 2/10000, 1.5, 2.3, EnergyMeV)\n ratio = 1.0\n elif Rcut >= 1.8613 and Rcut <= 2.9375:\n Flux = self.MizunoPlhump(0.3, 3.5, 1.6/1000, 2.0, 1.6, EnergyMeV)\n ratio = 1.0\n elif Rcut >= 1.0623 and Rcut <= 1.8613:\n Flux = self.MizunoPl(0.3, 2.5, EnergyMeV)\n ratio = 1.0\n\n return ratio*Flux/10**7",
"def _analytical_encircled_energy(fno, wavelength, points):\n p = points * e.pi / fno / wavelength\n return 1 - special.j0(p)**2 - special.j1(p)**2",
"def energy(self, state: np.ndarray):\r\n return -0.5 * state.dot(self.weights).dot(state) + np.sum(state * self.threshold)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Onsite energy of 1D superconductor, e.g. used for same purpose as hoppingy_2D_superconductor_pincher.
|
def onsite_1D_superconductor_pincher(site,p):
Ez_eff = p.Ez
return (2*p.ty_SC_pincher - p.mu_SC_pincher)*tau_z + Ez_eff*sigma_y/2. + p.Delta_pincher*tau_x
|
[
"def getEnergy(self) -> float:\n ...",
"def energy(self):\n return self.kinetic() + self.potential()",
"def energy(self,mu):\r\n\t\t\r\n\t\treturn -sum(sum(self.weight[i,j]*self.x[i]*self.x[j] for j in range(self.N)) for i in range(self.N))",
"def onsite_2D_superconductor_pincher(site,p):\n\n\treturn (2*(p.tx_SC_pincher+p.ty_SC_pincher) - p.mu_SC_pincher)*tau_z + p.Ez_2D_S*sigma_y/2. + p.Delta_pincher*tau_x",
"def energyMultiplier(self) -> float:\n return self._getMultiplier('energy')",
"def energy(self, state: np.ndarray):\r\n return -0.5 * state.dot(self.weights).dot(state) + np.sum(state * self.threshold)",
"def specific_energy_func(self):\n return self.P.val - self.inl[2].m.val_SI * self.e.val",
"def generationEnergy(self):\n return self.energy + BULLETKEFACTOR * self.energy * self.relativevelocity ** 2",
"def abs_energy(x):\n\treturn np.dot(x, x)",
"def get_specific_energy(self):\n raise NotImplementedError",
"def get_full_energy_simple(x):\n # print(x[..., 0])\n # print(x[..., 1])\n # The signal in frequency domain is symmetric and pytorch already\n # discards second half of the signal.\n squared = torch.add(torch.pow(x[..., 0], 2),\n torch.pow(x[..., 1], 2)).squeeze()\n # sum of squared values of the signal\n full_energy = torch.sum(squared).item()\n return full_energy, squared",
"def energy(signal):\n return np.sum(np.square(signal)) #change with np.mean to calculate mean energy",
"def onsite_2D_superconductor_lead(site,p):\n\n\n\treturn (2*(p.tx_SC_lead+p.ty_SC_lead) - p.mu_SC_lead)*tau_z + p.Ez_2D_S_lead*sigma_y/2. + p.Delta_SC_lead*tau_x",
"def __init__(self,rho,enemin=ENEMIN):\n self.rho = rho\n self.enemin=enemin\n # Read in the stopping power and interpolate.\n xesp_tbl = np.loadtxt(\"xe_estopping_power_NIST.dat\");\n self.evals = xesp_tbl[:,0]\n self.dEdxvals = xesp_tbl[:,1];\n self.evals = np.insert(self.evals,0,0.0);\n self.dEdxvals = np.insert(self.dEdxvals,0,self.dEdxvals[0]);\n self.xesp = sc_interpol(self.evals,self.dEdxvals*self.rho,kind='cubic')\n # this is the dE/dx(E) function\n return",
"def EnergyConsumption(self):\n req_reactants_sor_syn_kwargs = {'mol_LiOH_H2O': self.sor_syn.mol_LiOH_H2O,\n 'hc_LiOH': self.hC.hc_LiOH,\n 'mol_aluminium_hydroxide': self.sor_syn.mol_aluminium_hydroxide,\n 'hc_aluminium_hydroxide': self.hC.hc_aluminium_hydroxide_mol,\n 'mol_H2O': self.sor_syn.mol_H2O,\n 'hc_H2O': self.hC.hc_H2O,\n 'mol_HCl': self.sor_syn.mol_HCl,\n 'hc_HCl': self.hC.hc_HCl,\n 'reaction_temperature': self.reactor.reaction_temp}\n\n q_reactants_sor_syn = Sor_Syn_Chemicals.QReactants(**req_reactants_sor_syn_kwargs)\n\n req_reactor_sor_syn_kwargs = {'reaction_temperature': self.reactor.reaction_temp,\n 'reaction_time_1': self.reactor.reaction_time_1,\n 'reaction_time_2': self.reactor.reaction_time_2,\n 'surface_area': self.reactor.surface_area,\n 'thermal_conductivity': self.reactor.thermal_conductivity,\n 'wall_thickness': self.reactor.wall_thickness,\n 'liq_density_1': self.density_1,\n 'liq_density_2': self.density_2}\n\n q_reactor_sor_syn = Sor_Syn_Reactor.QReactor(**req_reactor_sor_syn_kwargs)\n\n q_reaction_sor_syn = q_reactants_sor_syn + (q_reactor_sor_syn * 10**(-3))\n\n\n req_stir_energy_sor_syn_kwargs = {'impeller_power_number': self.impeller.impeller_power_number,\n 'impeller_diameter': self.impeller.impeller_diameter,\n 'agitator_rotational_speed': self.impeller.agitator_rotational_speed,\n 'density_1': self.density_1 * 10**3,\n 'density_2': self.density_2 * 10**3,\n 'stirring_time_1': self.reactor.reaction_time_1 * 3600,\n 'stirring_time_2': self.reactor.reaction_time_2 * 3600,\n 'efficiency': self.impeller.efficiency}\n\n stirring_energy_sor_syn = uC.kiloWattHours(Impeller.StirringEnergySorSyn(**req_stir_energy_sor_syn_kwargs))\n\n grinding_energy_sor_syn = QProcesses.grinding_energy(uC.tonnes(self.total_mass_mix_2_sor_syn))\n\n filtration_energy_sor_syn = QProcesses.filtration_energy(uC.tonnes(self.total_mass_mix_2_sor_syn))\n\n pumping_energy_sor_syn = uC.kiloWattHours(QProcesses.pumping_energy(uC.tonnes(self.total_mass_mix_2_sor_syn) +\n self.water.sor_syn_washing))\n\n req_stir_energy_column_washing_kwargs = {'impeller_power_number': self.impeller.impeller_power_number,\n 'impeller_diameter': self.impeller.impeller_diameter,\n 'agitator_rotational_speed': self.impeller.agitator_rotational_speed,\n 'density': self.density_NaCl_washing * 10 ** 3,\n 'stirring_time': self.washing.stirring_time * 3600,\n 'efficiency': self.impeller.efficiency}\n stirring_energy_column_washing = uC.kiloWattHours\\\n (QProcesses.stirring_energy(**req_stir_energy_column_washing_kwargs))\n\n # assuming the brine has the density of water\n\n pumping_energy_column_extraction = uC.kiloWattHours(QProcesses.pumping_energy\n (uC.tonnes(((self.plant.brine_flow_day * 10**6 / 24) *\n self.plant.plant_uptime) * self.brine.brine_density) +\n ((self.washing.H2O_washing +\n self.stripping.H2O_stripping) * 10**3) +\n uC.tonnes(self.washing.mass_NaCl)))\n\n pumping_energy_effluent = uC.kiloWattHours\\\n (QProcesses.pumping_energy(uC.tonnes(((self.plant.brine_flow_day * 10**6 / 24) *\n self.plant.plant_uptime * self.brine.brine_density) +\n (self.washing.H2O_washing + self.stripping.H2O_stripping) *\n 10**3 + self.washing.mass_NaCl - self.stripping.Li_sol_output *\n 10**3 * self.density_LiCl_sol_stripping)))\n\n filtration_energy_FO = QProcesses.filtration_energy(self.FO.Li_sol_output * 10**(-3))\n\n pumping_energy_FO = uC.kiloWattHours(QProcesses.pumping_energy(uC.tonnes(self.stripping.Li_sol_output *\n 10**3 * self.density_LiCl_sol_stripping)))\n\n req_reactants_LC_processing_kwargs = {'mol_LiCl': uC.solidMol\n ('LiCl', self.reactant_flow.LC_processing_reactants['LiCl']),\n 'hc_LiCl': self.hC.hc_LiCl,\n 'mol_Na2CO3': uC.solidMol\n ('Na2CO3', self.reactant_flow.LC_processing_reactants['Na2CO3']),\n 'hc_Na2CO3': self.hC.hc_Na2CO3,\n 'reaction_temperature': self.LC_processing.reaction_temp}\n q_reactants_LC_processing = LC_processing.QReactants(**req_reactants_LC_processing_kwargs)\n\n q_reactor_LC_processing_kwargs = {'reaction_temperature': self.LC_processing.reaction_temp,\n 'reaction_time': self.LC_processing.reaction_time,\n 'surface_area': self.LC_processing.surface_area,\n 'thermal_conductivity': self.LC_processing.thermal_conductivity,\n 'wall_thickness': self.LC_processing.wall_thickness,\n 'liq_density': self.density_LC_processing}\n\n q_reactor_LC_processing = QReactors.batchReactor(**q_reactor_LC_processing_kwargs)\n\n q_reaction_LC_processing = q_reactants_LC_processing + (q_reactor_LC_processing[0] * 10**(-3))\n\n req_stir_energy_LC_processing_kwargs = {'impeller_power_number': self.impeller.impeller_power_number,\n 'impeller_diameter': self.impeller.impeller_diameter,\n 'agitator_rotational_speed': self.impeller.agitator_rotational_speed,\n 'density': self.density_LC_processing * 10**3,\n 'stirring_time': self.LC_processing.reaction_time * 3600,\n 'efficiency': self.impeller.efficiency}\n\n stirring_energy_LC_processing = uC.kiloWattHours(QProcesses.stirring_energy\n (**req_stir_energy_LC_processing_kwargs))\n\n filtration_energy_LC_processing = QProcesses.filtration_energy\\\n (uC.tonnes(self.reactant_flow.LC_processing_reactants['LiCl'] +\n self.reactant_flow.LC_processing_reactants['Na2CO3']))\n\n pumping_energy_LC_processing = uC.kiloWattHours(QProcesses.pumping_energy\n (uC.tonnes(self.FO.Li_sol_output * 10**3 +\n self.density_LiCl_sol_FO +\n self.reactant_flow.LC_processing_reactants['Na2CO3'])))\n\n req_reactants_LC_carbonation_kwargs = {'mol_Li2CO3': uC.solidMol\n ('Li2CO3', self.reactant_flow.LC_purification_reactants['impure Li2CO3']),\n 'hc_Li2CO3': self.hC.hc_Li2CO3_carbonation,\n 'mol_CO2': uC.solidMol\n ('CO2', self.reactant_flow.LC_purification_reactants['CO2']),\n 'hc_CO2': self.hC.hc_CO2_carbonation,\n 'mol_H2O': uC.solidMol\n ('H2O', self.reactant_flow.LC_purification_reactants['H2O']),\n 'hc_H2O': self.hC.hc_H2O,\n 'reaction_temperature': self.LC_purification.carbonation_temp}\n\n q_reactants_LC_carbonation = LC_purification.QReactants(**req_reactants_LC_carbonation_kwargs)\n\n req_reactor_LC_carbonation_kwargs = {'reaction_temperature': self.LC_purification.carbonation_temp,\n 'reaction_time': self.LC_purification.carbonation_time,\n 'surface_area': self.LC_purification.surface_area,\n 'thermal_conductivity': self.LC_purification.thermal_conductivity,\n 'wall_thickness': self.LC_purification.wall_thickness,\n 'liq_density': self.density_LC_purification}\n\n q_reactor_LC_carbonation = QReactors.batchReactor(**req_reactor_LC_carbonation_kwargs)\n\n q_reaction_LC_carbonation = q_reactants_LC_carbonation + (q_reactor_LC_carbonation[0] * 10**(-3))\n\n req_stir_energy_carbonation_kwargs = {'impeller_power_number': self.impeller.impeller_power_number,\n 'impeller_diameter': self.impeller.impeller_diameter,\n 'agitator_rotational_speed': self.impeller.agitator_rotational_speed,\n 'density': self.density_LC_purification * 10**3,\n 'stirring_time': self.LC_purification.carbonation_time * 3600,\n 'efficiency': self.impeller.efficiency}\n\n stirring_energy_carbonation = uC.kiloWattHours(QProcesses.stirring_energy(**req_stir_energy_carbonation_kwargs))\n\n filtration_energy_carbonation = QProcesses.filtration_energy\\\n (uC.tonnes(self.reactant_flow.LC_purification_intermediate['LiHCO3']))\n\n pumping_energy_carbonation = uC.kiloWattHours(QProcesses.pumping_energy\n (uC.tonnes(self.reactant_flow.LC_purification_reactants\n ['impure Li2CO3']) +\n self.reactant_flow.LC_purification_reactants['H2O'] +\n self.reactant_flow.LC_purification_reactants['CO2']))\n\n pumping_energy_carbonation_processing = uC.kiloWattHours(QProcesses.pumping_energy(uC.tonnes\n (self.reactant_flow.LC_purification_intermediate\n ['LiHCO3'])))\n\n req_reactants_LC_precipitation_kwargs = {'mol_Li2CO3': uC.solidMol\n ('Li2CO3', self.reactant_flow.LC_purification_intermediate['LiHCO3']),\n 'hc_Li2CO3': self.hC.hc_Li2CO3_carbonation,\n 'mol_CO2': uC.solidMol\n ('CO2', self.reactant_flow.LC_purification_reactants['CO2']),\n 'hc_CO2': self.hC.hc_CO2_carbonation,\n 'mol_H2O': uC.solidMol\n ('H2O', self.reactant_flow.LC_purification_reactants['H2O']),\n 'hc_H2O': self.hC.hc_H2O,\n 'reaction_temperature': self.LC_purification.precipitation_temp}\n\n q_reactants_LC_precipitation = LC_purification.QReactants(**req_reactants_LC_precipitation_kwargs)\n\n req_reactor_LC_precipitation_kwargs = {'reaction_temperature': self.LC_purification.precipitation_temp,\n 'reaction_time': self.LC_purification.precipitation_time,\n 'surface_area': self.LC_purification.surface_area,\n 'thermal_conductivity': self.LC_purification.thermal_conductivity,\n 'wall_thickness': self.LC_purification.wall_thickness,\n 'liq_density': self.density_LC_purification}\n\n q_reactor_LC_precipitation = QReactors.batchReactor(**req_reactor_LC_precipitation_kwargs)\n\n q_reaction_LC_precipitation = q_reactants_LC_precipitation + (q_reactor_LC_precipitation[0] * 10**(-3))\n\n req_stir_energy_precipitation_kwargs = {'impeller_power_number': self.impeller.impeller_power_number,\n 'impeller_diameter': self.impeller.impeller_diameter,\n 'agitator_rotational_speed': self.impeller.agitator_rotational_speed,\n 'density': self.density_LC_purification * 10**3,\n 'stirring_time': self.LC_purification.precipitation_time * 3600,\n 'efficiency': self.impeller.efficiency}\n\n stirring_energy_precipitation = uC.kiloWattHours(QProcesses.stirring_energy\n (**req_stir_energy_precipitation_kwargs))\n\n filtration_energy_precipitation = QProcesses.filtration_energy\\\n (uC.tonnes(self.reactant_flow.LC_purification_intermediate['LiHCO3']))\n\n req_drying_energy_LC_processing_kwargs = {'heat_capacity_solution': self.hC_LC_purification,\n 'mass_solution': self.total_mass_drying_LC_purification * 10**(-3),\n 'boiling_temperature': self.Tb_LC_purification,\n 'starting_temperature': self.LC_purification.washing_temperature,\n 'evaporation_enthalpy': self.Hvap_LC_purification,\n 'mass_vapour': (self.LC_purification.water_content_filtration *\n self.reactant_flow.LC_purification_product\n ['pure Li2CO3']) * 10**(-3)}\n\n drying_energy_LC_purification = uC.kiloWattHours(QProcesses.drying_energy\n (**req_drying_energy_LC_processing_kwargs))\n\n pumping_energy_precipitation_filtration = uC.kiloWattHours(QProcesses.pumping_energy\n (uC.tonnes(self.reactant_flow.LC_purification_product\n ['pure Li2CO3']) +\n self.reactant_flow.LC_purification_by_products\n ['H2O']))\n\n pumping_energy_LC_purification_wash = uC.kiloWattHours(QProcesses.pumping_energy\n (uC.tonnes(self.water.LC_purification_washing)))\n\n req_belt_conveyor_kwargs = {'belt_speed': self.BC.belt_speed, 'belt_length': self.BC.belt_length,\n 'gradient': self.BC.gradient, 'conveyor_output': self.BC.output,\n 'drive_train_efficiency': self.BC.efficiency}\n belt_conveyor_energy_average = QMachines.beltConveyor_requirement(**req_belt_conveyor_kwargs) * \\\n self.BC.hours_operation\n\n energy_df = pd.DataFrame(data={\"Reaction energy\": [q_reaction_sor_syn + q_reaction_LC_processing +\n q_reaction_LC_carbonation + q_reaction_LC_precipitation +\n stirring_energy_sor_syn + stirring_energy_column_washing +\n stirring_energy_LC_processing + stirring_energy_carbonation +\n stirring_energy_precipitation],\n \"Processing energy\": [filtration_energy_sor_syn + filtration_energy_FO +\n filtration_energy_LC_processing +\n filtration_energy_carbonation +\n filtration_energy_precipitation + grinding_energy_sor_syn +\n drying_energy_LC_purification],\n \"Transportation energy\": [pumping_energy_sor_syn +\n pumping_energy_column_extraction +\n pumping_energy_effluent + pumping_energy_FO +\n pumping_energy_LC_processing +\n pumping_energy_carbonation_processing +\n pumping_energy_carbonation +\n pumping_energy_carbonation_processing +\n pumping_energy_precipitation_filtration +\n pumping_energy_LC_purification_wash +\n belt_conveyor_energy_average]},\n index=['Geothermal_LDH'])\n energy_df['sum'] = energy_df.sum(axis=1)\n\n return energy_df",
"def energy_density(self):\n if self.is_energy:\n return self.values(\"MEAS:EDENsity?\")[0]\n else:\n raise Exception(\"%s is not a energy sensor\" % self.sensor_name)",
"def get_emb_energy(self):\n\n #Add all the components together to get an energy summary.\n energy_tot = 0\n for i in range(len(self.supersystems) - 1):\n sup = self.supersystems[i]\n sup_e = sup.get_supersystem_energy()\n sup.get_env_energy()\n sub_e = sup.subsystems[-1].env_energy\n print(f\"Supersystem {i + 1} Energy: {sup_e}\")\n print(f\"Higher level subsystem Energy: {sub_e}\")\n energy_tot += sup_e - sub_e\n\n sup = self.supersystems[-1]\n sup_e = sup.get_supersystem_energy()\n sup.get_env_in_env_energy()\n sup.get_hl_energy()\n sup.get_env_energy()\n energy_tot += sup_e\n for sub in sup.subsystems:\n #THIS IS VERY HACKY. NEED TO COME UP WITH A BETTER WAY TO GET SUBSYSTEM STUFF.\n if 'hl_energy' in vars(sub):\n energy_tot -= sub.env_energy\n energy_tot += sub.hl_energy\n\n print(\"\".center(80, '*'))\n print(f\"Total Embedding Energy: {energy_tot}\")\n print(\"\".center(80, '*'))\n return energy_tot",
"def einstein_energy(self, dbe):\n phase = dbe.phases[self.phase_name]\n param_search = dbe.search\n theta_param_query = (\n (where('phase_name') == phase.name) & \\\n (where('parameter_type') == 'THETA') & \\\n (where('constituent_array').test(self._array_validity))\n )\n lntheta = self.redlich_kister_sum(phase, param_search, theta_param_query)\n theta = exp(lntheta)\n if lntheta != 0:\n result = 1.5*v.R*theta + 3*v.R*v.T*log(1-exp(-theta/v.T))\n else:\n result = 0\n return result / self._site_ratio_normalization",
"def Energy(spins):\n center = spins\n sides = np.roll(spins, 1, 0) + np.roll(spins, 1, 1) + np.roll(spins, -1, 0) + np.roll(spins, -1, 1)\n return -J*np.sum(center*sides)/2"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Onsite energy of 2D superconducting lead, e.g. used for same purpose as hoppingy_2D_superconductor_lead.
|
def onsite_2D_superconductor_lead(site,p):
return (2*(p.tx_SC_lead+p.ty_SC_lead) - p.mu_SC_lead)*tau_z + p.Ez_2D_S_lead*sigma_y/2. + p.Delta_SC_lead*tau_x
|
[
"def getEnergy(self) -> float:\n ...",
"def onsite_2D_superconductor_pincher(site,p):\n\n\treturn (2*(p.tx_SC_pincher+p.ty_SC_pincher) - p.mu_SC_pincher)*tau_z + p.Ez_2D_S*sigma_y/2. + p.Delta_pincher*tau_x",
"def _analytical_encircled_energy(fno, wavelength, points):\n p = points * e.pi / fno / wavelength\n return 1 - special.j0(p)**2 - special.j1(p)**2",
"def dual_gradient_energy(img):\n R = img[:, :, 0]\n G = img[:, :, 1]\n B = img[:, :, 2]\n\n horizontal_red = filters.sobel_h(R)\n horizontal_green = filters.sobel_h(G)\n horizontal_blue = filters.sobel_h(B)\n\n vertical_red = filters.sobel_v(R)\n vertical_green = filters.sobel_v(G)\n vertical_blue = filters.sobel_v(B)\n\n horizontal_square_sum = add_squares(horizontal_red,\n horizontal_green, horizontal_blue)\n\n vertical_square_sum = add_squares(vertical_red,\n vertical_green, vertical_blue)\n\n energy = numpy.add(horizontal_square_sum, vertical_square_sum)\n\n return energy",
"def __nn_energy2D(self, grid, J):\n N = np.shape(grid)[0]\n Energy = 0\n # going to the right and down in the grid\n # each spin has two neigbhours to the left\n # and above\n for i in range(N):\n for j in range(N):\n up = i-1 # neighbour above\n if i == 0: # periodic BC\n up = N-1\n left = j-1 # neibour left\n if j == 0: # periodic BC\n left = N-1\n Energy += -J*grid[i, j]*(grid[up, j] + grid[i, left])\n return Energy",
"def Energy(spins):\n center = spins\n sides = np.roll(spins, 1, 0) + np.roll(spins, 1, 1) + np.roll(spins, -1, 0) + np.roll(spins, -1, 1)\n return -J*np.sum(center*sides)/2",
"def energy(self):\n return self.kinetic() + self.potential()",
"def abs_energy(x):\n\treturn np.dot(x, x)",
"def _compute_kinetic_energy_cell(self):\n b_cell_sq = torch.matmul(\n self.b_velocities_cell.transpose(2, 3), self.b_velocities_cell\n )\n # Einsum computes the trace\n return (\n self.b_masses_cell * torch.einsum(\"abii->ab\", b_cell_sq)[:, :, None, None]\n )",
"def generationEnergy(self):\n return self.energy + BULLETKEFACTOR * self.energy * self.relativevelocity ** 2",
"def get_emb_energy(self):\n\n #Add all the components together to get an energy summary.\n energy_tot = 0\n for i in range(len(self.supersystems) - 1):\n sup = self.supersystems[i]\n sup_e = sup.get_supersystem_energy()\n sup.get_env_energy()\n sub_e = sup.subsystems[-1].env_energy\n print(f\"Supersystem {i + 1} Energy: {sup_e}\")\n print(f\"Higher level subsystem Energy: {sub_e}\")\n energy_tot += sup_e - sub_e\n\n sup = self.supersystems[-1]\n sup_e = sup.get_supersystem_energy()\n sup.get_env_in_env_energy()\n sup.get_hl_energy()\n sup.get_env_energy()\n energy_tot += sup_e\n for sub in sup.subsystems:\n #THIS IS VERY HACKY. NEED TO COME UP WITH A BETTER WAY TO GET SUBSYSTEM STUFF.\n if 'hl_energy' in vars(sub):\n energy_tot -= sub.env_energy\n energy_tot += sub.hl_energy\n\n print(\"\".center(80, '*'))\n print(f\"Total Embedding Energy: {energy_tot}\")\n print(\"\".center(80, '*'))\n return energy_tot",
"def power_flow(self):\n e2 = np.real(np.conj(self.e_y)*self.e_y + np.conj(self.e_z)*self.e_z)\n E2 = np.real(np.conj(self.E) * self.E)\n c = cgs['c']\n if self._keepFFTz:\n dz = self.z_coords[1]-self.z_coords[0]\n E2_integrate_z = trapz(np.fft.fftshift(E2, axes=0),\n x=np.fft.fftshift(self.kz[:,0,0]), axis=0)\\\n * dz*dz/(2*np.pi)\n else:\n E2_integrate_z = trapz(E2, x=self.z_coords, axis=0)\n E2_integrate_yz = trapz(E2_integrate_z,x=self.y_coords, axis=0)\n power_norm = c/(8*np.pi)*E2_integrate_yz * (c*self.k_0/self.omega) *e2\n\n return power_norm",
"def onsite_1D_superconductor_pincher(site,p):\n\tEz_eff = p.Ez\n\treturn (2*p.ty_SC_pincher - p.mu_SC_pincher)*tau_z + Ez_eff*sigma_y/2. + p.Delta_pincher*tau_x",
"def elastic_energy(c1, c2, R, D):\n\n import numpy as np\n\n rho = R*R / D*D # Volume density of BZO. ** For further calculations, assume rho << 1. **\n\n lambda_1 = (c_1[(1,1)] + c_1[(1,2)]) / c_1[(1,3)]\n lambda_2 = (c_2[(1,1)] + c_2[(1,2)]) / c_2[(1,3)]\n\n # TODO: Does f_3 == f_z?? #####\n f_3 = (C2 - C1) / C1\n f_theta = np.sqrt(2)*f_x\n\n a_0 = (f_3(1+f_theta)+lambda_2*f_theta*(1+f3))/(c_1[(1,3)]*(lambda_1*(1+f_theta) - lambda_2*(1+f_3)))\n # b_0 = # DNE\n\n a_1 = a_0 / (np.ln(D) - np.ln(R))\n b_1 = ( f3 + lambda_1*f_theta ) / (c_2[(1,3)] * ( lambda_1*(1+f_theta)-lambda_2*(1+f_3) ))\n\n\n v_1 = 0.5 * ( c1[(1,1)] + c1[(1,2)] ) - ( 1/c1[(3,3)] ) * ( c1[(1,3)] * c1[(1,3)] )\n v_2 = 0.5 * ( c2[(1,2)] + c2[(1,2)] ) - ( 1/c2[(3,3)] ) * ( c2[(1,3)] * c2[(1,3)] )\n\n E = (c1[(1,1)] + c1[(1,2)])*c[(3,3)]*v_1*((2*(1-rho)+rho*np.ln(rho*(2-np.ln(rho))))/(np.ln(rho)*np.ln(rho)))*a_0*a_0 + (c_2[(1,1)]+c_2[(1,2)])*c_2[(3,3)]*v_2*b_1*b_1*rho",
"def specific_energy_func(self):\n return self.P.val - self.inl[2].m.val_SI * self.e.val",
"def _compute_kinetic_energy_cell(self):\n return self.b_masses_cell * self.b_velocities_cell ** 2",
"def getEnergyAt(self, step):\n pass;",
"def SecondaryPositrons(self, E):\n EnergyMeV = 0.001*np.copy(np.asarray(E, dtype=float))\n\n Rcut = self.AvGeomagCutOff\n\n if Rcut >= 10.3872 and Rcut <= 12.4706:\n Flux = self.MizunoBrokenpl(0.3, 2.2, 3000, 4.0, EnergyMeV)\n ratio = 3.3\n elif Rcut >= 5.7857 and Rcut <= 10.3872:\n Flux = self.MizunoPl(0.3, 2.7, EnergyMeV)\n ratio = 1.66\n elif Rcut >= 2.9375 and Rcut <= 5.7857:\n Flux = self.MizunoPlhump(0.3, 3.3, 2/10000, 1.5, 2.3, EnergyMeV)\n ratio = 1.0\n elif Rcut >= 1.8613 and Rcut <= 2.9375:\n Flux = self.MizunoPlhump(0.3, 3.5, 1.6/1000, 2.0, 1.6, EnergyMeV)\n ratio = 1.0\n elif Rcut >= 1.0623 and Rcut <= 1.8613:\n Flux = self.MizunoPl(0.3, 2.5, EnergyMeV)\n ratio = 1.0\n\n return ratio*Flux/10**7",
"def energy_function(image):\n H, W, _ = image.shape\n out = np.zeros((H, W))\n\n ### YOUR CODE HERE\n grayImg = color.rgb2gray(image)\n\n\n gradient = np.gradient(grayImg)\n out = np.abs(gradient[0]) + np.abs(gradient[1])\n\n # dx = np.gradient(grayImg, axis=0)\n # dy = np.gradient(grayImg, axis=1)\n # out = np.abs(dx) + np.abs(dy)\n ### END YOUR CODE\n\n return out"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Hopping energy in xdirection of 1D system with proximitized superconductivity. Parameters see onsite function
|
def hoppingx(site0,site1,p):
# print("%s: in hoppingx()" %str(misc.round_time(datetime.datetime.now(),round_to=60)))
return -p.tx*tau_z + 1j*p.alphahbar/(2.*p.ax)*sigma_ytau_z
|
[
"def onsite_1D_superconductor_pincher(site,p):\n\tEz_eff = p.Ez\n\treturn (2*p.ty_SC_pincher - p.mu_SC_pincher)*tau_z + Ez_eff*sigma_y/2. + p.Delta_pincher*tau_x",
"def onsite_2D_superconductor_pincher(site,p):\n\n\treturn (2*(p.tx_SC_pincher+p.ty_SC_pincher) - p.mu_SC_pincher)*tau_z + p.Ez_2D_S*sigma_y/2. + p.Delta_pincher*tau_x",
"def onsite_2D_superconductor_lead(site,p):\n\n\n\treturn (2*(p.tx_SC_lead+p.ty_SC_lead) - p.mu_SC_lead)*tau_z + p.Ez_2D_S_lead*sigma_y/2. + p.Delta_SC_lead*tau_x",
"def extract_extra_sites(self):\n\n # weighting arrays for the virtual sites should not be changed\n w1o, w2o, w3o = 1.0, 0.0, 0.0 # SUM SHOULD BE 1\n w1x, w2x, w3x = -1.0, 1.0, 0.0 # SUM SHOULD BE 0\n w1y, w2y, w3y = -1.0, 0.0, 1.0 # SUM SHOULD BE 0\n\n with open('xyz_with_extra_point_charges.xyz') as xyz_sites:\n lines = xyz_sites.readlines()\n\n sites = OrderedDict()\n sites_no = 0\n for i, line in enumerate(lines[2:]):\n # get the current element\n element = str(line.split()[0])\n\n if element != 'X':\n # search the following entries for sites connected to this atom\n for pos_site in lines[i + 3:]:\n if str(pos_site.split()[0]) != 'X':\n # if there are no sites break and start the next loop\n break\n else:\n # get the virtual site coords\n v_pos = array([float(pos_site.split()[x]) for x in range(1, 4)])\n # get parent index number for the topology network\n parent = i + 1 - sites_no\n # get the two closest atoms to the parent\n closet_atoms = list(self.molecule.topology.neighbors(parent))\n if len(closet_atoms) < 2:\n # find another atom if we only have one\n # dont want to get the parent as a close atom\n closet_atoms.append(list(self.molecule.topology.neighbors(closet_atoms[0]))[-1])\n\n # Get the xyz coordinates of the reference atoms\n parent_pos = array(self.molecule.molecule['qm'][parent - 1][1:])\n close_a = array(self.molecule.molecule['qm'][closet_atoms[0] - 1][1:])\n close_b = array(self.molecule.molecule['qm'][closet_atoms[1] - 1][1:])\n\n # work out the local coordinates site using rules from the OpenMM guide\n orig = w1o * parent_pos + w2o * close_a + close_b * w3o\n ab = w1x * parent_pos + w2x * close_a + w3x * close_b # rb-ra\n ac = w1y * parent_pos + w2y * close_a + w3y * close_b # rb-ra\n # Get the axis unit vectors\n z_dir = cross(ab, ac)\n z_dir = z_dir / sqrt(dot(z_dir, z_dir.reshape(3, 1)))\n x_dir = ab / sqrt(dot(ab, ab.reshape(3, 1)))\n y_dir = cross(z_dir, x_dir)\n # Get the local coordinates positions\n p1 = dot((v_pos - orig), x_dir.reshape(3, 1))\n p2 = dot((v_pos - orig), y_dir.reshape(3, 1))\n p3 = dot((v_pos - orig), z_dir.reshape(3, 1))\n\n charge = float(pos_site.split()[4])\n\n # store the site info [(parent top no, a, b), (p1, p2, p3), charge]]\n sites[sites_no] = [(parent - 1, closet_atoms[0] - 1, closet_atoms[1] - 1), (p1 / 10, p2 / 10, p3 / 10), charge]\n sites_no += 1\n\n self.molecule.sites = sites\n\n # get the parent non bonded values\n for value in sites.values():\n charge, sigma, eps = self.non_bonded_force[value[0][0]]\n # Change the charge on the first entry\n charge = float(charge) - value[2]\n self.non_bonded_force[value[0][0]] = [str(charge), sigma, eps]",
"def abs_energy(x):\n\treturn np.dot(x, x)",
"def __init__(self, *args, **kwargs):\n super(DischargedWaterBoxHsites, self).__init__(*args, **kwargs)\n\n # Zero charges.\n system = self.system\n forces = { system.getForce(index).__class__.__name__ : system.getForce(index) for index in range(system.getNumForces()) }\n force = forces['NonbondedForce']\n for index in range(force.getNumParticles()):\n [charge, sigma, epsilon] = force.getParticleParameters(index)\n charge *= 0\n if epsilon == 0.0 * unit.kilojoules_per_mole:\n # Add LJ site to hydrogens.\n epsilon = 0.0157 * unit.kilojoules_per_mole\n sigma = 0.06 * unit.angstroms\n force.setParticleParameters(index, charge, sigma, epsilon)\n for index in range(force.getNumExceptions()):\n [particle1, particle2, chargeProd, sigma, epsilon] = force.getExceptionParameters(index)\n chargeProd *= 0\n epsilon *= 0\n force.setExceptionParameters(index, particle1, particle2, chargeProd, sigma, epsilon)\n \n return",
"def Calculate_Xe(self):\n\t\tX_e_TempArray = [1]\n\t\tfor i in range(0,self.n_eta-1):\n\t\t\tif X_e_TempArray[i] > 0.99:\n\t\t\t\tX_e_TempArray.append(self.Saha_equation(self.x_eta[i]))\n\t\t\telse:\n\t\t\t\tPeebleXe = integrate.odeint(self.Peebles_equation, X_e_TempArray[i], self.x_eta[i:])\n\t\t\t\tbreak\n\n\t\tPeebleXe2 = []\n\t\tfor i in range(0, len(PeebleXe)-1):\n\t\t\tPeebleXe2.append(PeebleXe[i][0])\n\t\tself.X_e_array = np.concatenate([np.array(X_e_TempArray),np.array(PeebleXe2)])\t# Merges arrays",
"def opt_energy_env_2site(isos_012, h_mpo_2site, states_1site_above):\n def _ascend_op_2site_to_2site_many(mpo_2site, isos):\n ops = []\n for l in range(len(isos)):\n mpo_2site = ascend_op_2site_to_2site(mpo_2site, *isos[l])\n ops.append(mpo_2site)\n return ops\n\n def _mpo_with_state(iso_012, iso_021, h_mpo_2site, state_1site):\n \"\"\"Contract a 2-site MPO with a 1-site descended state. O(D^4)\"\"\"\n h2L, h2R = h_mpo_2site\n\n envL = [\n backend.ncon(\n [state_1site, iso_021, h, backend.conj(iso_012)],\n [(1, 3), (1, -1, 2), (4, 2), (3, 4, -2)]) # one transpose required\n for h in h2L\n ]\n\n envR = [\n backend.ncon(\n [state_1site, iso_012, h, backend.conj(iso_021)],\n [(1, 3), (1, -1, 2), (4, 2), (3, 4, -2)]) # one transpose required\n for h in h2R\n ]\n\n return envL, envR\n\n def _descend_energy_env_L(env, iso_021):\n return [descend_state_1site_L(e, iso_021) for e in env]\n\n def _descend_energy_env_R(env, iso_012):\n return [descend_state_1site_R(e, iso_012) for e in env]\n\n isos_wt = isos_with_transposes(isos_012)\n iso_012, iso_021 = isos_wt[0]\n isos_wt_above = isos_wt[1:]\n levels_above = len(isos_wt_above)\n\n # Ascend two-site Hamiltonian terms to the bottom of the final isometry\n h2s_above = _ascend_op_2site_to_2site_many(h_mpo_2site, isos_wt)\n\n # hamiltonian with isometry opposite the gap\n h2L, h2R = h_mpo_2site\n iso_h2R_012 = [\n backend.ncon([iso_021, h], [(-1, -3, 1), (-2, 1)]) for h in h2R\n ] # transpose to 012\n iso_h2L_012 = [\n backend.ncon([iso_012, h], [(-1, -2, 1), (-3, 1)]) for h in h2L\n ]\n\n def _compute_env(lvl, reflect=False):\n # TODO: Could shorten this a bit by doing only left or right at one time\n h2 = h2s_above[lvl]\n if reflect:\n h2 = reflect_mpo_2site(h2)\n\n envL, envR = _mpo_with_state(*isos_wt_above[lvl], h2,\n states_1site_above[lvl])\n\n # descend envs back down to the level of the gap\n for lvl2 in reversed(range(lvl)):\n iso_012_l2, iso_021_l2 = isos_wt_above[lvl2]\n if reflect:\n envR = _descend_energy_env_L(envR, iso_021_l2)\n envL = _descend_energy_env_R(envL, iso_012_l2)\n else:\n envL = _descend_energy_env_L(envL, iso_021_l2)\n envR = _descend_energy_env_R(envR, iso_012_l2)\n\n if reflect:\n iso_h2_L, iso_h2_R = iso_h2R_012, iso_h2L_012\n else:\n iso_h2_L, iso_h2_R = iso_h2L_012, iso_h2R_012\n\n # contract with the hamiltonian + isometry opposite the gap\n envL = sum(\n backend.ncon([eL, ihR], [(1, -1), (1, -2, -3)])\n for eL, ihR in zip(envL, iso_h2_R))\n\n envR = sum(\n backend.ncon([eR, ihL], [(1, -1), (1, -2, -3)])\n for eR, ihL in zip(envR, iso_h2_L))\n\n # weight each term according to the number of occurrences\n # in the translation-invariant tree\n weight = 1 / 2.0**(lvl + 1)\n return (envL + envR) * weight, weight\n\n weightsum = 0.0\n env_total = []\n for lvl in range(levels_above):\n env, weight = _compute_env(lvl)\n weightsum += weight\n env_total.append(env)\n\n # Now compute the boundary term\n env, weight = _compute_env(levels_above - 1, reflect=True)\n weightsum += weight\n env_total.append(env)\n\n env_total = sum(env_total)\n\n assert weightsum == 1.0\n\n return env_total",
"def opt_energy_env(isos_012,\n h_op_1site,\n h_mpo_2site,\n states_1site_above):\n if len(isos_012) == 1: # top of tree\n h_mpo_2site = add_mpos_2site(h_mpo_2site, reflect_mpo_2site(h_mpo_2site))\n env = opt_energy_env_1site(isos_012[0], h_op_1site, h_mpo_2site,\n states_1site_above[0])\n else:\n env1 = opt_energy_env_1site(isos_012[0], h_op_1site, h_mpo_2site,\n states_1site_above[0])\n env2 = opt_energy_env_2site(isos_012, h_mpo_2site, states_1site_above[1:])\n env = env1 + env2\n\n return env",
"def hoppingy_1D_semiconductor(site0,site1,p):\n\t#print(\"%s: in hoppingy_1D_semiconductor()\" %str(misc.round_time(datetime.datetime.now(),round_to=60)))\n\treturn -p.t_N*tau_z + 1j*p.alphahbar/(2*p.ay)*sigma_ytau_z",
"def energy(self, state: np.ndarray):\r\n return -0.5 * state.dot(self.weights).dot(state) + np.sum(state * self.threshold)",
"def prox_mapping(v, x0, sigma, dist_option=2):\n if dist_option == 1:\n x = x0 - sigma * v\n elif dist_option == 2:\n x = x0 * np.exp(-sigma * v)\n x = x / x.sum()\n return x",
"def prox_mapping2(v, x0, sigma, dist_option=2):\n lb = -25\n if dist_option == 1:\n x = x0 - sigma * v\n elif dist_option == 2:\n u = -sigma * v\n u_max = u.max()\n u = u - u_max\n u[u < lb] = lb\n # if u_max > 0:\n # x = x0 * np.exp(-sigma * v - u_max)\n # x = x / x.sum()\n # else:\n x = x0 * np.exp(u)\n x = x / x.sum()\n return x",
"def binding_energy(self,site,double_stranded=False):\n w = len(site)\n E_f = self.activation(site) * w * (-2/beta) - 0.05\n E_b = double_stranded and (self.activation(wc(site)) * w * (-2/beta) - 0.05)\n E_t = ((1 / -beta) * log(exp(-beta * E_f) + exp(-beta * E_b))\n if double_stranded\n else E_f)\n return E_t",
"def propagate_system(self, system):\n # Compute eigenvectors and values for matrix exponential operator\n # eigval -> (R x M x 3)\n # eigvec -> (R x M x 3 x 3)\n eigval, eigvec = torch.symeig(self.b_velocities_cell, eigenvectors=True)\n\n evaldt2 = 0.5 * eigval[:, :, None, :] * self.time_step\n\n # Compute exponential operator and sinh(x)/x operator (approximated)\n a_coeff = torch.exp(evaldt2)\n b_coeff = a_coeff * self.sinhdx.f(evaldt2)\n\n # Transform positons, velocities and cells via the eigenvectors\n positions_tmp = torch.matmul(system.positions, eigvec)\n velocities_tmp = torch.matmul(system.momenta / system.masses, eigvec)\n cells_tmp = torch.matmul(system.cells, eigvec)\n\n # Apply the propagator to the positions\n positions_tmp = (\n positions_tmp * a_coeff ** 2 + velocities_tmp * b_coeff * self.time_step\n )\n\n # Apply the propagator to the cells\n cells_tmp = cells_tmp * a_coeff ** 2\n\n # Transform everything back and update the system\n system.positions = torch.matmul(positions_tmp, eigvec.transpose(2, 3))\n system.cells = torch.matmul(cells_tmp, eigvec.transpose(2, 3))",
"def power_on(self):",
"def __init__(self,rho,enemin=ENEMIN):\n self.rho = rho\n self.enemin=enemin\n # Read in the stopping power and interpolate.\n xesp_tbl = np.loadtxt(\"xe_estopping_power_NIST.dat\");\n self.evals = xesp_tbl[:,0]\n self.dEdxvals = xesp_tbl[:,1];\n self.evals = np.insert(self.evals,0,0.0);\n self.dEdxvals = np.insert(self.dEdxvals,0,self.dEdxvals[0]);\n self.xesp = sc_interpol(self.evals,self.dEdxvals*self.rho,kind='cubic')\n # this is the dE/dx(E) function\n return",
"def energy(params,circuit):\n # setup circuit (resolve parameters to numerical values)\n resolver = cirq.ParamResolver({'theta'+str(j):params[j] for j in range(n_var_params)})\n resolved_circuit = cirq.resolve_parameters(circuit, resolver) \n u = resolved_circuit.unitary(qubit_order = qp+qb)\n unitary = u.reshape([2**nphys,2**nbond,2**nphys,2**nbond])\n # Convert to MPS and compute <H> \n # change the order of indices to [p, vL, vR] = [p_out, b_in, b_out] \n # (with p_in = 0 to go from unitary to isometry)\n B = np.swapaxes(unitary[:,:,0,:],1,2)\n psi = MPS.from_Bflat([site], [B], bc='infinite', dtype=complex, form=None)\n psi.canonical_form()\n psi.convert_form(psi.form)\n holo_E = (H.expectation_value(psi)).real\n \n return holo_E",
"def energy_inf(self):\n\n if self.x**2 != 1:\n print('Off axis orbits are not currently supported.')\n elif self.harmonic is None:\n print('Unable to compute energy values without setting modes.')\n # else:\n # self.harmonic_key = tuple((self.harmonic['ell'], self.harmonic['em']))\n # self.mode_key = tuple((self.mode['kay'], self.mode['en']))\n # print(self.harmonic_key)\n # print(self.mode_key)\n # if self.harmonic_key in self.mode_content.keys():\n # if self.mode_key in self.mode_content[self.harmonic_key].keys():\n # print('Mode has already been computed and has been skipped.')\n # TODO (aaron): add some logic to skip modes that have already been computed\n else:\n self.omega = fp_find_omega(self.omega_r, self.omega_theta, self.omega_phi, self.em, self.kay, self.en)\n self.re_nu, self.im_nu = calc_nu(self.aa, self.slr, self.ecc, self.x, self.ell, self.en, self.em, self.kay)\n\n self.eigen, self.Slm, self.Slmd, self.Slmdd = calc_swsh_eq(self.aa, self.omega, self.ell, self.em, -2)\n\n self.nu = self.re_nu + 1j * self.im_nu\n self.Bin = py_find_Bin(self.re_nu, self.im_nu, self.eigen, self.aa, self.omega, self.em)\n\n self.mode_dependent = {'gw_freq':self.omega, 'eigen':self.eigen, 'nu':self.nu, 'Bin':self.Bin}\n\n self.e_inf, self.Z = flux_inf(self.nu, self.Bin, self.eigen, self.slr, self.ecc, self.aa, self.ups_r, self.ups_theta,\n self.ups_phi, self.gamma, self.omega, self.em, self.Lz, self.En, self.Slm, self.Slmd,\n self.Slmdd, self.omega_r, self.r1, self.r2, self.r3, self.r4, self.zp, self.zm)\n if np.isnan(self.e_inf): # TODO (aaron): investigate why this can be nan\n print('Some value is NaN - this needs to be investigated.')\n self.e_inf = 0\n print('Energy at infinity stored as zero:', self.e_inf)\n\n elif self.double:\n self.e_inf = 2 * self.e_inf\n print('Energy at infinity:', self.e_inf)\n\n # put everything in a dict to save later as a json/hdf5\n self.harmonic_key = tuple((self.harmonic['ell'], self.harmonic['em']))\n self.mode_key = tuple((self.mode['kay'], self.mode['en']))\n\n if self.harmonic_key in self.mode_content.keys():\n self.mode_content[self.harmonic_key][self.mode_key] = self.e_inf\n else:\n self.mode_content[self.harmonic_key] = {self.mode_key: self.e_inf}"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Check if device is asymmetric (one Al strip) or symmetric (two Al strips). Returns
|
def check_asymm_device(p):
if len(p.right) == 0:
p.asymmetric = True # to be used when printing last blocks of the Hamiltonian
p.Nxasymmetric = len(p.left) + len(p.middle)
else:
p.asymmetric = False
return p.asymmetric
|
[
"def is_symmetric(self):\n return self._alph1 == self._alph2 \\\n and np.array_equal(self._matrix, np.transpose(self._matrix))",
"def is_symmetric(self):",
"def is_symmetric(self):\n M = self.parent().realization_of().Monomial()\n return M(self).is_symmetric()",
"def use_symmetry(self):\n symmetry = self.params[PARAM_SYMMETRY]\n if symmetry is None:\n #Default to false if no parameter.\n return False\n else:\n return symmetry.use_symmetry",
"def is_symmetric(self):\n matrix = Matrix(self.array)\n\n if len(self.array) == len(self.array[0]) and matrix == matrix.transposition():\n print(\"Matrix is symmetric\")\n return True\n else:\n print(\"Matrix is not symmetric\")\n return False",
"def issymmetrical(self):\n\n if self.width == 1 or self.height==1:\n return False\n\n h_opp, w_opp = self.get_player_location(self._inactive_player)\n h_active, w_active = self.get_player_location(self.active_player)\n\n if self.width == 3 and self.height == 3:\n if self._active_player == self._player_1:\n if self.check_center_sym(h_opp, w_opp, h_active, w_active):\n return True\n return False\n\n elif self.width % 2 == 1 and self.height % 2 == 1:\n if self.active_player == self._player_2:\n mid_i = self.width//2\n mid_j = self.height//2\n # check that middle square is filled\n if self._board_state[mid_i + mid_j * self.height] == Board.BLANK:\n off_center = self.__get_moves((mid_i, mid_j))\n if len(off_center) == 0:\n pass\n else:\n return False #strictly speaking the middle position needs to be unavailable rather than filled to guarantee no symmetry\n #however the check for symmetry needs to be fast and accuracy is sacrificed for speed\n if self.check_center_sym(h_opp, w_opp, h_active, w_active):\n return True\n if self.check_horizontal_sym(h_opp, w_opp, h_active, w_active):\n return True\n if self.check_vertical_sym(h_opp, w_opp, h_active, w_active):\n return True\n if self.width == self.height:\n if self.check_diag1_sym(h_opp, w_opp, h_active, w_active):\n return True\n if self.check_diag2_sym(h_opp, w_opp, h_active, w_active):\n return True\n return False\n elif self._active_player == self._player_1:\n if self.check_center_sym(h_opp, w_opp, h_active, w_active):\n return True\n if self.check_horizontal_sym(h_opp, w_opp, h_active, w_active):\n return True\n if self.check_vertical_sym(h_opp, w_opp, h_active, w_active):\n return True\n if self.width == self.height:\n if self.check_diag1_sym(h_opp, w_opp, h_active, w_active):\n return True\n if self.check_diag2_sym(h_opp, w_opp, h_active, w_active):\n return True\n\n return False",
"def checkValidSymmetry(self) -> bool:\n return (\n self.domain,\n self.boundary,\n self.isThroughCenterAssembly,\n ) in self.VALID_SYMMETRY",
"def is_symmetrical(self):\r\n\r\n if (not self.is_square()):\r\n raise ErrorInMatrix('This matrix is not square')\r\n else:\r\n for i in range(self.row):\r\n for j in range(self.col):\r\n if self.mat[i][j] != self.mat[j][i]:\r\n return False\r\n else:\r\n return True",
"def is_symmetric(self, diag='main'):\n if self.is_square():\n if diag == 'main':\n return self == self.transpose()\n elif diag == 'anti':\n to_compare = []\n for row in range(self.rows):\n to_compare.append(self.matrix[row][::-1])\n to_compare = Matrix(to_compare[::-1])\n return self == to_compare.transpose()\n else:\n raise ValueError(\"Wrong diag. Could be 'main' or 'anti\")\n else:\n raise ValueError(\"Non square matrix.\")",
"def is_non_strict_symmetric(use_symmetric_encodings: bool,\n use_strict_symmetric: bool,\n is_unsigned_symmetric: bool) -> bool:\n return use_symmetric_encodings and \\\n not use_strict_symmetric and \\\n not is_unsigned_symmetric",
"def is_symmetric(A):\n\tif A.ndim == 1:\n\t\tprint(\"This is a vector, not a matrix!\")\n\t\treturn False\n\tif A.ndim != 2:\n\t\tprint(\"This is not a matrix!\")\n\t\treturn False\n\telse:\n\t\treturn np.array_equal(A, A.T)",
"def _derive_layout_symmetry(self):\n self._sym_df = None # Default option\n if self.exploit_layout_symmetry:\n # Check symmetry of bounds & turbine_weights\n if np.unique(self.minimum_yaw_angle, axis=0).shape[0] > 1:\n print(\"minimum_yaw_angle is not equal over wind directions.\")\n print(\"Exploiting of symmetry has been disabled.\")\n return\n\n if np.unique(self.maximum_yaw_angle, axis=0).shape[0] > 1:\n print(\"maximum_yaw_angle is not equal over wind directions.\")\n print(\"Exploiting of symmetry has been disabled.\")\n return\n\n if np.unique(self.maximum_yaw_angle, axis=0).shape[0] > 1:\n print(\"maximum_yaw_angle is not equal over wind directions.\")\n print(\"Exploiting of symmetry has been disabled.\")\n return\n\n if np.unique(self.turbine_weights, axis=0).shape[0] > 1:\n print(\"turbine_weights is not equal over wind directions.\")\n print(\"Exploiting of symmetry has been disabled.\")\n return\n\n # Check if turbine_weights are consistently 1.0 everywhere\n if np.any(np.abs(self.turbine_weights - 1.0) > 0.001):\n print(\"turbine_weights are not uniformly 1.0.\")\n print(\"Exploiting of symmetry has been disabled.\")\n return\n\n x = self.fi.layout_x\n y = self.fi.layout_y\n df = find_layout_symmetry(x=x, y=y)\n\n # If no axes of symmetry, exit function\n if df.shape[0] <= 0:\n print(\"Wind farm layout in floris is not symmetrical.\")\n print(\"Exploitation of symmetry has been disabled.\")\n return\n\n wd_array = self.fi.floris.flow_field.wind_directions\n sym_step = df.iloc[0][\"wd_range\"][1]\n if ((0.0 not in wd_array) or(sym_step not in wd_array)):\n print(\"Floris wind direction array does not \" +\n \"intersect {:.1f} and {:.1f}.\".format(0.0, sym_step))\n print(\"Exploitation of symmetry has been disabled.\")\n return\n\n ids_minimal = (wd_array >= 0.0) & (wd_array < sym_step)\n wd_array_min = wd_array[ids_minimal]\n wd_array_remn = np.remainder(wd_array, sym_step)\n\n if not np.all([(x in wd_array_min) for x in wd_array_remn]):\n print(\"Wind direction array appears irregular.\")\n print(\"Exploitation of symmetry has been disabled.\")\n\n self._sym_mapping_extrap = np.array(\n [np.where(np.abs(x - wd_array_min) < 0.0001)[0][0]\n for x in wd_array_remn], dtype=int)\n\n self._sym_mapping_reduce = copy.deepcopy(ids_minimal)\n self._sym_df = df\n\n return",
"def is_symmetric(matrix):\r\n\r\n\ts = matrix.shape\r\n\tif s[0] != s[1]:\r\n\t\tb = False #Not diagonal since rows != cols\r\n\telse:\r\n\t\tb = np.allclose(matrix, matrix.T, equal_nan=True)\r\n\r\n\treturn(b)",
"def __eq__(self, other):\n if isinstance(other, SymmetryType):\n return (\n self.domain == other.domain\n and self.boundary == other.boundary\n and self.isThroughCenterAssembly == other.isThroughCenterAssembly\n )\n elif isinstance(other, str):\n otherSym = SymmetryType.fromStr(other)\n return (\n self.domain == otherSym.domain\n and self.boundary == otherSym.boundary\n and self.isThroughCenterAssembly == otherSym.isThroughCenterAssembly\n )\n else:\n raise NotImplementedError",
"def run_symmetric_encryption(self) -> bool:\n try:\n alice_message = self.qc.generate_message(self.message_length)\n\n alice_cipher = self.qc.cipher_message(alice_message,\n self.alice_key)\n bob_message = self.qc.cipher_message(alice_cipher, self.bob_key)\n\n print(\"------------------------------------------------------\")\n print(\"Alice's Message\\n{}\\n\".format(\n self.qc.list_to_string(alice_message)))\n print(\"Cipher\\n{}\\n\".format(self.qc.list_to_string(alice_cipher)))\n print(\"Bob's Message\\n{}\\n\".format(\n self.qc.list_to_string(bob_message)))\n\n if self.run_type == \"attack\":\n eve_message = self.qc.cipher_message(alice_cipher,\n self.eve_key)\n\n print(\"Eve's Cracked Message\\n{}\\n\".format(\n self.qc.list_to_string(alice_message)))\n\n return self.qc.list_to_string(\n alice_message) == self.qc.list_to_string(\n eve_message) and self.qc.list_to_string(\n bob_message) == self.qc.list_to_string(eve_message)\n\n return self.qc.list_to_string(\n alice_message) == self.qc.list_to_string(bob_message)\n\n except TypeError:\n print(\"Error: No keys have been generated yet!\\n\")",
"def SupportsEncryption(self):\n return self.path_spec.type_indicator in (\n definitions.TYPE_INDICATORS_WITH_ENCRYPTION_SUPPORT)",
"def check_center_sym(self, h_opp, w_opp, h_active, w_active):\n\n # position symmetrical to h, w is self.height - h - 1, self.width -w - 1 or to idx : boardArea-idx\n\n # player locations are symmetrical\n if (h_active, w_active) == (self.height - h_opp -1, self.width - w_opp -1):\n # all squares are filled symmetrically\n for idx in range((self.width*self.height)//2-1):\n if self._board_state[idx] != self._board_state[self.width*self.height-1-idx]:\n return False\n #print ('Found center sym')\n return True\n return False",
"def check_symmetry(self, tol=1e-5, verbose=True):\n Ctemp = self.Cvoigt.copy()\n dC = Ctemp.T - Ctemp\n maxdC = (np.abs(dC)).max()\n if maxdC > tol: raise ValueError('Elastic tensor is not symmetric !')\n if verbose: print 'Symmetry checked! Maximum element in dC =', maxdC\n return",
"def is_matrix_symmetric(self, M, rtol=1e-05, atol=1e-08):\n return(np.allclose(M, M.T, rtol=rtol, atol=atol))"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Make NN(S) subject to the calibration of the NS(Heff) system created in make_1D_NLeft_1D_S_Heff_No_NRight. Notes xcoordinate of the 1D semiconducting system is taken to be zero. xcoordinate of the 2D pincher layer is taken to be at +1. So the pincher layer is 1D, but implemented as a 2D Hamiltonian because it needs to have couplings between it and the middle N.
|
def make_1D_Nleft_1D_N_2D_S_2D_SMiddle_No_NRight(p,ppar):
print("%s: in make_1D_Nleft_1D_N_2D_S_2D_SMiddle_No_NRight()" %str(misc.round_time(datetime.datetime.now(),round_to=60)))
import kwant
sys = kwant.Builder()
sys[(lat(x,y) for x in [0] for y in range(p.Ny))] = onsite_1D_semiconductor
sys[kwant.builder.HoppingKind((0,1),lat)] = hoppingy_1D_semiconductor
if ppar.pincher_SC_lead == True:
print(" - Adding SC layer (2D Hamiltonian and 1D line of sites) at N system - S lead boundary.")
"""Attaching extra sites with hoppings p.tx_SC_pincher and p.ty_SC_pincher:"""
sys[(lat(x,y) for x in [1] for y in range(p.Ny))] = onsite_2D_superconductor_pincher
sys[kwant.builder.HoppingKind((1,0),lat)] = hoppingx_2D_superconductor_pincher
sys[kwant.builder.HoppingKind((0,1),lat)] = hoppingy_2D_superconductor_pincher
"""Attaching Left lead to the middle region:"""
lead = make_lead_onesite_wide_1D(p)
sys.attach_lead(lead)
"""
Adding SC lead last. In that way, the indexing of the smatrix will work as before when wanting to access the other leads. In order to access from the SC lead, acces the 2nd lead index in e.g. the smatrix.
"""
if ppar.SClead == True:
SClead = make_SC_lead_Ny_wide(p)
sys.attach_lead(SClead)
print(" - Attached SC lead")
return sys
|
[
"def change_cell(nsys0,X0):\n if X0.dtype != int:\n raise TypeError('X0.dtype is wrong.')\n if X0.shape != (3,3):\n raise TypeError('X0 has wrong shape.')\n X = np.array(X0,dtype=float)\n ncp = np.zeros(3,dtype=int)\n ncp[0] = X0[0,:].max()\n ncp[1] = X0[1,:].max()\n ncp[2] = X0[2,:].max()\n\n nsys = replicate(nsys0,ncp[0],ncp[1],ncp[2])\n hmat0 = nsys0.get_hmat()\n hmat = np.dot(hmat0,X0)\n print(nsys)\n sposs = nsys.get_scaled_positions()\n spnews = np.array(sposs)\n nsys.set_hmat(hmat)\n #...Since hmat0 is that of extended system,\n #...X should correspond to it.\n X[0,:] /= ncp[0]\n X[1,:] /= ncp[1]\n X[2,:] /= ncp[2]\n Xi = np.linalg.inv(X)\n for i,p in enumerate(sposs):\n pnew = np.dot(Xi,p)\n for l in range(3):\n pnew[l] = nappy.util.pbc(pnew[l])\n spnews[i,:] = pnew[:]\n nsys.set_scaled_positions(spnews)\n return nsys",
"def _fermion_solver(self):\n self.kcut = len(self.offsets) - 1\n\n nhe, he2idx, idx2he = _heom_state_dictionaries(\n [2] * len(self.flat_ck), self.N_cut\n )\n self.nhe = nhe\n self.he2idx = he2idx\n self.idx2he = idx2he\n \n\n # Separate cases for Hamiltonian and Liouvillian\n if self.isHamiltonian:\n if self.isTimeDep:\n self.N = self.H_sys_list.shape[0]\n self.L = liouvillian(self.H_sys_list[0], []).data\n \n else:\n self.N = self.H_sys.shape[0]\n self.L = liouvillian(self.H_sys, []).data\n \n else:\n \n if self.isTimeDep: \n self.N = int(np.sqrt(self.H_sys_list[0].shape[0])) \n self.L = self.H_sys_list[0].data\n \n else:\n self.N = int(np.sqrt(self.H_sys.shape[0]))\n self.L = self.H_sys.data\n \n self.L_helems = sp.csr_matrix(\n (self.nhe * self.N ** 2, self.nhe * self.N ** 2), dtype=np.complex\n )\n # Set coupling operators\n spreQ = []\n spostQ = []\n spreQdag = []\n spostQdag = []\n for coupOp in self.coup_op:\n spreQ.append(spre(coupOp).data)\n spostQ.append(spost(coupOp).data)\n spreQdag.append(spre(coupOp.dag()).data)\n spostQdag.append(spost(coupOp.dag()).data)\n\n self.spreQ = spreQ\n self.spostQ = spostQ\n self.spreQdag = spreQdag\n self.spostQdag = spostQdag\n # make right hand side\n self.fermion_rhs()\n\n # return output\n return self.L_helems, self.nhe",
"def apply_syndrome(N):\n circ=HammingCircuit(N, ancillas=N)\n nqubits=2**N\n count=np.zeros(N)\n for i in range(1,nqubits):\n count=count+1\n for j in range(N):\n count[j]=count[j]%(2**j)\n if count[j]==0 and i!=1: circ.x(nqubits+j)\n if i==1 and j!=0: circ.x(nqubits+j)\n circ.mct([*range(nqubits,nqubits+N)],i)\n return circ.to_gate(label='Correction')",
"def init_stn(self, stn_fc2: nn.Linear) -> None:\n margin = 0.01\n sampling_num_per_side = int(self.num_control_points / 2)\n ctrl_pts_x = np.linspace(margin, 1. - margin, sampling_num_per_side)\n ctrl_pts_y_top = np.ones(sampling_num_per_side) * margin\n ctrl_pts_y_bottom = np.ones(sampling_num_per_side) * (1 - margin)\n ctrl_pts_top = np.stack([ctrl_pts_x, ctrl_pts_y_top], axis=1)\n ctrl_pts_bottom = np.stack([ctrl_pts_x, ctrl_pts_y_bottom], axis=1)\n ctrl_points = np.concatenate([ctrl_pts_top, ctrl_pts_bottom],\n axis=0).astype(np.float32)\n stn_fc2.weight.data.zero_()\n stn_fc2.bias.data = torch.Tensor(ctrl_points).view(-1)",
"def makeHomography(Sxy, Txy):\n\n assert len(Sxy) >= 4, 'at least 4 source points required.'\n assert len(Txy) >= 4, 'at least 4 target points required.'\n assert len(Sxy) == len(Txy), 'same number of source and target points (at least 4) required.'\n\n n = len(Sxy)\n b = np.zeros(2 * n + 1)\n # this coupled with constraint 3 makes h33 = 1\n b[-1] = 1\n\n i = np.arange(n)\n A = np.zeros((2 * n + 1, 9))\n\n # 1. x constraints:\n # -sx*h11 - sy*h12 - h13 + 0 + 0 + 0 + sx*tx*h31 + sy*tx*h32 + tx*h33\n A[2 * i] = np.array([\n -Sxy[i, 0], -Sxy[i, 1], [-1]*n,\n [0]*n, [0]*n, [0]*n,\n Sxy[i, 0] * Txy[i, 0], Sxy[i, 1] * Txy[i, 0], Txy[i, 0]\n ]).T\n\n # 2. y constraints:\n # 0 + 0 + 0 -sx*h21 - sy*h22 - h23 + sx*tx*h31 + sy*tx*h32 + tx*h33\n A[2 * i + 1] = np.array([\n [0]*n, [0]*n, [0]*n,\n -Sxy[i, 0], -Sxy[i, 1], [-1]*n,\n Sxy[i, 0] * Txy[i, 1], Sxy[i, 1] * Txy[i, 1], Txy[i, 1]\n ]).T\n\n # 3. constant scale constraint:\n # 0h11 + 0h12 + 0h13 + 0h21 + 0h22 + 0h23 + 0h31 + 0h32 + h33\n A[-1, -1] = 1\n\n H = np.linalg.lstsq(A, b, rcond=None)[0].reshape(3, 3)\n H_ = H / H[-1, -1]\n return H_",
"def create_spn_neuron(n_gaussians: int):\n\n class SPNNeuron(nn.Module):\n def __init__(self, in_features):\n \"\"\"\n Initialize the SPNNeuron.\n\n Args:\n in_features: Number of input features.\n n_mv: Number of different pairwise independence mixtures of the leaf nodes.\n \"\"\"\n # Init\n super(SPNNeuron, self).__init__()\n\n # Create random sequence of scopes\n scopes = np.random.permutation(in_features)\n\n sums = []\n\n # For two consecutive (random) scopes\n for i in range(0, in_features, 2):\n scope_1 = scopes[i]\n scope_2 = scopes[i + 1]\n\n # Create n_mv MultivariateGaussian from these two scopes\n mvs = []\n for _ in range(n_gaussians):\n # TODO: MVG are currently not trainable\n # mv = MultivariateGaussian(n_vars=2, scope=[scope_1, scope_2])\n # mvs.append(mv)\n\n g1 = GaussianNode(scope=scope_1)\n g2 = GaussianNode(scope=scope_2)\n\n prod = ProductNode([g1, g2])\n mvs.append(prod)\n\n sumnode = SumNode(children=mvs)\n sums.append(sumnode)\n\n self.root = ProductNode(children=sums)\n\n def forward(self, x):\n x = self.root(x)\n return x\n\n return SPNNeuron",
"def test_kron_1x2_conv():\n u.seed_random(1)\n\n n, Xh, Xw = 1, 1, 4\n Kh, Kw = 1, 2\n dd = [1, 1, 1]\n o = dd[-1]\n\n model: u.SimpleModel = u.StridedConvolutional2(dd, kernel_size=(Kh, Kw), nonlin=False, bias=True)\n data = torch.tensor([0, 1., 1, 1]).reshape((n, dd[0], Xh, Xw))\n\n model.layers[0].bias.data.zero_()\n model.layers[0].weight.data.copy_(torch.tensor([1, 2]))\n\n model.layers[1].bias.data.zero_()\n model.layers[1].weight.data.copy_(torch.tensor([1, 2]))\n\n sample_output = model(data)\n\n autograd_lib.clear_backprops(model)\n autograd_lib.add_hooks(model)\n output = model(data)\n autograd_lib.backprop_hess(output, hess_type='LeastSquares')\n autograd_lib.compute_hess(model, method='kron', attr_name='hess_kron')\n autograd_lib.compute_hess(model, method='exact')\n autograd_lib.disable_hooks()\n\n for i in range(len(model.layers)):\n layer = model.layers[i]\n H = layer.weight.hess\n Hk = layer.weight.hess_kron\n Hk = Hk.expand()\n print(u.symsqrt_dist(H, Hk))",
"def twoSiteGate(self, m, n, tau):\n\n if n < m:\n mpo1 = self._mpo[n][-1, :, :, :]\n mpo2 = self._mpo[m][:, 0, :, :]\n nl = n\n mr = m\n if n > m:\n mpo1 = self._mpo[m][-1, :, :, :]\n mpo2 = self._mpo[n][:, 0, :, :]\n nl = m\n nr = n\n assert (mpo1.shape[0] == mpo2.shape[0])\n d1 = mpo1.shape[1]\n d2 = mpo2.shape[1]\n if nl != 0 and nr != (self._N - 1):\n h = np.kron(mpo1[0, :, :] / 2.0, mpo2[0, :, :])\n for s in range(1, mpo1.shape[0] - 1):\n h += np.kron(mpo1[s, :, :], mpo2[s, :, :])\n h += np.kron(mpo1[-1, :, :], mpo2[-1, :, :] / 2.0)\n\n elif nl != 0 and nr == (self._N - 1):\n h = np.kron(mpo1[0, :, :] / 2.0, mpo2[0, :, :])\n for s in range(1, mpo1.shape[0]):\n h += np.kron(mpo1[s, :, :], mpo2[s, :, :])\n elif nl == 0 and nr != (self._N - 1):\n h = np.kron(mpo1[0, :, :], mpo2[0, :, :])\n for s in range(1, mpo1.shape[0] - 1):\n h += np.kron(mpo1[s, :, :], mpo2[s, :, :])\n h += np.kron(mpo1[-1, :, :], mpo2[-1, :, :] / 2.0)\n Gate = np.reshape(sp.linalg.expm(tau * h), (d1, d2, d1, d2))\n #Gate=np.reshape(np.eye(4),(d1,d2,d1,d2))\n\n return Gate",
"def H(N, W1, c1, phi1, J1=1, W2=0, c2=0, phi2=0, J2=0, nleg=1, mode='open'):\n\n # try to load Sx, Sy, Sz from the Globals dictionary if they have been\n # generated\n try:\n Sx, Sy, Sz = G['sigmas']\n except KeyError:\n Sx, Sy, Sz = c.sigmax(), c.sigmay(), c.sigmaz()\n G['sigmas'] = [Sx, Sy, Sz]\n\n # try to load the full Hilbert space operators from the Globals\n # dictionary if they have been generated\n if not G.__contains__('full_S'):\n G['full_S'] = {}\n try:\n full_S = G['full_S'][N]\n except KeyError:\n full_S = [[half.full_matrix(S, k, N) for k in range(N)]\n for S in [Sx, Sy, Sz]]\n G['full_S'][N] = full_S\n\n # The following section describes a hamiltonian of a 2-D latice that\n # we label the following way\n # 0 l2 2*l2 ... (l1-1)*l2\n # 1 l2+1 2*l2+1 ... (l1-1)*l2+1\n # 2 l2+2 2*l2+2 ... (l1-1)*l2+2\n # ...\n # l2-1 2*l2-1 3*l2-1 ... l1*l2-1\n l1 = N // nleg # number of sites along the \"horizontal\"\n l2 = nleg # number of sites along the \"vertical\" (number of legs)\n # Nearest neighbor contributions along the horizontal direction (along\n # which J1 is the coupling constant)\n if nleg == N:\n J1 = 0 # interaction=0 if there's only 1 site along direction\n # mode == 'periodic' is self-explanatory. l1==2 and lb1=0 would imply\n # adjacent sites along adjacent legs interact with each other twice,\n # not exactly what we are looking for.\n lb1 = 0 if (mode == 'periodic' and not l1 == 2) else l2\n inter_terms1 = J1 * sum(full_S[i][j - l2] * full_S[i][j]\n for j in range(lb1, N) for i in range(3))\n\n # Nearest neighbor contributions along the vertical direction (along\n # which J2 is the coupling constant)\n if nleg == 1:\n J2 = 0 # interaction=0 if there's only 1 site along direction\n # mode == 'periodic' is self-explanatory. l2==2 and js looping over\n # every index would imply adjacent sites interact with each other\n # twice, not exactly what we are looking for.\n if (mode == 'periodic' and not l2 == 2):\n # if periodic BC, loop over every site\n js = range(0, l2)\n else:\n # if open BC, skip indices that are at the start of a column\n js = range(1, l2)\n # \"vert_os\" is the offset -- \"distance\" in our indices between\n # adjacent sites along the same rung. It is in general the number\n # of legs of the lattice.\n inter_terms2 = J2 * sum(full_S[i][vert_os: vert_os + l2][j - 1] *\n full_S[i][vert_os: vert_os + l2][j]\n for j in js for vert_os in range(0, N, l2)\n for i in range(3))\n\n inter_terms = inter_terms1 + inter_terms2\n\n # Contributions from the disorder field\n # --- along horizontal direction ---\n if l1 == 1: # field contrib=0 if length of leg=1 aka 1D\n field1 = np.zeros([1])\n else:\n field1 = W1 * np.cos(2 * np.pi * c1 * np.arange(1, l1 + 1) + phi1)\n # --- along vertical direction ---\n if l2 == 1: # field contrib=0 if length of leg=1 aka 1D\n field2 = np.zeros([1])\n else:\n field2 = W2 * np.cos(2 * np.pi * c2 * np.arange(1, l2 + 1) + phi2)\n\n field = field1.repeat(l2) + field2.repeat(l1).reshape(l2, l1).T.flatten()\n field_terms = sum(field * full_S[2])\n\n # Total\n H = inter_terms + field_terms\n return H.real",
"def __init__(self, ni, nhl, nhmax, no, N=0.5, lower=-0.2, upper=0.2):\n self.N = N\n self.ni = ni+1\n self.nhl = int(round(nhl))\n self.nhmax = int(round(nhmax))\n self.no = no\n\n self.layer = []\n # input layer's value\n self.layer.append([1.0]*self.ni)\n nls = [nhmax]*self.nhl +[self.no]\n # hidden and output value\n for num in nls:\n self.layer.append([0.0]*num)\n\n # weight matrixs \n self.wms = []\n colsnum = self.ni\n\n for rowsnum in nls:\n self.wms.append(makeMatrix(colsnum, rowsnum, lower, upper))\n colsnum = rowsnum",
"def run_sin():\n network = FFBPNetwork(1, 1)\n network.add_hidden_layer(3)\n sin_X = [[0], [0.01], [0.02], [0.03], [0.04], [0.05], [0.06], [0.07], [0.08], [0.09], [0.1], [0.11], [0.12],\n [0.13], [0.14], [0.15], [0.16], [0.17], [0.18], [0.19], [0.2], [0.21], [0.22], [0.23], [0.24], [0.25],\n [0.26], [0.27], [0.28], [0.29], [0.3], [0.31], [0.32], [0.33], [0.34], [0.35], [0.36], [0.37], [0.38],\n [0.39], [0.4], [0.41], [0.42], [0.43], [0.44], [0.45], [0.46], [0.47], [0.48], [0.49], [0.5], [0.51],\n [0.52], [0.53], [0.54], [0.55], [0.56], [0.57], [0.58], [0.59], [0.6], [0.61], [0.62], [0.63], [0.64],\n [0.65], [0.66], [0.67], [0.68], [0.69], [0.7], [0.71], [0.72], [0.73], [0.74], [0.75], [0.76], [0.77],\n [0.78], [0.79], [0.8], [0.81], [0.82], [0.83], [0.84], [0.85], [0.86], [0.87], [0.88], [0.89], [0.9],\n [0.91], [0.92], [0.93], [0.94], [0.95], [0.96], [0.97], [0.98], [0.99], [1], [1.01], [1.02], [1.03],\n [1.04], [1.05], [1.06], [1.07], [1.08], [1.09], [1.1], [1.11], [1.12], [1.13], [1.14], [1.15], [1.16],\n [1.17], [1.18], [1.19], [1.2], [1.21], [1.22], [1.23], [1.24], [1.25], [1.26], [1.27], [1.28], [1.29],\n [1.3], [1.31], [1.32], [1.33], [1.34], [1.35], [1.36], [1.37], [1.38], [1.39], [1.4], [1.41], [1.42],\n [1.43], [1.44], [1.45], [1.46], [1.47], [1.48], [1.49], [1.5], [1.51], [1.52], [1.53], [1.54], [1.55],\n [1.56], [1.57]]\n sin_Y = [[0], [0.00999983333416666], [0.0199986666933331], [0.0299955002024957], [0.0399893341866342],\n [0.0499791692706783], [0.0599640064794446], [0.0699428473375328], [0.0799146939691727],\n [0.089878549198011], [0.0998334166468282], [0.109778300837175], [0.119712207288919],\n [0.129634142619695], [0.139543114644236], [0.149438132473599], [0.159318206614246],\n [0.169182349066996], [0.179029573425824], [0.188858894976501], [0.198669330795061], [0.2084598998461],\n [0.218229623080869], [0.227977523535188], [0.237702626427135], [0.247403959254523],\n [0.257080551892155], [0.266731436688831], [0.276355648564114], [0.285952225104836], [0.29552020666134],\n [0.305058636443443], [0.314566560616118], [0.324043028394868], [0.333487092140814],\n [0.342897807455451], [0.35227423327509], [0.361615431964962], [0.370920469412983], [0.380188415123161],\n [0.389418342308651], [0.398609327984423], [0.40776045305957], [0.416870802429211], [0.425939465066],\n [0.43496553411123], [0.44394810696552], [0.452886285379068], [0.461779175541483], [0.470625888171158],\n [0.479425538604203], [0.488177246882907], [0.496880137843737], [0.505533341204847],\n [0.514135991653113], [0.522687228930659], [0.531186197920883], [0.539632048733969],\n [0.548023936791874], [0.556361022912784], [0.564642473395035], [0.572867460100481],\n [0.581035160537305], [0.58914475794227], [0.597195441362392], [0.60518640573604], [0.613116851973434],\n [0.62098598703656], [0.628793024018469], [0.636537182221968], [0.644217687237691], [0.651833771021537],\n [0.659384671971473], [0.666869635003698], [0.674287911628145], [0.681638760023334],\n [0.688921445110551], [0.696135238627357], [0.70327941920041], [0.710353272417608], [0.717356090899523],\n [0.724287174370143], [0.731145829726896], [0.737931371109963], [0.744643119970859],\n [0.751280405140293], [0.757842562895277], [0.764328937025505], [0.770738878898969],\n [0.777071747526824], [0.783326909627483], [0.78950373968995], [0.795601620036366], [0.801619940883777],\n [0.807558100405114], [0.813415504789374], [0.819191568300998], [0.82488571333845], [0.83049737049197],\n [0.836025978600521], [0.841470984807897], [0.846831844618015], [0.852108021949363],\n [0.857298989188603], [0.862404227243338], [0.867423225594017], [0.872355482344986],\n [0.877200504274682], [0.881957806884948], [0.886626914449487], [0.891207360061435],\n [0.895698685680048], [0.900100442176505], [0.904412189378826], [0.908633496115883],\n [0.912763940260521], [0.916803108771767], [0.920750597736136], [0.92460601240802], [0.928368967249167],\n [0.932039085967226], [0.935616001553386], [0.939099356319068], [0.942488801931697],\n [0.945783999449539], [0.948984619355586], [0.952090341590516], [0.955100855584692],\n [0.958015860289225], [0.960835064206073], [0.963558185417193], [0.966184951612734],\n [0.968715100118265], [0.971148377921045], [0.973484541695319], [0.975723357826659],\n [0.977864602435316], [0.979908061398614], [0.98185353037236], [0.983700814811277], [0.98544972998846],\n [0.98710010101385], [0.98865176285172], [0.990104560337178], [0.991458348191686], [0.992712991037588],\n [0.993868363411645], [0.994924349777581], [0.99588084453764], [0.996737752043143], [0.997494986604054],\n [0.998152472497548], [0.998710143975583], [0.999167945271476], [0.999525830605479],\n [0.999783764189357], [0.999941720229966], [0.999999682931835]]\n data = NNData(sin_X, sin_Y, .1)\n network.train(data, 10001, order=NNData.Order.RANDOM)\n network.test(data)\n\n # creating a matplotib graph of the the produced sine grap and actual sine graph\n # plt.plot(test_x, test_y, label='Produced Sine Graph')\n #\n # x = np.arange(0, (np.pi/2), 0.1)\n # y = np.sin(x)\n # plt.plot(x, y, label='Actual Sine Graph')\n #\n # plt.title('Sine Function')\n # plt.xlabel('Input values')\n # plt.ylabel('Output values')\n # plt.legend(loc='upper right')\n # plt.grid(True, which='both')\n #\n # plt.show()",
"def Model3():\n M2 = Model()\n tan = M2.GetGroupByName(\"TAN\")\n sn = M2.GetGroupByName(\"SN\")\n sp = M2.GetGroupByName(\"SP\")\n da = M2.GetGroupByName(\"Da\")\n context = M2.GetGroupByName(\"Context\")\n snr = M2.GetGroupByName(\"SNr/GPi\")\n\n \n \n c2tan = M2.GetProjectionsBetweenGroups(context, tan)[0]\n tan2sn = M2.GetProjectionsBetweenGroups(tan, sn)[0]\n tan2sp = M2.GetProjectionsBetweenGroups(tan, sp)[0]\n da2tan = M2.GetProjectionsBetweenGroups(da, tan)[0]\n\n sn.SetActivationFunction(neu.Tanh_plus)\n sp.SetActivationFunction(neu.Tanh_plus)\n snr.SetActivationFunction(neu.Tanh_plus)\n\n W = np.zeros((6, 3))\n W[0:2,0] = W[2:4,1] = W[4:6,2] = 1.0\n tan2sn.mask = np.copy(W)\n tan2sp.mask = np.copy(W)\n tan2sn.weights = W*-1\n tan2sp.weights = W*-1\n\n sn2tan = sn.ConnectTo(tan)\n sp2tan = sp.ConnectTo(tan)\n sn2tan.weights = W.T/-10\n sp2tan.weights = W.T/-10\n da2tan.weights = np.ones(da2tan.weights.shape)*-0.25\n \n tan.SetActivationFunction(np.vectorize(lambda x: SSigmoid(x, tgain)))\n tan.thresholds=0.5*np.ones(tan.inputs.shape)\n hb = np.average(sn.thresholds)/-tan.size\n HB = np.ones(tan.inputs.shape)*hb\n sn.thresholds = 0.1*np.ones(sn.activations.shape)\n sp.thresholds = 0.1*np.ones(sp.activations.shape)\n #sn.thresholds = -1*tan.GetActivationFunction()(np.ones(sn.inputs.shape)-1)\n #sp.thresholds = -1*tan.GetActivationFunction()(np.ones(sp.inputs.shape)-1)\n #sn.thresholds = -0.1*tan.GetActivationFunction()(np.zeros(sn.inputs.shape))\n #sp.thresholds = -0.1*tan.GetActivationFunction()(np.zeros(sp.inputs.shape))\n #c2tan.weights = np.random.random(c2tan.weights.shape)\n c2tan.weights = np.ones(c2tan.weights.shape)*1.5\n c2tan.mask = np.dot(np.ones(tan.inputs.shape),\n np.array([[1,1,1,0,0,0,0,0,0]]))\n c2tan.learningEnabled = True\n c2tan.learningFunction = TAN_LearningRule\n\n M2.SetParameter(\"TRACE_TAN\", True)\n M2.SetParameter(\"HB\", HB)\n return M2",
"def __init__(self, n):\n self.sfs = np.zeros(n+1,dtype=int)\n self.n_hap = n\n\n\n self._pi = None\n self._td = None\n self._S = None\n self._FWH = None\n self._ns = None\n self._theta_h = None",
"def _setup_training_graph(self):\n # First sweep \n n1 = self.MPS.nodes.read(1)\n n1.set_shape([None, None, None, None])\n C1s, n1 = self._one_sweep(n1, self.C1, self.C2s)\n\n # Second sweep\n C2 = self.C2s.read(self.MPS.input_size-4)\n C2.set_shape([None, None])\n self.C2s, _ = self._one_sweep(n1, C2, C1s)",
"def __init__(self, ni, nh, no):\n\t\t\n\t\tself.ni = ni + 1 # +1 for the bias node (to be replaced in the future)\n\t\tself.nh = nh\n\t\tself.no = no\n\t\t\n\t\t# create the node objects\n\t\tself.ai = np.ndarray(self.ni, object)\n\t\tself.ah = np.ndarray(self.nh, object)\n\t\tself.ao = np.ndarray(self.no, object)\n\t\tfor x in xrange(self.ni): self.ai[x] = node()\n\t\tfor x in xrange(self.nh): self.ah[x] = node()\n\t\tfor x in xrange(self.no): self.ao[x] = node()\n\t\t\n\t\t# create the weight matrices and set them to random values\n\t\tself.wi = np.ndarray( (self.nh, self.ni), object )\n\t\tself.wo = np.ndarray( (self.no, self.nh), object )\n\t\tfor x in xrange(self.nh):\n\t\t\tfor y in xrange(self.ni):\n\t\t\t\tself.wi[x,y] = edge(random.rand(), self.ah[x], self.ai[y])\n\t\t\tfor z in xrange(self.no):\n\t\t\t\tself.wo[z,x] = edge(random.rand(), self.ao[z], self.ah[x])\n\t\t\n\t\t# create hidden weight matrix, a symmetric matrix with all diagonal\n\t\t# entries equal to zero\n\t\tself.wh = np.ndarray( (self.nh, self.nh), object )\n\t\t\n\t\tfor i in xrange(self.nh):\n\t\t\tfor j in xrange(i, self.nh):\n\t\t\t\tif i == j: self.wh[i,j] = edge(0, self.ah[i], self.ah[j])\n\t\t\t\telse: self.wh[i,j] = self.wh[j,i] = edge(random.rand(), self.ah[i], self.ah[j])",
"def make_channel(S):\n\n assert S._hilb_space is not None\n spc = S._hilb_space\n assert S.is_hermitian()\n assert spc.eye() in S\n\n if S.dim() == 1:\n return CP_Map.identity(spc)\n\n # Hermitian basis for all but identity\n B = (S - spc.eye().span()).hermitian_basis()\n # Add identity to make a PSD basis\n B = [ b - spc.eye() * b.eigvalsh()[0] for b in B ]\n # Make everything in the basis sum to a bounded operator\n m = np.sum(B).eigvalsh()[-1]\n B = [ b/m for b in B ]\n # Add a final element to make a complete POVM\n B += [ spc.eye() - np.sum(B) ]\n # Make Kraus operators\n J = [ b.sqrt() for b in B ]\n # Remove a unitary degree of freedom\n # Is this needed or just here to make a nicer answer?\n J = [ j.svd()[0].H * j for j in J ]\n\n # Add basis index to channel output (eliminates interference between different basis\n # elements).\n hk = qudit('k', len(J))\n J = [ hk.ket(k) * j for (k,j) in enumerate(J) ]\n\n Kspc = TensorSubspace.from_span(J)\n assert S.equiv(Kspc.H * Kspc)\n\n chan = CP_Map.from_kraus(J)\n assert chan.is_cptp()\n\n return chan",
"def Graph_powerICA(X, nonlin, Ws, b=0.5, seed=None, Huber_param=1.345,lp_param=1.5,fair_param=1.3998, radical=0):\n \n [d,n] = np.shape(X)\n I = np.eye(d)\n C = (X @ X.T)/n - I\n flg = 0\n #print(C)\n W = np.zeros((d,d), dtype=X.dtype)\n\n # initial guess for unmixing Matrix\n if(radical == 1):\n W0 = RADICAL(X, K=50, sweeps=1)\n else:\n W0 = scipy.stats.ortho_group.rvs(d)\n\n\n Stilde, K = GraphAutoCorrelation(X.T, Ws)\n #print(Stilde)\n if d>n:\n print('Data has invalid shape! Should be d × n array with d < n!')\n if not np.isreal(X).all():\n print('Data is not real!')\n # if np.max(np.abs(C[:]))> 1e-10:\n # print('Data is not whitened!')\n # if np.max(np.abs((np.mean(X,axis=1))))>1e-10:\n # print('Data is not centered!')\n\n for k in range(0,d-1): \n ## (1) Initialization\n w0 = W0[k,:].reshape(1,d).T\n ## (2) Compute the orthogonal operator\n Orth = (I - W.T.dot(W))\n ## (3-6) compute Node:1 and Node:2 in series\n w1, delta1, flg1 = Node1(X, nonlin, w0, Stilde, K, b, Orth, Huber_param, lp_param, fair_param)\n w2, delta2, flg2 = Node2(X, nonlin, w0, Stilde, K, b, Orth, Huber_param, lp_param, fair_param)\n\n #print('Orth',Orth,'W',W)\n flg = flg1*flg2\n ## (7) choose the unmixing vector with larger delta\n if flg == 1:\n if np.linalg.norm(delta1) > np.linalg.norm(delta2):\n W[k,:] = w1.T\n \n else:\n W[k,:] = w2.T\n else:\n W[k:d-1,:] = np.zeros((1,d))\n flg = 0\n break\n ## (8) compute the last demixing vector\n if flg == 1:\n W[d-1,:] = (W0[d-1,:] @ (I - W.T @ W))/np.linalg.norm(W0[d-1,:] @ (I - W.T @ W))\n return W, flg",
"def createNeurons(self, verbose=False):\n\t\t# Depending on the set_reduction_method, we use different algorithms to calculate prototypes\n\t\tif self.set_reduction_method == \"means\":\n\t\t\tprint(\"Calculating centers for Gaussian function by means...\")\n\t\t\tself.prototypes = Cluster.byMeans(self.training_set, number_of_clusters=self.cluster_count,\n\t\t\t\t\t\t\t\t\t\t\t class_header=self.class_header, verbosity=0)\n\t\telif self.set_reduction_method == \"medoids\":\n\t\t\tprint(\"Calculating centers for Gaussian function by medoids...\")\n\t\t\tself.prototypes = Cluster.byMedoids(self.training_set, self.cluster_count, self.class_header, verbosity=0)\n\n\t\telif self.set_reduction_method == \"condensed\":\n\t\t\tprint(\"Calculating centers for Gaussian function using condensed nearest neighbor...\")\n\t\t\tself.prototypes = NearestNeighbor.condensedNearestNeighbor(self.training_set, self.class_header)\n\n\t\telse:\n\t\t\tprint(\"'%s' is an invalid set reduction method, please check it and try again.\" % self.set_reduction_method)\n\t\t\tsys.exit()\n\n\t\tif not self.regression:\n\t\t\tprint(\"Generating output layer of size %d with sigmoid activation functions...\" % self.output_count) if verbose else None\n\t\t\tself.output_layer = FFNetwork(len(self.prototypes),\n\t\t\t\t\t\t\t\t\t\t [self.output_count, 'sigmoid'],\n\t\t\t\t\t\t\t\t\t\t self.training_set,\n\t\t\t\t\t\t\t\t\t\t class_header=self.class_header,\n\t\t\t\t\t\t\t\t\t\t learning_rate=self.learning_rate,\n\t\t\t\t\t\t\t\t\t\t use_momentum=self.use_momentum,\n\t\t\t\t\t\t\t\t\t\t regression=self.regression)\n\t\telse:\n\t\t\tprint(\"Generating output layer with a single linear activation function for regression...\") if verbose else None\n\t\t\tself.output_layer = FFNetwork(len(self.prototypes),\n\t\t\t\t\t\t\t\t\t\t [self.output_count, 'linear'],\n\t\t\t\t\t\t\t\t\t\t self.training_set,\n\t\t\t\t\t\t\t\t\t\t class_header=self.class_header,\n\t\t\t\t\t\t\t\t\t\t learning_rate=self.learning_rate,\n\t\t\t\t\t\t\t\t\t\t use_momentum=self.use_momentum,\n\t\t\t\t\t\t\t\t\t\t regression=self.regression)\n\n\t\tprint(\"Generating widths for basis functions using nearest neighbor proximity...\") if verbose else None\n\t\tsigma_list = self.findSigma()\n\n\t\t# for every point in prototype list, create a neuron and store that point and sigma in said neuron\n\t\tprint(\"Generating layer of Gaussian basis functions of size %d...\" % len(self.prototypes)) if verbose else None\n\t\tfor i in range(len(self.prototypes)):\n\t\t\tself.function_layer.append(RBFNeuron(self.prototypes.iloc[i], sigma_list[i], self.class_header))\n\n\t\tprint(\"\\nTRAINING NEURONS ON TRAINING DATA OF %d ENTRIES\" % len(self.training_set)) if verbose else None\n\t\tself.training_set.apply(lambda row: self.train(row), axis=1)",
"def build_hessian(self,x,y):\n #Precalculate entries of hessian\n x_sum = np.sum(x)\n x_squared_sum = np.sum(x*x)\n y_sum = np.sum(y)\n y_squared_sum = np.sum(y*y)\n xy_sum = np.sum(x*y)\n n = len(x)\n\n hessian = np.array([\n [n,0,x_sum,y_sum,0,0],\n [0,n,0,0,x_sum,y_sum],\n [x_sum,0,x_squared_sum,xy_sum,0,0],\n [y_sum,0,xy_sum,y_squared_sum,0,0],\n [0,x_sum,0,0,x_squared_sum,xy_sum],\n [0,y_sum,0,0,xy_sum,y_squared_sum]\n ])\n return hessian"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Make metallic lead that can be attached to sys (Builder) object with the same conservation_law and particle_hole symmetry as the 2D proximitized topological superconductor being considered. Has the width of par.middle, and is translationally invariant in the ydirection.
|
def make_lead(p):
sys_ = kwant.Builder(kwant.TranslationalSymmetry([0,1]),conservation_law=tinyarray.array(np.kron(s_z,I_x)),particle_hole=sigma_ytau_y) ## ???: symmetries - implementing complex conjugation?
sys_[(lat(x,0) for x in par.middle)] = (2*(p.tx+p.ty) - p.mu)*tau_z
sys_[kwant.builder.HoppingKind((1,0),lat)] = -p.tx*tau_z
sys_[kwant.builder.HoppingKind((0,1),lat)] = -p.ty*tau_z
return sys_
|
[
"def make_1D_Nleft_1D_N_2D_S_2D_SMiddle_No_NRight(p,ppar):\n\tprint(\"%s: in make_1D_Nleft_1D_N_2D_S_2D_SMiddle_No_NRight()\" %str(misc.round_time(datetime.datetime.now(),round_to=60)))\n\n\timport kwant\n\n\tsys = kwant.Builder()\n\n\tsys[(lat(x,y) for x in [0] for y in range(p.Ny))] = onsite_1D_semiconductor \n\tsys[kwant.builder.HoppingKind((0,1),lat)] = hoppingy_1D_semiconductor\n\n\tif ppar.pincher_SC_lead == True:\n\t\tprint(\" - Adding SC layer (2D Hamiltonian and 1D line of sites) at N system - S lead boundary.\")\n\t\t\"\"\"Attaching extra sites with hoppings p.tx_SC_pincher and p.ty_SC_pincher:\"\"\"\n\t\tsys[(lat(x,y) for x in [1] for y in range(p.Ny))] = onsite_2D_superconductor_pincher\n\t\tsys[kwant.builder.HoppingKind((1,0),lat)] = hoppingx_2D_superconductor_pincher\n\t\tsys[kwant.builder.HoppingKind((0,1),lat)] = hoppingy_2D_superconductor_pincher\n\n\t\"\"\"Attaching Left lead to the middle region:\"\"\"\n\tlead = make_lead_onesite_wide_1D(p)\n\tsys.attach_lead(lead)\n\n\t\"\"\" \n\tAdding SC lead last. In that way, the indexing of the smatrix will work as before when wanting to access the other leads. In order to access from the SC lead, acces the 2nd lead index in e.g. the smatrix.\n\t\"\"\"\n\tif ppar.SClead == True:\n\t\tSClead = make_SC_lead_Ny_wide(p)\n\t\tsys.attach_lead(SClead)\n\t\tprint(\" - Attached SC lead\")\n\n\treturn sys",
"def wrinkle(randomness=\"string\", axis=\"string\", envelope=\"string\", uvSpace=\"string\", wrinkleCount=int, branchDepth=int, thickness=\"string\", branchCount=int, style=\"string\", crease=\"string\", wrinkleIntensity=\"string\", dropoffDistance=\"string\", center=\"string\"):\n pass",
"def pole_bending_modeling(model1,leftsupportx,rightsupportx,supporty,leftplatecenterx,rightplatecenterx,plateheighty,lengthx,heighty,stiffness):\r\n \r\n \r\n # add loading plate\r\n model1 = pole_contact_plate(model1,'rightloadplate',(rightplatecenterx,heighty,0),lengthx,1000,plateheighty,stiffness)\r\n model1 = pole_contact_plate(model1,'leftloadplate',(leftplatecenterx,heighty,0),lengthx,1000,plateheighty,stiffness)\r\n \r\n \r\n # add support\r\n model1 = add_support(model1,'leftsupport',leftsupportx,supporty,0,lengthx * 2,10000,default=[1,1,1,0,0,0]) # due to fact that only one side of plate will be selected\r\n model1 = add_support(model1,'rightsupport',rightsupportx,supporty,0,lengthx * 2,10000,default=[0,1,1,0,0,0]) # big width number to seelct all nodes\r\n \r\n \r\n model1 = add_material(model1)\r\n model1.table('loadtable',1,['time'],[[0,0],[1,1]])\r\n model1.load('leftrightload',{'xyz':[0,1,0,0,0,0],'DOF':6,'scalar':-1,'setnamelist':['leftloadplate_plate','rightloadplate_plate'],'tabletag':'loadtable'})\r\n \r\n\r\n model1.section('sec_1','shell_section',{'thickness':0.1875})\r\n\r\n \r\n model1.property('prop1','quad4',{'type':75,'thinkness':0.01})\r\n model1.property('prop_dent','quad4',{'type':75})\r\n \r\n \r\n model1.elemset_sub_setname('surface_elements','dentelems')\r\n \r\n model1.link_prop_conn('prop1',setnamelist=['surface_elements-dentelems'])\r\n model1.link_prop_conn('prop_dent',setnamelist=['dentelems','extension_elements_surface_leftend','extension_elements_surface_rightend'])\r\n \r\n model1.link_sec_prop('sec_1','prop1')\r\n model1.link_sec_prop('sec_1','prop_dent')\r\n \r\n # associate the material\r\n model1.link_mat_prop('pole_alum','prop1')\r\n model1.link_mat_prop('pole_alum_dent','prop_dent')\r\n \r\n model1.loadcase('loadcase1','static_arclength',{'boundarylist':['leftsupport','rightsupport','leftrightload'],'para':{'nstep':50}})\r\n \r\n #model1.job('job1','static_job',{'loadcaselist':['loadcase0','loadcase1'],'submit':True,'reqresultslist':['stress','total_strain','plastic_strain']})\r\n model1.job('job1','static_job',{'loadcaselist':['loadcase0','loadcase1'],'submit':False,'reqresultslist':['stress','total_strain','plastic_strain']})\r\n \r\n return model1",
"def __init__(self, central_blackhole_mass, initial_outer_semi_major_axis, mass_one=30. | units.MSun, mass_two=30. | units.MSun,\n initial_outer_eccentricity=0.6, inner_eccentricity=0.6, inclination=0.0,\n orbital_fraction_timestep=0.5):\n self.central_blackhole = Particle(1)\n self.central_blackhole.mass = central_blackhole_mass\n\n self.blackholes = Particles(2)\n self.blackholes[0].mass = mass_one\n self.blackholes[1].mass = mass_two\n self.total_mass = self.blackholes.mass.sum()\n\n self.initial_outer_semi_major_axis = initial_outer_semi_major_axis\n self.initial_outer_eccentricity = initial_outer_eccentricity\n\n # Calculating the hill radius to act as a maximum boundary for the initial inner semi major axis and therefore the inner orbital period\n self.hill_radius = self.get_hill_radius(self.initial_outer_semi_major_axis, self.initial_outer_eccentricity,\n self.total_mass, self.central_blackhole.mass)\n self.binary_max_orbital_period = self.get_orbital_period(0.5 * self.hill_radius, self.total_mass)\n self.binary_min_orbital_period = self.get_orbital_period(\n 1000000 * self.get_schwarzschild_radius(self.blackholes[0].mass), self.total_mass)\n # Restricting the initial inner orbital period\n self.orbital_period = numpy.random.uniform(self.binary_min_orbital_period.value_in(units.yr),\n self.binary_max_orbital_period.value_in(units.yr), size=1) | units.yr\n\n self.inner_semi_major_axis = self.get_semi_major_axis(self.total_mass, self.orbital_period)\n self.inner_eccentricity = inner_eccentricity\n self.inclination = inclination\n\n self.timestep = self.orbital_period * orbital_fraction_timestep\n\n # Create the binary blackholes and set them in orbit around each other\n binary_position, binary_velocity = get_position(self.blackholes[0].mass, self.blackholes[1].mass,\n self.inner_eccentricity, self.inner_semi_major_axis,\n 180, self.inclination, 180, 0, self.timestep)\n self.blackholes[1].position = binary_position\n self.blackholes[1].velocity = binary_velocity\n\n self.blackholes_distance = (self.blackholes[0].position - self.blackholes[1].position).length()\n self.minimum_distance = 100 * self.get_schwarzschild_radius(self.blackholes[0].mass)\n # self.merged_blackhole = Particle()\n\n self.blackholes.move_to_center()\n # Set the (inner binary) center of mass and center of mass velocity in orbit around the supermassive black hole\n self.initial_outer_semi_major_axis, self.initial_outer_eccentricity = self.set_in_orbit_around_central_blackhole(\n central_blackhole_mass,\n self.initial_outer_semi_major_axis,\n self.initial_outer_eccentricity,\n time_to_advance=(self.orbital_period/2.))",
"def add_L(self, space):\r\n rotation_center_body = pm.Body(body_type=pm.Body.STATIC)\r\n rotation_center_body.position = (300, 300)\r\n\r\n rotation_limit_body = pm.Body(body_type=pm.Body.STATIC)\r\n rotation_limit_body.position = (300, 300)\r\n body = pm.Body(650, 650)\r\n body.position = (300, 600)\r\n l1 = pm.Segment(rotation_limit_body, (25, -20), (25, 200.0), 1.0)\r\n l2 = pm.Segment(rotation_limit_body, (-25, -20), (-25, 200.0), 1.0)\r\n\r\n l3 = pm.Segment(rotation_limit_body, (25, -20), (85.0, -90.0), 1.3)\r\n l4 = pm.Segment(rotation_limit_body, (-25, -20), (-85.0, -90.0), 1.3)\r\n l8 = pm.Segment(body, (-250, -200), (200.0, -200.0), 5.0)\r\n\r\n rotation_center_joint = pm.PinJoint(body, rotation_center_body, (0, -200), (0, -200))\r\n joint_limit = .03\r\n rotation_limit_joint = pm.SlideJoint(body, rotation_limit_body, (-20, -200), (0, -200), 0, joint_limit)\r\n\r\n space.add(l1, l2, l3, l4, l8, rotation_limit_body, rotation_center_body, body, rotation_center_joint,\r\n rotation_limit_joint)\r\n return l8",
"def lumped_cpw(freq,\n line_width,\n line_gap,\n substrate_thickness,\n film_thickness,\n dielectric_constant=11.45,\n loss_tangent=10**-5,\n london_penetration_depth=30 * 10**-9):\n s = line_width\n w = line_gap\n h = substrate_thickness\n t = film_thickness\n eRD = dielectric_constant\n tanD = loss_tangent\n lambdaLT = london_penetration_depth\n wfreq = freq * 2 * np.pi\n\n Kk0, Kk01, Kk1, Kk11 = elliptic_int_constants(s, w, h)\n\n C = 2 * e0 * (eRD - 1) * (Kk1 / Kk11) + 4 * e0 * (Kk0 / Kk01)\n\n #filling factor\n q = 0.5 * (Kk1 * Kk01) / (Kk11 * Kk0)\n\n #Admittance\n G = wfreq * C * q * tanD\n\n #Effective Dielectric Constant\n etfSqrt = effective_dielectric_constant(freq, s, w, h, t, q, Kk0, Kk01, eRD)\n\n #External Inducatance\n Z0 = (30 * np.pi / etfSqrt) * Kk01 / Kk0\n Lext = Z0**2 * C\n Cstar = 2 * e0 * (etfSqrt**2 - 1) * (Kk1 / Kk11) + 4 * e0 * (Kk0 / Kk01)\n\n #Kinetic Inductance\n A1 = (-t / np.pi) + (1 / 2) * np.sqrt((2 * t / np.pi)**2 + s**2)\n B1 = s**2 / (4 * A1)\n C1 = B1 - (t / np.pi) + np.sqrt((t / np.pi)**2 + w**2)\n D1 = 2 * t / np.pi + C1\n\n LkinStep = (u0 * lambdaLT * C1 / (4 * A1 * D1 * Kk0))\n\n Lkin1 = LkinStep * 1.7 / (np.sinh(t / (2 * lambdaLT)))\n Lkin2 = LkinStep * 0.4 / (np.sqrt(\n (((B1 / A1)**2) - 1) * (1 - (B1 / D1)**2)))\n\n Lk = Lkin1 + Lkin2\n\n return Lk, Lext, C, G, Z0, etfSqrt**2, Cstar",
"def make_cross_wall(self):\n if self.orient == \"e\":\n self.cross_wall = self.coord1.wall_south\n if self.orient == \"s\":\n self.cross_wall = self.coord1.wall_east",
"def make_water_splash(inst: Entity) -> None:\n pos1 = Vec(conf_pos1)\n splash_pos = Vec(conf_pos1)\n\n if calc_type == 'track_platform':\n lin_off = inst.fixup.float('$travel_distance')\n travel_ang = Angle.from_str(inst.fixup['$travel_direction'])\n start_pos = inst.fixup.float('$starting_position')\n if start_pos:\n start_pos = round(start_pos * lin_off)\n pos1 += Vec(x=-start_pos) @ travel_ang\n\n pos2 = Vec(x=lin_off) @ travel_ang + pos1\n elif calc_type.startswith('piston'):\n # Use piston-platform offsetting.\n # The number is the highest offset to move to.\n max_pist = srctools.conv_int(calc_type.split('_', 2)[1], 4)\n bottom_pos = inst.fixup.int('$bottom_level')\n top_pos = min(inst.fixup.int('$top_level'), max_pist)\n\n pos2 = pos1.copy()\n pos1 += Vec(z=128 * bottom_pos)\n pos2 += Vec(z=128 * top_pos)\n LOGGER.info('Bottom: {}, top: {}', bottom_pos, top_pos)\n else:\n # Directly from the given value.\n pos2 = Vec.from_str(conditions.resolve_value(inst, conf_pos2))\n\n origin = Vec.from_str(inst['origin'])\n orient = Matrix.from_angstr(inst['angles'])\n splash_pos.localise(origin, orient)\n pos1.localise(origin, orient)\n pos2.localise(origin, orient)\n\n # Since it's a straight line and you can't go through walls,\n # if pos1 and pos2 aren't in goo we aren't ever in goo.\n\n check_pos = [pos1, pos2]\n\n if pos1.z < origin.z:\n # If embedding in the floor, the positions can both be below the\n # actual surface. In that case check the origin too.\n check_pos.append(Vec(pos1.x, pos1.y, origin.z))\n\n if pos1.z == pos2.z:\n # Flat - this won't do anything...\n return\n\n for pos in check_pos:\n grid_pos = pos // 128.0 * 128.0\n grid_pos += (64.0, 64.0, 64.0)\n\n if BLOCK_POS.lookup_world(pos).is_goo:\n break\n else:\n return # Not in goo at all\n\n water_pos = grid_pos + (0.0, 0.0, 32.0)\n\n # Check if both positions are above or below the water..\n # that means it won't ever trigger.\n if max(pos1.z, pos2.z) < water_pos.z - 8:\n return\n if min(pos1.z, pos2.z) > water_pos.z + 8:\n return\n\n # Pass along the water_pos encoded into the targetname.\n # Restrict the number of characters to allow direct slicing\n # in the script.\n enc_data = f'_{water_pos.z + 12.0:09.3f}{\"f\" if fast_check else \"s\"}'\n\n vmf.create_ent(\n classname='env_splash',\n targetname=conditions.local_name(inst, name) + enc_data,\n parentname=conditions.local_name(inst, parent),\n origin=splash_pos + (0.0, 0.0, 16.0),\n scale=scale,\n vscripts='BEE2/water_splash.nut',\n thinkfunction='Think',\n spawnflags='1', # Trace downward to water surface.\n )",
"def jointLattice(before=bool, exclusive=\"string\", after=bool, widthLeft=float, joint=\"string\", includeHiddenSelections=bool, creasing=float, frontOfChain=bool, prune=bool, widthRight=float, geometryIndices=bool, split=bool, lowerTransform=\"string\", geometry=\"string\", upperBindSkin=\"string\", name=\"string\", rounding=float, parallel=bool, ignoreSelected=bool, afterReference=bool, remove=bool, upperTransform=\"string\", lengthOut=float, deformerTools=bool, lengthIn=float, lowerBindSkin=\"string\"):\n pass",
"def onsite_2D_superconductor_lead(site,p):\n\n\n\treturn (2*(p.tx_SC_lead+p.ty_SC_lead) - p.mu_SC_lead)*tau_z + p.Ez_2D_S_lead*sigma_y/2. + p.Delta_SC_lead*tau_x",
"def create_logic_bricks():\n sensors = bpy.context.scene.objects['Cylinder'].game.sensors\n controllers = bpy.context.scene.objects['Cylinder'].game.controllers\n actuators = bpy.context.scene.objects['Cylinder'].game.actuators\n bpy.ops.logic.sensor_add(type='ALWAYS', object=\"Cylinder\",name=\"sensor1\")\n sensors['sensor1'].use_pulse_true_level = True\n bpy.ops.logic.controller_add(type='PYTHON',object=\"Cylinder\",name=\"controller1\")\n controllers['controller1'].text = bpy.data.texts['pistonMover.py']\n sensors['sensor1'].link(controllers['controller1'])\n bpy.ops.logic.actuator_add(type=\"GAME\",object=\"Cylinder\",name=\"actuator1\")\n actuators['actuator1'].mode = \"QUIT\"\n controllers['controller1'].link(actuator = actuators['actuator1'])\n bpy.context.scene.game_settings.logic_step_max = 50\n bpy.context.scene.game_settings.physics_step_max = 50\n bpy.context.scene.game_settings.physics_step_sub = 5",
"def build_geometry(self, sym=1, alpha=0, delta=0):\n\n if self.is_stator:\n label = \"Lamination_Stator\" # Label lamination\n else:\n label = \"Lamination_Rotor\"\n if self.is_internal:\n lb = \"Ext\" # label for the bore\n ly = \"Int\" # label for the yoke\n else:\n lb = \"Int\"\n ly = \"Ext\"\n label_bore = label + \"_Bore_Radius_\" + lb\n label_yoke = label + \"_Yoke_Radius_\" + ly\n\n Ryoke = self.get_Ryoke()\n H_yoke = self.comp_height_yoke()\n\n if self.slot is not None and self.slot.Zs != 0:\n # getting Number of Slot\n Zs = self.slot.Zs\n\n # Check for symmetry\n assert (Zs % sym) == 0, (\n \"ERROR, Wrong symmetry for \"\n + label\n + \" \"\n + str(Zs)\n + \" slots and sym=\"\n + str(sym)\n )\n\n bore_desc = self.get_bore_desc(sym=sym)\n bore_list = list()\n for bore in bore_desc:\n if type(bore[\"obj\"]) is Arc1:\n bore_list.append(bore[\"obj\"])\n elif \"lines\" in bore: # Duplicated slot\n for line in bore[\"lines\"]:\n bore_list.append(type(line)(init_dict=line.as_dict()))\n bore_list[-1].rotate((bore[\"begin_angle\"] + bore[\"end_angle\"]) / 2)\n else: # Notches\n lines = bore[\"obj\"].build_geometry()\n for line in lines:\n line.rotate((bore[\"begin_angle\"] + bore[\"end_angle\"]) / 2)\n bore_list.extend(lines)\n # Set line label\n for line in bore_list:\n line.label = label_bore\n else: # No slot\n return Lamination.build_geometry(self, sym=sym, alpha=alpha, delta=delta)\n\n # Create the lamination surface(s)\n surf_list = list()\n if sym == 1: # Complete lamination\n if self.is_internal:\n point_ref = Ryoke + (H_yoke / 2)\n else:\n point_ref = Ryoke - (H_yoke / 2)\n # Create Slot surface\n surf_slot = SurfLine(line_list=bore_list, label=label_bore, point_ref=point_ref)\n # Create yoke circle surface\n surf_yoke = Circle(\n radius=Ryoke, label=label_yoke, line_label=label_yoke, center=0\n )\n if self.Rint == 0 and len(bore_list) > 0:\n surf_list = [surf_slot]\n elif self.Rint == 0 and len(bore_list) == 0:\n surf_list = list()\n elif self.is_internal:\n surf_list.append(\n SurfRing(\n out_surf=surf_slot,\n in_surf=surf_yoke,\n label=label,\n point_ref=point_ref,\n )\n )\n else:\n surf_list.append(\n SurfRing(\n out_surf=surf_yoke,\n in_surf=surf_slot,\n label=label,\n point_ref=point_ref,\n )\n )\n else: # Only one surface\n # Add the Yoke part\n Zy1 = Ryoke\n Zy2 = Ryoke * exp(1j * 2 * pi / sym)\n bore_list.append(\n Segment(bore_list[-1].get_end(), Zy2, label=label + \"_Yoke_Side_Left\")\n )\n if Ryoke > 0: # For internal lamination\n bore_list.append(\n Arc1(\n begin=Zy2,\n end=Zy1,\n radius=-Ryoke,\n is_trigo_direction=False,\n label=label_yoke,\n )\n )\n bore_list.append(\n Segment(Zy1, bore_list[0].get_begin(), label=label + \"_Yoke_Side_Right\")\n )\n # Create a Surface for the slot\n if self.is_internal:\n point_ref = (Ryoke + H_yoke / 2) * exp(1j * pi / sym)\n else:\n point_ref = (Ryoke - H_yoke / 2) * exp(1j * pi / sym)\n surf_slot = SurfLine(line_list=bore_list, label=label_bore, point_ref=point_ref)\n surf_list.append(surf_slot)\n\n # Apply the transformations\n for surf in surf_list:\n surf.rotate(alpha)\n surf.translate(delta)\n\n # Adding the ventilation surfaces\n for vent in self.axial_vent:\n surf_list += vent.build_geometry(\n sym=sym, alpha=alpha, delta=delta, is_stator=self.is_stator\n )\n return surf_list",
"def add_pol_leakage_manual(self):\n\n if self.parang_corrected == False:\n # Compute P-Jones matrices\n self.pjones_mat = np.zeros((self.Nant,self.time_unique.shape[0],2,2),dtype=complex)\n self.djones_mat = np.zeros((self.Nant,self.time_unique.shape[0],2,2),dtype=complex)\n\n for ant in range(self.Nant):\n self.djones_mat[ant,:,0,0] = 1\n self.djones_mat[ant,:,0,1] = self.leakR_real[ant]+1j*self.leakR_imag[ant]\n self.djones_mat[ant,:,1,0] = self.leakL_real[ant]+1j*self.leakL_imag[ant]\n self.djones_mat[ant,:,1,1] = 1\n\n if self.mount[ant] == 'ALT-AZ':\n self.pjones_mat[ant,:,0,0] = np.exp(-1j*self.parallactic_angle[ant,:]) # INI: opposite of feed angle i.e. parang +/- elev\n self.pjones_mat[ant,:,0,1] = 0\n self.pjones_mat[ant,:,1,0] = 0\n self.pjones_mat[ant,:,1,1] = np.exp(1j*self.parallactic_angle[ant,:])\n elif self.mount[ant] == 'ALT-AZ+NASMYTH-L':\n self.pjones_mat[ant,:,0,0] = np.exp(-1j*(self.parallactic_angle[ant,:]-self.elevation_copy_dterms[ant,:]))\n self.pjones_mat[ant,:,0,1] = 0\n self.pjones_mat[ant,:,1,0] = 0\n self.pjones_mat[ant,:,1,1] = np.exp(1j*(self.parallactic_angle[ant,:]-self.elevation_copy_dterms[ant,:]))\n elif self.mount[ant] == 'ALT-AZ+NASMYTH-R':\n self.pjones_mat[ant,:,0,0] = np.exp(-1j*(self.parallactic_angle[ant,:]+self.elevation_copy_dterms[ant,:]))\n self.pjones_mat[ant,:,0,1] = 0\n self.pjones_mat[ant,:,1,0] = 0\n self.pjones_mat[ant,:,1,1] = np.exp(1j*(self.parallactic_angle[ant,:]+self.elevation_copy_dterms[ant,:]))\n \n data_reshaped = self.data.reshape((self.data.shape[0],self.data.shape[1],2,2))\n\n for a0 in range(self.Nant):\n for a1 in range(a0+1,self.Nant):\n bl_ind = self.baseline_dict[(a0,a1)]\n time_ind = 0\n for ind in bl_ind:\n data_reshaped[ind] = np.matmul(self.djones_mat[a0,time_ind], np.matmul(self.pjones_mat[a0,time_ind], np.matmul(data_reshaped[ind], \\\n np.matmul(np.conjugate(self.pjones_mat[a1,time_ind].T), np.conjugate(self.djones_mat[a1,time_ind].T)))))\n time_ind = time_ind + 1\n\n self.data = data_reshaped.reshape(self.data.shape) \n self.save_data()\n\n elif self.parang_corrected == True:\n # Add P-Jones corruptions (parallactic angle rotation) using meqtrees\n # add_pjones(self.output_column)\n\n # Construct station-based leakage matrices (D-Jones)\n #self.pol_leak_mat = np.zeros((self.Nant,2,2),dtype=complex) # To serve as both D_N and D_C\n self.pol_leak_mat = np.zeros((self.Nant,self.time_unique.shape[0],2,2),dtype=complex)\n #self.rotation_mat = np.zeros((self.Nant,self.time_unique.shape[0],2,2),dtype=complex) # To serve as Rot(theta=parang+/-elev)\n \n # Set up D = D_N = D_C, Rot(theta = parallactic_angle +/- elevation). Notation following Dodson 2005, 2007.\n for ant in range(self.Nant):\n if self.mount[ant] == 'ALT-AZ':\n self.pol_leak_mat[ant,:,0,0] = 1\n self.pol_leak_mat[ant,:,0,1] = (self.leakR_real[ant]+1j*self.leakR_imag[ant])*np.exp(1j*2*(self.parallactic_angle[ant,:]))\n self.pol_leak_mat[ant,:,1,0] = (self.leakL_real[ant]+1j*self.leakL_imag[ant])*np.exp(-1j*2*(self.parallactic_angle[ant,:]))\n self.pol_leak_mat[ant,:,1,1] = 1\n\n elif self.mount[ant] == 'ALT-AZ+NASMYTH-LEFT':\n self.pol_leak_mat[ant,:,0,0] = 1\n self.pol_leak_mat[ant,:,0,1] = (self.leakR_real[ant]+1j*self.leakR_imag[ant])*np.exp(1j*2*(self.parallactic_angle[ant,:]-self.elevation_copy_dterms[ant,:]))\n self.pol_leak_mat[ant,:,1,0] = (self.leakL_real[ant]+1j*self.leakL_imag[ant])*np.exp(-1j*2*(self.parallactic_angle[ant,:]-self.elevation_copy_dterms[ant,:]))\n self.pol_leak_mat[ant,:,1,1] = 1\n \n elif self.mount[ant] == 'ALT-AZ+NASMYTH-RIGHT':\n self.pol_leak_mat[ant,:,0,0] = 1\n self.pol_leak_mat[ant,:,0,1] = (self.leakR_real[ant]+1j*self.leakR_imag[ant])*np.exp(1j*2*(self.parallactic_angle[ant,:]+self.elevation_copy_dterms[ant,:]))\n self.pol_leak_mat[ant,:,1,0] = (self.leakL_real[ant]+1j*self.leakL_imag[ant])*np.exp(-1j*2*(self.parallactic_angle[ant,:]+self.elevation_copy_dterms[ant,:]))\n self.pol_leak_mat[ant,:,1,1] = 1\n\n # Save to external file as numpy array\n # np.save(II('$OUTDIR')+'/pol_leakage', self.pol_leak_mat)\n\n data_reshaped = self.data.reshape((self.data.shape[0],self.data.shape[1],2,2))\n\n for a0 in range(self.Nant):\n for a1 in range(a0+1,self.Nant):\n bl_ind = self.baseline_dict[(a0,a1)]\n time_ind = 0\n for ind in bl_ind:\n data_reshaped[ind] = np.matmul(self.pol_leak_mat[a0,time_ind], np.matmul(data_reshaped[ind], \\\n np.conjugate(self.pol_leak_mat[a1,time_ind].T)))\n time_ind = time_ind + 1\n \n self.data = data_reshaped.reshape(self.data.shape) \n self.save_data()",
"def Build_pwld_2d(self) :\n\n self.mass_matrix = np.zeros((4,4))\n self.x_grad_matrix = np.zeros((4,4))\n self.y_grad_matrix = np.zeros((4,4))\n self.stiffness_matrix = np.zeros((4,4))\n\n# Build the matrices by looping over the ``sides''\n mass_side = np.array([[2.,1.,1.],[1.,2.,1.],[1.,1.,2.]])\n for side in xrange(0,4) :\n a = side\n b = (side+1)%4\n x0 = self.x[a]\n x1 = self.x[b]\n x2 = self.x_c\n y0 = self.y[a]\n y1 = self.y[b]\n y2 = self.y_c\n\n x2_x1 = x2-x1\n x1_x2 = x1-x2\n x0_x2 = x0-x2\n x2_x0 = x2-x0\n x1_x0 = x1-x0\n x0_x1 = x0-x1\n y1_y2 = y1-y2\n y2_y1 = y2-y1\n y2_y0 = y2-y0\n y0_y2 = y0-y2\n y0_y1 = y0-y1\n y1_y0 = y1-y0\n\n a_00 = 0.5*(y2_y1**2+x2_x1**2)\n a_01 = -0.5*(y2_y0*y2_y1+x2_x0*x2_x1)\n a_02 = -0.5*(y0_y1*y2_y1+x0_x1*x2_x1)\n a_11 = 0.5*(y2_y0**2+x2_x0**2)\n a_12 = 0.5*(y2_y0*y0_y1+x0_x2*x1_x0)\n a_22 = 0.5*(y0_y1**2+x1_x0**2)\n\n jacobian = np.abs(x1_x0*y2_y0-y1_y0*x2_x0)\n area = 0.5*jacobian\n\n mass_matrix = area/12*mass_side\n x_grad_matrix = 1./6.*np.array([[y1_y2,y1_y2,y1_y2],[y2_y0,y2_y0,y2_y0],\n [y0_y1,y0_y1,y0_y1]])\n y_grad_matrix = 1./6.*np.array([[x2_x1,x2_x1,x2_x1],[x0_x2,x0_x2,x0_x2],\n [x1_x0,x1_x0,x1_x0]])\n stiffness_matrix = 1./jacobian*np.array([[a_00,a_01,a_02],\n [a_01,a_11,a_12],[a_02,a_12,a_22]])\n\n self.mass_matrix[a,a] += mass_matrix[0,0]\n self.mass_matrix[a,b] += mass_matrix[0,1]\n self.mass_matrix[b,a] += mass_matrix[1,0]\n self.mass_matrix[b,b] += mass_matrix[1,1]\n\n self.x_grad_matrix[a,a] += x_grad_matrix[0,0]\n self.x_grad_matrix[a,b] += x_grad_matrix[0,1]\n self.x_grad_matrix[b,a] += x_grad_matrix[1,0]\n self.x_grad_matrix[b,b] += x_grad_matrix[1,1]\n\n self.y_grad_matrix[a,a] += y_grad_matrix[0,0]\n self.y_grad_matrix[a,b] += y_grad_matrix[0,1]\n self.y_grad_matrix[b,a] += y_grad_matrix[1,0]\n self.y_grad_matrix[b,b] += y_grad_matrix[1,1]\n\n self.stiffness_matrix[a,a] += stiffness_matrix[0,0]\n self.stiffness_matrix[a,b] += stiffness_matrix[0,1]\n self.stiffness_matrix[b,a] += stiffness_matrix[1,0]\n self.stiffness_matrix[b,b] += stiffness_matrix[1,1]\n \n for i in xrange(0,4) :\n self.mass_matrix[a,i] += 0.25*mass_matrix[0,2]\n self.mass_matrix[b,i] += 0.25*mass_matrix[1,2]\n self.mass_matrix[i,a] += 0.25*mass_matrix[2,0]\n self.mass_matrix[i,b] += 0.25*mass_matrix[2,1]\n\n self.x_grad_matrix[a,i] += 0.25*x_grad_matrix[0,2]\n self.x_grad_matrix[b,i] += 0.25*x_grad_matrix[1,2]\n self.x_grad_matrix[i,a] += 0.25*x_grad_matrix[2,0]\n self.x_grad_matrix[i,b] += 0.25*x_grad_matrix[2,1]\n\n self.y_grad_matrix[a,i] += 0.25*y_grad_matrix[0,2]\n self.y_grad_matrix[b,i] += 0.25*y_grad_matrix[1,2]\n self.y_grad_matrix[i,a] += 0.25*y_grad_matrix[2,0]\n self.y_grad_matrix[i,b] += 0.25*y_grad_matrix[2,1]\n\n self.stiffness_matrix[a,i] += 0.25*self.stiffness_matrix[0,2]\n self.stiffness_matrix[b,i] += 0.25*self.stiffness_matrix[1,2]\n self.stiffness_matrix[i,a] += 0.25*self.stiffness_matrix[2,0]\n self.stiffness_matrix[i,b] += 0.25*self.stiffness_matrix[2,1]\n\n for j in xrange(0,4) :\n self.mass_matrix[i,j] += 0.25**2*mass_matrix[2,2]\n self.x_grad_matrix[i,j] += 0.25**2*x_grad_matrix[2,2]\n self.y_grad_matrix[i,j] += 0.25**2*y_grad_matrix[2,2]\n self.stiffness_matrix[i,j] += 0.25**2*self.stiffness_matrix[2,2]",
"def create_wall(\n grid: np.ndarray,\n thickness: float,\n height: float,\n origin: Sequence[float] = (0, 0, 0), # (x, y, theta)\n) -> bpy.types.Object:\n # create the wall object and add it to the scene\n h, w = grid.shape\n verts, faces = [], []\n for y in range(h + 1):\n for x in range(w + 1):\n verts.append((x, y, 0))\n if y < h and x < w and grid[y][x]:\n bottom_left = x + (w + 1) * y\n top_left = bottom_left + w + 1\n top_right, bottom_right = top_left + 1, bottom_left + 1\n faces.append([bottom_left, bottom_right, top_right, top_left])\n\n mesh = bpy.data.meshes.new(name=\"Wall\")\n mesh.from_pydata(verts, [], faces)\n obj = bpy.data.objects.new(mesh.name, mesh)\n collection = bpy.data.collections.get('Collection')\n collection.objects.link(obj)\n\n # activate the object for following operations\n obj.select_set(True)\n bpy.context.view_layer.objects.active = obj\n\n # remove redundant geometry\n bpy.ops.object.mode_set(mode='EDIT')\n bpy.ops.mesh.delete_loose()\n bpy.ops.mesh.select_all(action='SELECT')\n bpy.ops.mesh.dissolve_limited()\n bpy.ops.object.mode_set(mode='OBJECT')\n\n # model transformation (according to origin, thickness, and height)\n bpy.ops.transform.resize(value=(thickness, thickness, 1))\n origin_x, origin_y, origin_theta = origin\n if origin_x or origin_y:\n bpy.ops.transform.translate(value=(origin_x, origin_y, 0))\n if origin_theta:\n bpy.context.scene.tool_settings.transform_pivot_point = 'CURSOR'\n bpy.ops.transform.rotate(value=origin_theta, orient_axis='Z')\n\n bpy.ops.object.mode_set(mode='EDIT')\n bpy.ops.mesh.extrude_region_move(TRANSFORM_OT_translate={\"value\": (0, 0, height)})\n bpy.ops.object.mode_set(mode='OBJECT')\n\n return obj",
"def construct_single_ply_piece(self, fraction=1.0):\n th_nom = np.radians(self.fiber_angle)\n # Step 1: Define origin line L0\n origin_point = Point2D(self.starting_position, 0.0)\n L0 = Line2D.from_point_angle(origin_point, th_nom)\n # Step 2: Define line L2, perpendicular to L0, tangent to circle s4\n tangent_point = Point2D.from_polar(self.cg.s4, th_nom)\n L2 = Line2D.from_point_angle(tangent_point, th_nom + np.pi/2)\n P0 = L0.intersection_line(L2)\n\n # Step 3: Position P2 and P3 based on max_width and eccentricity\n P2_dist = self.max_width * self.eccentricity\n P3_dist = self.max_width * (1 - self.eccentricity)\n P2 = P0 + Point2D.from_polar(P2_dist, L2.angle())\n P3 = P0 + Point2D.from_polar(P3_dist, L2.angle() + np.pi)\n\n # Step 4: Calculate the spanned angle (both deltas should be >= 0)\n T2 = L0.intersection_circle_near(P2.norm(), P0)\n T3 = L0.intersection_circle_near(P3.norm(), P0)\n delta_phi_1 = fraction*(P2.angle() - T2.angle())\n delta_phi_2 = fraction*(T3.angle() - P3.angle())\n\n # Step 5: Calculate the side lines L1 and L3\n L1 = L0.rotate(delta_phi_1)\n L3 = L0.rotate(-delta_phi_2)\n near_pt = Point2D(self.cg.s1, 0)\n P1a = L1.intersection_circle_near(self.cg.s1, near_pt)\n P4a = L3.intersection_circle_near(self.cg.s1, near_pt)\n # Redefine P2 and P3 if needed (for rest pieces)\n if fraction != 1.0:\n P2 = L2.intersection_line(L1)\n P3 = L2.intersection_line(L3)\n\n # Step 6: Construct L4, parallel to L2, through either P1a or P4a,\n # whichever is furthest from L2\n if L2.distance_point(P1a) > L2.distance_point(P4a):\n L4_through_point = P1a\n else:\n L4_through_point = P4a\n L4 = Line2D.from_point_angle(L4_through_point, L2.angle())\n # now redefine P1 and P4 as the intersection points:\n P1b = L4.intersection_line(L1)\n P4b = L4.intersection_line(L3)\n\n ip_L1_L3 = L1.intersection_line(L3)\n if L2.distance_point(ip_L1_L3) < L2.distance_point(P4b):\n # Line segments L1 and L3 intersect within the polygon, so we have\n # a 'hourglass' shape. Move P1 and P4 to the intersection point,\n # effectively forming a triangle. We could just drop P4, if not\n # for some other code expeccting 4-point polygons.\n P1, P4 = ip_L1_L3, ip_L1_L3\n else:\n P1, P4 = P1b, P4b\n\n # Step 7: Return the final ply piece\n return PlyPiece(Polygon2D((P1, P2, P3, P4)), 0.0, -delta_phi_2, delta_phi_1)",
"def construct(self, geom):\n\n main_shape = geom.shapes.Tubs(self.name, rmin = self.halfDimension[\"rmin\"],\n rmax = self.halfDimension[\"rmax\"], dz = self.halfDimension[\"dz\"])\n main_lv = geom.structure.Volume(self.name+\"_lv\", material=self.Material, shape=main_shape)\n if isinstance(self.Sensitive,str):\n main_lv.params.append((\"SensDet\",self.Sensitive))\n self.add_volume(main_lv)\n\n straw_shape = geom.shapes.Tubs(self.name+\"_straw\", rmin = self.halfSTDimension[\"rmin\"],\n rmax = self.halfSTDimension[\"rmax\"], dz = self.halfSTDimension[\"dz\"])\n straw_lv = geom.structure.Volume(self.name+\"_straw_lv\", material=self.STMaterial, shape=straw_shape)\n\n wire_shape = geom.shapes.Tubs(self.name+\"_wire\", self.halfWireDimension[\"rmin\"],\n rmax = self.halfWireDimension[\"rmax\"], dz = self.halfWireDimension[\"dz\"])\n wire_lv = geom.structure.Volume(self.name+\"_wire_lv\", material=self.WireMaterial, shape=wire_shape)\n\n straw_pla = geom.structure.Placement( self.name+\"_straw_pla\", volume = straw_lv )\n wire_pla = geom.structure.Placement( self.name+\"_wire_pla\", volume = wire_lv )\n main_lv.placements.append( straw_pla.name )\n main_lv.placements.append( wire_pla.name )",
"def boneLattice(before=bool, exclusive=\"string\", after=bool, bicep=float, joint=\"string\", includeHiddenSelections=bool, frontOfChain=bool, prune=bool, widthRight=float, geometryIndices=bool, transform=\"string\", split=bool, geometry=\"string\", name=\"string\", parallel=bool, ignoreSelected=bool, afterReference=bool, remove=bool, tricep=float, widthLeft=float, lengthOut=float, deformerTools=bool, lengthIn=float):\n pass",
"def use_lennard_jones(self):\n edat = self.env.edat\n edat.contact_shell = 8.00\n edat.dynamic_sphere = False\n edat.dynamic_lennard = True"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Run dynamic baseline policy.
|
def run_dynamic_policy(results_path, benchmark_name, num_episodes, seeds=np.arange(10)):
if benchmark_name not in NON_OPTIMAL_POLICIES:
print("No dynamic policy found for this benchmark")
policy = NON_OPTIMAL_POLICIES[benchmark_name]
run_policy(results_path, benchmark_name, num_episodes, policy, seeds)
|
[
"def add_baseline_op(self, scope = \"baseline\"):\n ######################################################\n ######### YOUR CODE HERE - 4-8 lines. ############\n\n self.baseline = build_mlp(self.observation_placeholder,\n 1,\n scope,\n self.config.n_layers,\n self.config.layer_size,\n self.config.activation)\n loss = tf.losses.mean_squared_error(self.baseline_target_placeholder, tf.squeeze(self.baseline))\n optimizer = tf.train.AdamOptimizer(learning_rate=self.lr)\n self.update_baseline_op = optimizer.minimize(loss)\n\n #######################################################\n ######### END YOUR CODE. ############",
"def update_baseline(self, returns, observations):\n #######################################################\n ######### YOUR CODE HERE - 1-5 lines. ############\n\n self.sess.run(self.update_baseline_op, feed_dict={self.baseline_target_placeholder : returns,\n self.observation_placeholder : observations})\n\n # TODO\n #######################################################\n ######### END YOUR CODE. ############",
"def eval_baseline(self, baseline_sparsity: float):\n node_sparsities = self._get_nodes_optimized_sparsities(\n baseline_sparsity, balance_perf_loss=1.0, settings=None\n )\n\n for node_id, sparsity in node_sparsities.items():\n self._nodes_settings[node_id].baseline_sparsity = sparsity",
"def test_baseline_attributes(self):\n self.assertIs(self.dataset.first_stage, \"\")\n self.assertIs(self.dataset.wavelet, \"\")\n self.assertEqual(self.dataset.level, 0)\n self.assertEqual(self.dataset.niter, 0)\n\n self.dataset.compute_baseline(\n first_stage=\"sym6\", wavelet=\"qshift3\", level=1, mode=\"periodic\"\n )\n\n self.assertEqual(self.dataset.first_stage, \"sym6\")\n self.assertEqual(self.dataset.wavelet, \"qshift3\")\n self.assertEqual(self.dataset.level, 1)",
"def run(self):\n pre_policy = deepcopy(self.__policy)\n self.__policy_improvement()\n count = 0\n\n while self.__if_policy_diff(pre_policy) or count < 5:\n pre_policy = deepcopy(self.__policy)\n self.__policy_evaluation()\n self.__policy_improvement()\n\n if not self.__if_policy_diff(pre_policy):\n count += 1\n else:\n count = 0",
"def baseline():\n global state\n draw, image = clear_screen()\n\n data[\"new_user\"] = False\n data[\"tests\"] = {\"0\": None}\n data[\"number_of_tests\"] = -1\n update_data()\n\n update_buttons(draw, image, \"Start\", \"Start\", \"Record a \", \"baseline.\")\n state = \"Test\"",
"def create_baseline(target, save_baseline=to_csv, **kwargs):",
"def run_same_policy():\n\n tune.run(\"PG\", config={\"env\": RockPaperScissorsEnv})",
"def do_baseline_run(self, target_config: TargetConfig) -> RunResultSeries:\n L.get_logger().log('SlurmScalingRunner::do_baseline_run', level=\"debug\")\n\n # saving the batch interface from the config, to restore it later\n config_batch_interface = self.batch_interface.interface\n\n args = self._config.get_args(target_config.get_build(), target_config.get_target())\n\n # List of command_result_maps for all args\n cmd_maps = []\n jobs = []\n\n # check if interface for dispatching adheres to rule 1), see class docstring\n if self.batch_interface.interface == SlurmInterfaces.SBATCH_WAIT:\n L.get_logger().log(\n \"SlurmScalingRunner::do_baseline_run: Interface 'sbatch-wait' is a blocking \"\n \"dispatch interface, which cannot be used with scaling experiments. \"\n \"Downgrading to 'os'.\",\n level=\"warn\")\n self.batch_interface.interface = SlurmInterfaces.OS\n # dispatch job for each arg\n for i, arg in enumerate(args):\n # setup args for invocation\n target_config.set_args_for_invocation(arg)\n # List of tupels (iteration number, key)\n command_result_map: typing.List[typing.Tuple[int, str]] = []\n # if force sequential: add dependency to job_id before\n if self.force_sequential and i > 0:\n self.batch_interface.generator.config.dependencies = f\"afterok:{jobs[i-1]}\"\n else:\n self.batch_interface.generator.config.dependencies = \"\"\n job_id = self.dispatch_run(target_config, InstrumentConfig(), command_result_map)\n jobs.append(job_id)\n cmd_maps.append(command_result_map)\n\n # waiting needs to be done with non-blocking wait 'os' - rule 2)s\n if self.batch_interface.interface != SlurmInterfaces.OS:\n L.get_logger().log(\n f\"SlurmScalingRunner::do_baseline_run: {str(self.batch_interface.interface)} is a blocking \"\n \"wait interface, which cannot be used with scaling experiments.\"\n \" Downgrading to 'os'.\",\n level=\"warn\")\n self.batch_interface.interface = SlurmInterfaces.OS\n # wait for the group of all jobs to finish\n self.wait_run()\n\n run_result = M.RunResultSeries(reps=self.get_num_repetitions(), num_data_sets=5)\n for map in cmd_maps:\n time_series = M.RunResultSeries(reps=self.get_num_repetitions())\n self.collect_run(map, time_series)\n run_result.add_from(time_series)\n\n self.batch_interface.cleanup()\n # restore the batch interface\n self.batch_interface.interface = config_batch_interface\n\n return run_result",
"def run_evaluate_policy(script_path: str, sample: str, action_log_file: str):\n cmd = [\n \"python3\",\n script_path,\n sample,\n action_log_file,\n ]\n subprocess.run(cmd, check=True)",
"def make_baseline(start_year, records_url):\r\n policy_cl = Policy()\r\n behavior_cl = Behavior()\r\n records_cl = Records(records_url)\r\n calc_cl = Calculator(policy_cl, records_cl, behavior_cl)\r\n for i in range(start_year - 2013):\r\n calc_cl.increment_year()\r\n assert calc_cl.current_year == start_year\r\n calc_cl.calc_all()\r\n return(calc_cl)",
"def run_policy(dir):\n\n # create a model configuration\n\n # load the config as a json file\n with open(join(dir, \"run.conf\"), \"r\") as file_conf:\n file_str = file_conf.read()\n conf = json.loads(file_str)\n\n mc = ModelConfiguration(conf)\n conf = mc['conf']\n\n # create an environment wrapper\n with conf.ns('env'):\n env = MCMCEnvWrapper(mc)\n mc.add_environment(env)\n\n # policy neural_modules\n with conf.ns('policy'):\n policy = UnivariateGaussianPolicy(mc)\n policy.load_state_dict(torch.load(join(dir, \"model/last\", f\"policy.data\")))\n\n while True: env.execute_policy_once(10000, policy, True, True)",
"def main():\n parser = argparse.ArgumentParser()\n parser.add_argument('--config', default=\"configs.baseline\",\n help='experiment configuration dict')\n parser.add_argument('--train', action='store_true',\n help='whether to train')\n parser.add_argument('--test', action='store_true', help='whether to test')\n args = parser.parse_args()\n\n config_module = importlib.import_module(args.config)\n trainer = Trainer(config_module.config)\n if args.train:\n trainer.run()\n if args.test:\n test_report = trainer.test()\n print(test_report)",
"def execute_policy(self, policy):\r\n return self.manager.execute_policy(scaling_group=self, policy=policy)",
"def update_baseline(name, base, session):\r\n sql = update(TuningTable).where(TuningTable.tuning_name == name).values(baseline=base)\r\n res = session.execute(sql)\r\n return res is not None",
"def run_baselines(self, X, y, pass_n='0', targets=None, label_col='majority_type'):\n models = self.baseline_models[int(pass_n)]\n b_acc = []\n for m in models:\n pred = m.predict(X)\n pred = pd.Series(pred).apply(lambda x: step[x] if type(x) is not bool else x).values\n score = m.score(pred, y, scoring=['accuracy', 'recall', 'precision'])\n b_acc.append(score)\n print(\"Baseline scores on pass {}: {}\".format(pass_n+1, b_acc))\n return b_acc",
"def create_baseline(interval, running_time, moving_average_time_period):\n moving_average_time_period = int(moving_average_time_period)\n running_time = int(running_time)\n\n if moving_average_time_period >= running_time:\n print(\"Running time must be more than rolling average period\")\n exit()\n # get running time in minutes, div by interval plus 1 sec for network baseline\n num_of_polls = int((running_time * 60) / (interval + 1))\n moving_average_num_of_polls = int((moving_average_time_period * 60) / (interval + 1))\n cpu_utilisation = list()\n network_usage = list()\n memory_usage = list()\n cpu_utilisation_max = list()\n network_usage_max = list()\n memory_usage_max = list()\n i = 0\n max_cpu_average = 0\n max_network_average = 0\n max_memory_average = 0\n\n while i < num_of_polls:\n # create a list containing the CPU utilisation, memory usage and network usage over the entire period the\n # baseline is ran for.\n cpu = sysmon.get_cpu_utilisation()\n network = sysmon.get_network_interface_traffic(NETWORK_ADAPTOR)\n memory = sysmon.get_memory_usage()['memory_in_use']\n cpu_utilisation.append(cpu)\n network_usage.append(network)\n memory_usage.append(memory)\n\n # get the maximum values for the maximum cpu utilisation, network usage and memory usage. These values\n # are calculated using a move average over a specified period of time\n # first the minimum number of values are collected\n if i <= moving_average_num_of_polls:\n cpu_utilisation_max.append(cpu)\n network_usage_max.append(network)\n memory_usage_max.append(memory)\n # once the minimum number of values have been collected to calculate the average over. The size of the\n # list is maintained by dropping the first value and adding one to the end\n else:\n del cpu_utilisation_max[0]\n cpu_utilisation_max.append(cpu)\n cpu_average = get_mean(cpu_utilisation_max)\n if cpu_average > max_cpu_average:\n max_cpu_average = cpu_average\n del network_usage_max[0]\n network_usage_max.append(network)\n network_average = get_mean(network_usage_max)\n if network_average > max_network_average:\n max_network_average = network_average\n del memory_usage_max[0]\n memory_usage_max.append(memory)\n memory_average = get_mean(memory_usage_max)\n if memory_average > max_memory_average:\n max_memory_average = memory_average\n\n time.sleep(interval)\n i += 1\n\n # calculate the mean average from all the values in the list\n average_cpu_utilisation = get_mean(cpu_utilisation)\n average_network_usage = get_mean(network_usage)\n average_memory_usage = get_mean(memory_usage)\n\n # print the results to the console and write them to server_stats.txt\n resource_stats = \"CPU Average: %0.2f %%\\nCPU Max %0.2f %%\\nNetwork Average: %0.2f bytes per second\\n\" \\\n \"Network Max: %0.2f bytes per second\\nMemory Average: %0.2f MB\\nMemory Max: %0.2f MB\" % \\\n (average_cpu_utilisation*100, max_cpu_average*100, average_network_usage,\n max_network_average, average_memory_usage/1000, max_memory_average/1000)\n directory = 'resources'\n if not os.path.exists(directory):\n os.makedirs(directory)\n f = open('resources/server_stats.txt', 'w')\n f.write(resource_stats)\n f.close()\n print_results()",
"def load_baseline(self) -> bool:\n\n if 'sw-versipon' not in self.facts:\n raise LoaderException('Could not determine sw-version to load baseline configuration!')\n\n version = self.facts['sw-version']\n if '8.0' in version:\n # load the 8.0 baseline with\n pass\n elif '8.1' in version:\n # load the 8.1 baseline with\n pass\n elif '9.0' in version:\n # load the 9.0 baseline with\n pass\n else:\n print('Could not determine sw-version for baseline load')\n return False\n\n return True",
"def test_baseline_limits(self):\n\n self.dataset.compute_baseline(\n first_stage=\"sym6\", wavelet=\"qshift3\", level=1, mode=\"periodic\"\n )\n\n # Test that the baseline is always positive\n baseline = self.dataset.powder_baseline(None)\n self.assertTrue(np.all(np.greater_equal(baseline, 0)))\n\n data_bgr = self.dataset.powder_data(None, bgr=True)\n self.assertTrue(np.all(np.greater_equal(data_bgr, 0)))"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
1 BruteForce Traverse a and b, and use two variables x and y to store two integers. Let z = x + y. Create a new list c, representing z. x and y can be very large, refused by the interviewer. 2 List Operation O(M + N) O(M + N) Add x and y digit by digit from the start is not simple. We can not align two lists and we need an array to store carries(d1 + d2 >= 10). If we are given doubly linked list, the situation will become friendly. Ask the interviewer whether we can change the original lists. Reverse two lists at first. Add them digit by digit from the end to the beginning while generating a new list c. Notice carries. Reverse c and return.
|
def solution(self, a, b):
def reverse_list(head):
p1 = None
p2 = head
while p2 is not None:
t = p2
p2 = p2.next
t.next = p1
p1 = t
return p1
a_r = reverse_list(a)
b_r = reverse_list(b)
flag_carry = False
# sentinel
dummy = self.Node(None)
p = dummy
# traverse a and b
while a_r is not None and b_r is not None:
v = a_r.val + b_r.val
# notice the carry
if flag_carry:
v += 1
# update the flag
flag_carry = v >= 10
# create new node, notice the module operation
n = self.Node(v % 10)
# link the new list
p.next = n
# move the pointer
p = n
# iterate
a_r = a_r.next
b_r = b_r.next
# traverse the remaining of a list
if a_r is not None or b_r is not None:
rem = a_r if a_r is not None else b_r
while rem is not None:
v = rem.val
if flag_carry:
v += 1
flag_carry = v >= 10
n = self.Node(v % 10)
p.next = n
p = n
rem = rem.next
# a_r and b_r are both None
# notice there may exist a carry
if flag_carry:
n = self.Node(1)
p.next = n
p = n
# end the new list with None
p.next = None
return reverse_list(dummy.next)
|
[
"def sum_list_lsd(first_list: LinkedList, second_list: LinkedList) -> int:\n result = 0\n carry = 0\n order = 1\n\n current_0 = first_list.head\n current_1 = second_list.head\n\n while current_0 and current_1:\n result += ((current_0.data + current_1.data + carry) % 10) * order\n carry = (current_0.data + current_1.data + carry) // 10\n order *= 10\n current_1 = current_1.next\n current_0 = current_0.next\n\n for current in [current_1, current_0]:\n while current:\n result += ((current.data + carry) % 10) * order\n\n carry = current.data + carry // 10\n order *= 10\n current = current.next\n\n return result",
"def sum_linked_lists_reverse(node1, node2, carry=0):\n\n def get_length(head):\n \"\"\"Find length of linked list\n\n :param head head of the linked list\n :returns number of elements in the linked list\n\n \"\"\"\n num = 0\n curr = head\n while curr is not None:\n curr = curr.next\n num += 1\n return num\n\n def pad_zeroes(head, num):\n \"\"\"Pad zeroes to the front of the linked list\n\n :param head head of the linked list\n :param num number of zeroes to add\n :returns linked list with zeroes padded to the front\n\n \"\"\"\n new = curr = Node(0)\n num -= 1\n\n while num > 0:\n curr.next = Node(0)\n curr = curr.next\n num -= 1\n curr.next = head\n return new\n\n def sum_helper(node1, node2):\n \"\"\"Sum helper function to recursively sum elements of equal length linked lists\n\n :param node1 head of first linked list\n :param node2 head of second linked list\n\n :returns sum of first and second linked lists as a set of nodes\n\n \"\"\"\n if node1 is None and node2 is None:\n return\n curr = sum_helper(node1.next, node2.next)\n\n if curr is None:\n curr = Node(0)\n data = node1.data + node2.data + curr.data\n curr.data = data % 10\n\n next = Node(int(data >= 10))\n next.next = curr\n\n return next\n\n if node1 is None and node2 is None:\n return None\n\n len1 = get_length(node1)\n len2 = get_length(node2)\n\n if len1 < len2:\n node1 = pad_zeroes(node1, len2 - len1)\n elif len2 < len1:\n node2 = pad_zeroes(node2, len1 - len2)\n\n tmp = sum_helper(node1, node2)\n\n if tmp.data == 0 and tmp.next is not None:\n tmp = tmp.next\n\n return tmp",
"def digit_exchange(a, b):\n\n if ((a<1 or a>10000000) or (b<1 or b>10000000)):\n return -1\n\n list_a = []\n string_a=str(a) \n \n # for i in string_a: \n # digit=int(i)\n # list_a.append(digit)\n \n # Alternative for above code snippet\n list_a = list(string_a)\n\n count_dict = collections.Counter(str(a))\n \n list_a_copy=list_a\n\n output_list = find_combinations(list_a_copy, list_a, count_dict)\n temp_set = set(output_list)\n output_list=list(temp_set)\n \n while len(str(output_list[0])) < len(str(a)):\n output_list = find_combinations(output_list, list_a,count_dict)\n \n output_set = set(output_list)\n output_list = list(output_set)\n\n result=[]\n for num in output_list:\n if num>b:\n result.append(num)\n result.sort()\n output=result[0]\n print(output)",
"def sum_ll(ll1: LinkedList, ll2: LinkedList) -> LinkedList:\n ll3 = LinkedList(None)\n ll = ll3\n count = 0\n while count < 2:\n count = 0\n if not ll.data:\n ll.data = (ll1.data + ll2.data) % 10\n remainder = (ll1.data + ll2.data) // 10\n else:\n ll.next = LinkedList((ll1.data + ll2.data) % 10 + remainder)\n remainder = (ll1.data + ll2.data) // 10\n ll = ll.next\n\n ll1 = ll1.next\n if ll1 is None:\n count += 1\n ll1 = LinkedList(0)\n ll2 = ll2.next\n if ll2 is None:\n count += 1\n ll2 = LinkedList(0)\n\n if remainder:\n ll.next = LinkedList(remainder)\n\n return ll3",
"def _add_listelements(a, b):\r\n for i in range(len(a)):\r\n a[i] += b[i]\r\n \r\n return a",
"def convert(a, b):\n\n global dic\n if dic.get((a,b), (0,0)) != (0,0):\n return dic[(a,b)][0]\n cost = 1000\n index = -1\n for i in range(min(len(a), len(b))):\n if a[i] != b[i]:\n index = i\n break\n \n if index == -1:\n cost = max(len(a), len(b)) - min(len(a), len(b))\n cost *= 20\n res = \"insert or remove\"\n# print (\"just remove or insert\")\n else:\n res = \"None\"\n curcost = 5 + convert(a[index+1:], b[index+1:])\n if curcost < cost:\n cost = curcost\n res = \"copy\"\n curcost = 20 + convert(a[index:], b[index+1:])\n if curcost < cost:\n cost = curcost\n res = \"insert\"\n curcost = 20 + convert(a[index+1:], b[index:])\n if curcost < cost:\n cost = curcost\n res = \"cost\"\n dic[(a,b)] = (cost, res)\n return cost",
"def permut2lists(a,b):\n solucao = []\n for i,j in itertools.product(a,b):\n solucao.append([i,j])\n return solucao",
"def part_b():\n\n def calcPermute(numbers):\n return calcPermuteHelper(set(numbers), set(), numbers[0], numbers[-1])\n\n def calcPermuteHelper(numbers, visited, current, goal):\n if current == goal:\n return 1\n visited = deepcopy(visited)\n visited.add(current)\n next_options = ({current - x for x in [-2, -1, 1, 2, 3]} & numbers) - visited\n return sum(calcPermuteHelper(numbers, visited, x, goal) for x in next_options)\n\n def solve(numbers):\n try:\n nextdelta3ix = next((i for i in range(1, len(numbers)) if numbers[i] - numbers[i - 1] == 3))\n return calcPermute(numbers[:nextdelta3ix]) * solve(numbers[nextdelta3ix:])\n except StopIteration:\n return calcPermute(numbers)\n\n numbers = [0] + sorted([int(x) for x in read_input_lines()])\n\n print(solve(numbers))",
"def addTwoNumbers(self, l1, l2):\n if not l1:\n return l2\n if not l2:\n return l1\n\n head = ListNode(0)\n head.next = l1\n res = head\n\n addition = False\n while l1 and l2:\n head.next.val = l1.val + l2.val\n if addition:\n head.next.val += 1\n if head.next.val > 9:\n head.next.val -= 10\n addition = True\n else:\n addition = False\n\n head = head.next\n l1 = l1.next\n l2 = l2.next\n\n if l2:\n head.next = l2\n l1 = l2\n\n while l1:\n head.next.val = l1.val\n if addition:\n head.next.val += 1\n if head.next.val > 9:\n head.next.val -= 10\n addition = True\n else:\n addition = False\n head = head.next\n l1 = l1.next\n\n if addition:\n head.next = ListNode(1)\n\n return res.next",
"def distances(a, b):\n mem = [[]]\n ca = [0]\n mem.append(ca)\n ans = editDist(a, b, mem)\n return ans",
"def add(x, y):\n\tcarry = 0\n\tfor i, elem in enumerate(y):\n\t\tx[i], carry = (x[i] + elem + carry) % 10, (x[i] + elem + carry) / 10\n\treturn x",
"def addTwoNumbers(l1, l2):\n if not l1 and not l2:\n return None\n\n else:\n if l1 and not l2:\n v = l1.val\n elif l2 and not l1:\n v = l2.val\n l1, l2 = l2, None\n else:\n v = l1.val + l2.val\n\n if v >= 10:\n v -= 10\n if l1.next is None:\n if l2 is None or l2.next is None:\n l1.next = ListNode(1)\n else:\n l2.next.val += 1\n else:\n l1.next.val += 1\n\n l1.val = v\n\n if not l2:\n l1.next = self.addTwoNumbers(l1.next, None)\n else:\n l1.next = self.addTwoNumbers(l1.next, l2.next)\n \n return l1",
"def cross(a,b):\r\n return [s + t for s in a for t in b]",
"def triplets(a, b, c):\n\n # using multiplication principle of disjoint events (quadratic)\n \n num_trips = 0\n a.sort()\n b.sort()\n c.sort()\n qs = OrderedDict()\n for q in b:\n if q not in qs:\n qs[q] = True\n \n index_a = index_c = 0\n for q in qs:\n while index_a < len(a):\n if a[index_a] <= q:\n index_a += 1\n else:\n break\n while index_c < len(c):\n if c[index_c] <= q:\n index_c += 1\n else:\n break\n num_trips += index_a * index_c\n return num_trips",
"def sum(str1: str, str2: str) -> str:\n\n print(\"str1=\" + str(str1) + \", str2=\" + str(str2))\n\n if not str1.isdigit() or not str2.isdigit() or str1 is None or str2 is None:\n return None\n\n list1 = list(str1)\n list2 = list(str2)\n print(\"list1=\" + str(list1))\n print(\"list2=\" + str(list2))\n result_str = \"\"\n\n if len(str1) > len(str2):\n smaller_number = str2\n larger_number = str1\n else:\n smaller_number = str1\n larger_number = str2\n\n larger_index = len(larger_number) - 1\n\n digit_in_memory = 0\n\n for index in range(len(smaller_number), 0, -1):\n digit1 = int(smaller_number[index - 1])\n digit2 = int(larger_number[larger_index])\n\n cur_sum = digit1 + digit2 + digit_in_memory\n\n if cur_sum > 9:\n result_str += str(cur_sum)[-1]\n digit_in_memory = int(str(cur_sum)[0])\n else:\n result_str += str(cur_sum)\n digit_in_memory = 0\n\n if index == 1 and digit_in_memory != 0:\n if len(str1) == len(str2):\n result_str += str(digit_in_memory)\n else:\n cur_sum = int(larger_number[larger_index - 1]) + digit_in_memory\n result_str += str(cur_sum)\n\n larger_index -= 1\n\n reverse_result = result_str[::-1]\n first_part = \"\"\n\n if len(str1) != len(str2):\n first_part = larger_number[0:len(larger_number) - len(reverse_result):1]\n result_number = first_part + reverse_result\n\n return result_number",
"def sort_ab(a, b):\n\n outlist = []\n\n ia = 0\n ib = 0\n\n while ia < len(a) and ib < len(b):\n\n if a[ia] < b[ib]:\n outlist.append(a[ia])\n ia += 1\n\n else:\n outlist.append(b[ib])\n ib += 1\n\n # Add any remaining items:\n outlist.extend(a[ia:])\n outlist.extend(b[ib:])\n\n\n return outlist # Come back",
"def swap(a, b):\r\n for itemA in a:\r\n\r\n for itemB in b:\r\n\r\n if(abs(sum(a) - sum(b)) > abs((sum(a) - itemA + itemB) - (sum(b) + itemA - itemB))):\r\n return itemA, itemB\r\n\r\n return False",
"def steps_from(self,a: list, b: list):\n steps = \"\"\n if a[0] > b[0]:\n while a[0] != b[0]:\n a[0] -= 1\n steps += \"L\"\n if a[0] < b[0]:\n while a[0] != b[0]:\n a[0] += 1\n steps += \"R\"\n if a[1] > b[1]:\n while a[1] != b[1]:\n a[1] -= 1\n steps += \"U\"\n if a[1] < b[1]:\n while a[1] != b[1]:\n a[1] += 1\n steps += \"D\"\n\n return steps",
"def sort_ab(a, b):\n #[1,2,3], [4,5] --> [1,2,3,4,5]\n\n sorted_ab = []\n #Strategy: \n # If either list is empty, append the rest of other list. \n while len(a) > 0 or len(b) > 0:\n if a == []:\n sorted_ab.append(b.pop(0))\n elif b == []:\n sorted_ab.append(a.pop(0))\n elif a[0] < b[0]:\n sorted_ab.append(a.pop(0))\n else:\n sorted_ab.append(b.pop(0))\n\n return sorted_ab\n\n\n\n # compare first number of each, append bigger to a new list. "
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Intuition BFS O((MN) 2) O((MN) 2) Finding whether there exists a path or the shortest unweighted path, try BFS. Since we are trying to find the shortest path and the leaking will expand, there is no need to consider repeatedly visiting a grid. Hint 1 Use another queue to represent leakage, do not search the whole matrix at each iteration. O(MN) O(MN) auxiliary matrices visit and leakage Initialization q_l = deque()
|
def solution(self, grid, m, n, x0, y0, x1, y1):
def check_exceed(x, y, m, n):
if x < 0 or x >= m:
return False
if y < 0 or y >= n:
return False
return True
def check_leak(leakage, x, y):
return leakage[x][y] == "*"
# BFS initialization (queue + visit + path_len)
from collections import deque
q = deque()
q.append([x0, y0])
path_len = 1
# without visit matrix, BFS will be stuck in an infinite loop
visit = [[False] * n for _ in range(m)]
visit[x0][y0] = True
# leakage matrix
leakage = grid[:][:]
# BFS
while q:
# iterate path level by level
for _ in range(len(q)):
coordinates = q.popleft()
if coordinates == [x1, y1]:
return path_len
x = coordinates[0]
y = coordinates[1]
# left
if not check_exceed(x - 1, y, m, n) and not check_leak(leakage, x - 1, y):
if not visit[x - 1][y]:
visit[x - 1][y] = True
q.append([x - 1, y])
# right
if not check_exceed(x + 1, y, m, n) and not check_leak(leakage, x + 1, y):
if not visit[x + 1][y]:
visit[x + 1][y] = True
q.append([x + 1, y])
# top
if not check_exceed(x, y - 1, m, n) and not check_leak(leakage, x, y - 1):
if not visit[x][y - 1]:
visit[x][y - 1] = True
q.append([x, y - 1])
# bottom
if not check_exceed(x, y + 1, m, n) and not check_leak(leakage, x, y + 1):
if not visit[x][y + 1]:
visit[x][y + 1] = True
q.append([x, y + 1])
path_len += 1
# iterate leakage
temp = leakage[:][:]
for i in range(m):
for j in range(n):
if check_leak(leakage, i, j):
# left
if not check_exceed(i - 1, j, m, n):
temp[i - 1][j] = "*"
# right
if not check_exceed(i + 1, j, m, n):
temp[i + 1][j] = "*"
# top
if not check_exceed(i, j - 1, m, n):
temp[i][j - 1] = "*"
# bottom
if not check_exceed(i, j + 1, m, n):
temp[i][j + 1] = "*"
leakage = temp[:][:]
return -1
|
[
"def bfs(adj_matrix, Board, Source, Destination):\r\n\t\t# Initialize a queue and an array for storing whether the node has\r\n\t\t# been visited or not\r\n\t\tqueue = deque()\r\n\t\tvisited = [False for x in range(len(adj_matrix[0]))]\r\n\r\n\t\t# Distance array for storing the path length and prev_vert array\r\n\t\t# for storing the vertex used to get to that vertex\r\n\t\tdist = [sys.maxsize for x in range(len(adj_matrix[0]))]\r\n\t\tprev_vert = [-1 for x in range(len(adj_matrix[0]))]\r\n\t\r\n\t\t# Start position\r\n\t\tqueue.append(src)\r\n\t\tvisited[src] = True\r\n\t\tdist[src] = 0\r\n\r\n\t\t# BFS search\r\n\t\twhile queue:\r\n\t\t\tvert = queue.popleft()\r\n\t\t\trow = adj_matrix[vert]\r\n\r\n\t\t\tfor node in range(len(row)):\r\n\t\t\t\t# Unvisited nodes are added to the queue\r\n\t\t\t\tif visited[node] == False and row[node] == 1:\r\n\r\n\t\t\t\t\tvisited[node] = True\t# Set flag\r\n\t\t\t\t\tdist[node] = dist[vert] + 1\t# Calculate distance\r\n\t\t\t\t\tprev_vert[node] = vert\t# Set predecessor\r\n\r\n\t\t\t\t\tqueue.append(node)\t# Add to queue\r\n\r\n\t\t\t\t\t# If destination is found, end search\r\n\t\t\t\t\tif dest == node:\r\n\t\t\t\t\t\treturn dist, prev_vert\r\n\r\n\t\treturn False, False\t# Path could not be reached\t\t\t\t\r",
"def bfs(start, goal, fn_neighbours, maxcount=None):\n queue = [(start, [start])]\n seen = set()\n results = []\n minimum = sys.maxint\n while queue:\n current, path = queue.pop(0)\n if len(path) > minimum:\n return results\n if current == goal:\n minimum = min(minimum, len(path))\n results.append(path)\n if maxcount and len(results) >= maxcount:\n return results\n for n in fn_neighbours(current):\n if current not in seen:\n npath = path + [n]\n queue.append((n, npath))\n seen.add(current)\n if results:\n return results\n return NoPathExists",
"def breadth_first_search(self, graph: MatrixGraph, start: tuple, target: tuple,\n surface: pygame.Surface, display: pygame.Surface) \\\n -> list[tuple[int, int]]:\n queue = []\n visited = set()\n paths = {} # A dictionary that maps new nodes to the previous node\n queue.extend(graph.get_valid_neighbours(start[0], start[1]))\n visited.update(graph.get_valid_neighbours(start[0], start[1]))\n\n # Update paths with the original visited set\n for node in graph.get_valid_neighbours(start[0], start[1]):\n paths[node] = start\n found = False\n\n # Counter to store current iteration\n counter = 0\n\n # Pygame clock\n clock = Timer()\n\n while queue != [] and not found:\n # Draw and update the loop iteration counter\n counter += 1\n iteration_counter = f'Nodes Searched: {counter}'\n self._draw_loop_iterations(iteration_counter, surface)\n\n # Pop the current node\n curr = queue.pop(0)\n\n # Visualize step\n _ = pygame.event.get() # Call event.get to stop program from crashing on clicks\n curr_x = curr[0] + self._maze_x_offset + 1\n curr_y = curr[1] + self._maze_y_offset + 1\n pygame.draw.circle(surface, (255, 0, 0), (curr_x, curr_y), 3)\n display.blit(surface, (0, 0))\n pygame.display.flip()\n\n if curr == target:\n found = True\n for node in graph.get_valid_neighbours(curr[0], curr[1]):\n if node not in visited:\n queue.append(node)\n visited.add(node)\n\n # Add the node as a key with the current node as the value\n paths[node] = curr\n\n clock.update_time()\n self._draw_timer(clock, surface)\n\n if found is False:\n return []\n else:\n return self._find_and_draw_final_path(paths, start, target, surface, display)",
"def bfs(graph,start,end):\n #structure used to put nodes to visit\n queue=[]\n #my path\n path=[]\n #init the structure\n path.append(start)\n queue.append(path)\n\n #you loop on the queue where you put your nodes\n while len(queue) != 0:\n tmpPath=queue.pop(0)\n lastNode=tmpPath[len(tmpPath)-1]\n print(printPath(tmpPath))\n #we're done\n if lastNode == end: return tmpPath\n #else we must run through children\n for node in graph.neighbours(lastNode):\n if node not in tmpPath:\n newPath=tmpPath+[node]\n queue.append(newPath)",
"def BFS(self, graph):\r\n # keep records of all visited nodes : [config1, config2]\r\n explored = []\r\n # keep records of need check nodes : [[config,config],[config,config]]\r\n initial = self.initial\r\n goal_config = self.goal\r\n queue = [[initial]]\r\n\r\n while len(queue) > 0:\r\n # pop first node in queue # queue = [[config1]]\r\n node = queue.pop(0) # node : [config1]\r\n if node[-1] not in explored: # node[-1] : config1\r\n # add node to explored list\r\n explored.append(node[-1])\r\n # if the current node has children\r\n if node[-1] in graph.keys():\r\n for child in graph[node[-1]]: # for each child in children of a frontier\r\n node_duplicate = copy.deepcopy(node)\r\n node_duplicate.append(child)\r\n if test_config_equality(child, goal_config, self.problem_spec):\r\n return node_duplicate, True\r\n else:\r\n queue.append(node_duplicate)\r\n # if the current node has no child : do nothing\r\n return [], False",
"def depth_first_branch_and_bound_search(start_grid, use_manhattan):\n limit = INFINITY # Initialize limit to infinity\n\n \"\"\"\n Open list contains the live nodes \n \"\"\"\n open_list = PriorityQueue()\n root = Node(start_grid, goal_grid, use_manhattan, '')\n open_list.insert(root)\n result_node = None\n num_nodes_expanded = 0\n start_time = time.perf_counter()\n exec_time_str = '' # Execution time string for measuring execution time in seconds rounded to 4 decimal places\n\n \"\"\"\n While the open_list is not empty,\n Pull out the min f cost node.\n if the node is equal to the goal state, update the limit to the solution's f value\n Otherwise, generate the children, iterate through each child and only insert those elements into the queue with\n an f value <= the current limit\n \n \"\"\"\n while open_list.size() > 0:\n min_node = open_list.delete()\n num_nodes_expanded += 1\n if min_node.h == 0:\n if min_node.f <= limit:\n end_time = time.perf_counter()\n exec_time = end_time - start_time\n exec_time_str = f'Execution Time: {exec_time:0.4f} seconds'\n limit = min_node.f\n result_node = min_node\n else:\n successors = min_node.generate_successors()\n temp_list = PriorityQueue()\n for successor in successors:\n if successor.f <= limit:\n temp_list.insert(successor)\n while temp_list.size() > 0:\n open_list.insert(temp_list.delete())\n\n trace_and_print(root, result_node, num_nodes_expanded, exec_time_str)",
"def bfs(initial_node, dest_node):\n return queue_search(initial_node, dest_node, queue.Queue())",
"def prm_bfs(self, graph):\r\n # keep records of all visited nodes : [config1, config2]\r\n explored = []\r\n # keep records of need check nodes : [[config,config],[config,config]]\r\n initial = self.initial\r\n goal_config = self.goal\r\n queue = [[initial]]\r\n\r\n while len(queue) > 0:\r\n # pop first node in queue # queue = [[config1]]\r\n node = queue.pop(0) # node : [config1]\r\n if node[-1] not in explored: # node[-1] : config1\r\n # add node to explored list\r\n explored.append(node[-1])\r\n # if the current node has children\r\n if node[-1] in graph.keys():\r\n for child in graph[node[-1]]: # for each child in children of a frontier\r\n node_duplicate = copy.deepcopy(node)\r\n node_duplicate.append(child)\r\n if test_config_equality(child, goal_config, self.problem_spec):\r\n return node_duplicate, True\r\n else:\r\n queue.append(node_duplicate)\r\n # if the current node has no child : do nothing\r\n return [], False",
"def bfs_shortest_path(graph, start, goal):\n # keep track of all visited nodes\n visited = []\n\n # keep track of the nodes to be explored, starting with the starting node\n # provided\n queue = deque([[start]])\n\n if start == goal:\n return \"The start element is the goal element\"\n\n while queue:\n # get the first element of the current path\n path = queue.popleft()\n\n # get the last node from the path\n node = path[-1]\n\n if node not in visited:\n neighbors = graph[node]\n\n # create a new path for all the neighbors and push it into the queue\n for neighbor in neighbors:\n new_path = list(path)\n new_path.append(neighbor)\n queue.append(new_path)\n\n # return path to goal if neighbor is goal\n if neighbor == goal:\n return new_path\n\n visited.append(node)\n \n return \"There is no path between {} and {}\".format(start, goal)",
"def bfs_visited(ugraph, start_node):\r\n if ugraph.get(start_node,0) == 0:\r\n return set([])\r\n bfs_que = Queue()\r\n bfs_que.enqueue(start_node) \r\n visited = set([start_node])\r\n while len(bfs_que) > 0:\r\n node = bfs_que.dequeue()\r\n for neigh in ugraph[node]:\r\n if neigh not in visited:\r\n visited.add(neigh)\r\n bfs_que.enqueue(neigh)\r\n\r\n return visited",
"def bfs(drawer, map, start, goal):\n ### START: 1c\n visited = map.copy()\n visited[start] = 1\n new_paths = [[start]]\n end_reached = False\n while not end_reached:\n paths = new_paths\n new_paths = []\n for path in paths:\n adj_nodes = get_adjacent_nodes(path[-1], map.shape)\n for node in adj_nodes:\n if visited[node]:\n continue\n visited[node] = 1\n new_paths.append(path + [node])\n drawer.draw_path(path + [node])\n if node == goal:\n final_path = new_paths[-1]\n end_reached = True\n break\n return final_path\n ### END: 1c",
"def a_star_euclidean(self):\r\n visited = set()\r\n parent = {}\r\n path = []\r\n\r\n _queue = queue.PriorityQueue()\r\n current_cost = {}\r\n i = 0\r\n\r\n _queue.put((0,self.start_point))\r\n visited.add(self.start_point)\r\n current_cost[self.start_point] = 0\r\n\r\n while not _queue.empty():\r\n if _queue.qsize() > i:\r\n i = _queue.qsize()\r\n\r\n current_node = _queue.get()\r\n coordinate_current_node = current_node[1]\r\n if coordinate_current_node == self.end_point:\r\n path = self.buildpath(parent)\r\n self.maze.solution = dict(find_path_or_not=\"YES\",\r\n number_of_nodes_visited=len(visited),\r\n visited_nodes=visited,\r\n path_length=len(path),\r\n path=path,\r\n max_fringe_size=i)\r\n return\r\n for child_node in self.maze.neighbor(coordinate_current_node):\r\n next_cost = current_cost[coordinate_current_node] + 1\r\n if child_node not in visited:\r\n current_cost[child_node] = next_cost\r\n parent[child_node] = coordinate_current_node\r\n visited.add(child_node)\r\n # cost so far + h\r\n h = math.sqrt(\r\n (child_node[0] - self.end_point[0]) ** 2 +\r\n (child_node[1] - self.end_point[1]) ** 2\r\n )\r\n\r\n total_cost = h + next_cost\r\n _queue.put((total_cost,child_node))\r\n\r\n self.maze.solution = dict(find_path_or_not=\"NO\",\r\n number_of_nodes_visited=0,\r\n visited_nodes=visited,\r\n path_length=len(path),\r\n path=path,\r\n max_fringe_size=0)\r\n return",
"def shortest_path(M, start, goal):\n\n # 1.Initialization parameters\n frontier, explored, g_score, f_score, path = set([start]), set(), {}, {}, {}\n g_score[start] = 0\n\n while len(frontier) != 0:\n\n # 2. Get prioritize exploration of frontier;\n current_state = get_lowest(frontier, f_score, start)\n\n # 6.Whether the path reaches the goal;\n if current_state == goal:\n best_path = get_path(path, goal)\n return best_path\n\n # 3. Update forntier and explored\n frontier.remove(current_state)\n explored.add(current_state)\n\n # 4. Get adjacent point of the current boundary point;\n neighbor_state = actions(M, current_state)\n\n # 5. Explore the neighbors of the current boundary point ;\n for neighbor in neighbor_state:\n\n # Record the cost value of the current neighbor;\n current_gscore = g_score[current_state] + disBetween(M, current_state, neighbor)\n\n # The neighbor not in expored and not in frontier;\n if neighbor not in explored and neighbor not in frontier:\n g_score[neighbor] = current_gscore\n f_score[neighbor] = current_gscore + disBetween(M, neighbor, goal)\n path[neighbor] = current_state\n frontier.add(neighbor)\n\n # The neighbor in frontier;\n elif neighbor in frontier:\n if current_gscore < g_score[neighbor]:\n g_score[neighbor] = current_gscore\n f_score[neighbor] = current_gscore + disBetween(M, neighbor, goal)\n path[neighbor] = current_state\n\n\n\n print(\"shorest path called\")\n\n return 0",
"def solve(self):\n # add starting cell to open heap queue\n heapq.heappush(self.opened, (self.start.f, self.start))\n while len(self.opened):\n # pop cell from heap queue\n f, cell = heapq.heappop(self.opened)\n # add cell to closed list so we don't process it twice\n self.closed.add(cell)\n # if ending cell, return found path\n if cell is self.end:\n self.path = self.get_path()\n pathlen = np.shape(self.path)[0]\n return self.path, pathlen\n # get adjacent cells for cell\n adj_cells = self.get_adjacent_cells(cell)\n for adj_cell in adj_cells:\n if not adj_cell.iswall and adj_cell not in self.closed:\n if (adj_cell.f, adj_cell) in self.opened:\n # if adj cell in open list, check if current path is\n # better than the one previously found\n # for this adj cell.\n if adj_cell.g > cell.g + 1:\n self.update_cell(adj_cell, cell)\n else:\n self.update_cell(adj_cell, cell)\n # add adj cell to open list\n heapq.heappush(self.opened, (adj_cell.f, adj_cell))\n if len(self.opened)==0:\n print \"Warning: impossible maze!\"\n return None, 0",
"def bft(self, starting_vertex):\n # Create a q and enqueue starting vertex\n qq = Queue()\n qq.enqueue([starting_vertex])\n\n # Create a set of traversed vertices\n visited = set()\n\n # While queue is not empty:\n while qq.size() > 0:\n # dequeue/pop the first vertex\n path = qq.dequeue()\n \n # if not visited\n if path[-1] not in visited:\n # DO THE THING!!!!!!!\n print(path[-1])\n # mark as visited\n visited.add(path[-1])\n # enqueue all neightbors\n for next_vert in self.get_neighbors(path[-1]):\n new_path = list(path)\n new_path.append(next_vert)\n qq.enqueue(new_path)\n pass # TODO",
"def bfs(s,e,g):\n q=[]\n seen=[]\n finished_paths=[]\n q.append([(s,0)])\n while(q):\n path=q.pop(0)\n node=path[-1]\n if(node[0]==e):\n finished_paths.append(path)\n for a in g.get(node[0],[]):\n if(tuple(a) in seen):\n continue\n seen.append(tuple(a))\n new_path=list(path)\n new_path.append(a)\n q.append(new_path)\n return finished_paths",
"def breadth_first_search(graph, initial, projected_crystal):\n\n projection_tags = projected_crystal.info['projection']\n\n # get lattice vectors to hopp along through graph\n projected_unit_cell = projected_crystal.cell[:2, :2]\n a_lattice_vector = projected_unit_cell[0]/10\n b_lattice_vector = projected_unit_cell[1]/10\n print(a_lattice_vector, b_lattice_vector)\n main = np.array([a_lattice_vector, -a_lattice_vector, b_lattice_vector, -b_lattice_vector]) # vectors of unit cell\n near = np.append(main, projection_tags['near_base'], axis=0) # all nearest atoms\n # get k next nearest neighbours for each node\n neighbour_tree = scipy.spatial.cKDTree(graph)\n distances, indices = neighbour_tree.query(graph, # let's get all neighbours\n k=8) # projection_tags['number_of_nearest_neighbours']*2 + 1)\n # print(projection_tags['number_of_nearest_neighbours'] * 2 + 1)\n visited = [] # the atoms we visited\n ideal = [] # atoms at ideal lattice\n sub_lattice = [] # atoms in base and disregarded\n queue = [initial]\n ideal_queue = [graph[initial]]\n\n while queue:\n node = queue.pop(0)\n ideal_node = ideal_queue.pop(0)\n\n if node not in visited:\n visited.append(node)\n ideal.append(ideal_node)\n # print(node,ideal_node)\n neighbors = indices[node]\n for i, neighbour in enumerate(neighbors):\n if neighbour not in visited:\n distance_to_ideal = np.linalg.norm(near + graph[node] - graph[neighbour], axis=1)\n\n if np.min(distance_to_ideal) < projection_tags['allowed_variation']:\n direction = np.argmin(distance_to_ideal)\n if direction > 3: # counting starts at 0\n sub_lattice.append(neighbour)\n elif distances[node, i] < projection_tags['distance_unit_cell'] * 1.05:\n queue.append(neighbour)\n ideal_queue.append(ideal_node + near[direction])\n\n return graph[visited], ideal",
"def BFS(g,s,discovered):\n level = [s] # first level includes only s\n while len(level) > 0:\n next_level = [] # prepare to gather newly found vertices\n for u in level:\n for e in g.incident_edges(u): # for every outgoing edge from u\n v = e.opposite(u)\n if v not in discovered: # v is an unvisited vertex\n discovered[v] = e # e is the tree edge that discovered v\n next_level.append(v)# v will be further consider in next pass\n level = next_level",
"def bfs_paths(self, start, goal):\n queue = [(start, [start])]\n while queue:\n (vertex, path) = queue.pop(0)\n for next in self.get_adj(vertex) - set(path):\n if next == goal:\n yield path + [next]\n else:\n queue.append((next, path + [next]))"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Create GUI for train model tab
|
def create_train_tab(self, tab_control):
train_tab = ttk.Frame(tab_control)
# Data dir selection
train_tab_data_dir_label = ttk.Label(train_tab, text="Data Dir : ").place(x=20, y=20)
train_tab_data_dir_entry = ttk.Entry(train_tab, width=70)
train_tab_data_dir_entry.place(x=110, y=20) # have to place in a new line for use insert
train_tab_data_dir_browse_button = ttk.Button(train_tab, text="Select Dir", command=lambda: self.select_dir(train_tab_data_dir_entry)).place(x=550, y=20)
# Log dir selection
train_tab_log_dir_label = ttk.Label(train_tab, text="Log Dir : ").place(x=20, y=50)
train_tab_log_dir_entry = ttk.Entry(train_tab, width=70)
train_tab_log_dir_entry.place(x=110, y=50) # have to place in a new line for use insert
train_tab_log_dir_browse_button = ttk.Button(train_tab, text="Select Dir", command=lambda: self.select_dir(train_tab_log_dir_entry)).place(x=550, y=50)
# Model output dir selection
train_tab_model_out_dir_label = ttk.Label(train_tab, text="Model Out Dir : ").place(x=20, y=80)
train_tab_model_out_dir_entry = ttk.Entry(train_tab, width=70)
train_tab_model_out_dir_entry.place(x=110, y=80) # have to place in a new line for use insert
train_tab_model_out_dir_browse_button = ttk.Button(train_tab, text="Select Dir", command=lambda: self.select_dir(train_tab_model_out_dir_entry)).place(x=550, y=80)
# Batch size
train_tab_batch_size_label = ttk.Label(train_tab, text="Batch Size : ").place(x=20, y=110)
train_tab_batch_size_entry = ttk.Entry(train_tab, width=20)
train_tab_batch_size_entry.place(x=110, y=110)
# Epoch size
train_tab_epoch_size_label = ttk.Label(train_tab, text="Epoch Size : ").place(x=20, y=140)
train_tab_epoch_size_entry = ttk.Entry(train_tab, width=20)
train_tab_epoch_size_entry.place(x=110, y=140)
train_tab_start_train_button = ttk.Button(train_tab, text="Start Train", command=lambda: self.start_train_model(train_tab_data_dir_entry,
train_tab_log_dir_entry,
train_tab_model_out_dir_entry,
train_tab_batch_size_entry,
train_tab_epoch_size_entry))
train_tab_start_train_button.place(x=constants.GUI_WIDTH - 100, y=constants.GUI_HEIGHT - 75)
tab_control.add(train_tab, text=" Train Model ")
|
[
"def create_classifier_tab(self, tab_control):\n # Classifier data tab\n classifier_tab = ttk.Frame(tab_control)\n classifier_tab_data_dir_label = ttk.Label(classifier_tab, text=\"Data Dir : \").place(x=20, y=20)\n classifier_tab_data_dir_entry = ttk.Entry(classifier_tab, width=70)\n classifier_tab_data_dir_entry.place(x=110, y=20)\n classifier_tab_data_dir_browse_button = ttk.Button(classifier_tab, text=\"Select Dir\", command=lambda: self.select_dir(classifier_tab_data_dir_entry)).place(x=550, y=20)\n\n # output dir selection\n classifier_tab_model_dir_label = ttk.Label(classifier_tab, text=\"Model Dir : \").place(x=20, y=50)\n classifier_tab_model_dir_entry = ttk.Entry(classifier_tab, width=70)\n classifier_tab_model_dir_entry.place(x=110, y=50)\n classifier_tab_model_dir_browse_button = ttk.Button(classifier_tab, text=\"Select Dir\", command=lambda: self.select_dir(classifier_tab_model_dir_entry)).place(x=550, y=50)\n\n # output dir selection\n classifier_tab_output_dir_label = ttk.Label(classifier_tab, text=\"Output Dir : \").place(x=20, y=80)\n classifier_tab_output_dir_entry = ttk.Entry(classifier_tab, width=70)\n classifier_tab_output_dir_entry.place(x=110, y=80)\n classifier_tab_output_dir_browse_button = ttk.Button(classifier_tab, text=\"Select Dir\", command=lambda: self.select_dir(classifier_tab_output_dir_entry)).place(x=550, y=80)\n\n # Text Area\n # Horizontal (x) Scroll bar\n xscrollbar = Scrollbar(classifier_tab, orient=HORIZONTAL)\n xscrollbar.place(x=20, y=320, width=530)\n\n # Vertical (y) Scroll Bar\n yscrollbar = Scrollbar(classifier_tab, orient=VERTICAL)\n yscrollbar.place(x=550, y=140, height=210)\n\n classifier_tab_textarea = Text(classifier_tab, wrap=NONE, xscrollcommand=xscrollbar.set, yscrollcommand=yscrollbar.set)\n classifier_tab_textarea.place(x=20, y=140, width=530, height=180)\n xscrollbar.config(command=classifier_tab_textarea.xview)\n yscrollbar.config(command=classifier_tab_textarea.yview)\n\n # Classifier button\n align_data_start_train_button = ttk.Button(classifier_tab, text=\"Start generate classifier\",\n command=lambda: self.start_classifier_data(classifier_tab_data_dir_entry, classifier_tab_model_dir_entry, classifier_tab_output_dir_entry, classifier_tab_textarea))\n align_data_start_train_button.place(x=110, y=110, width=425)\n\n tab_control.add(classifier_tab, text=\" Generate Classifier \")",
"def create_image_recognition_tab(self, tab_control):\n image_recog_tab = ttk.Frame(tab_control)\n image_recog_tab_data_dir_label = ttk.Label(image_recog_tab, text=\"Image file\").place(x=20, y=20)\n image_recog_tab_data_dir_entry = ttk.Entry(image_recog_tab, width=70)\n image_recog_tab_data_dir_entry.place(x=110, y=20)\n image_recog_tab_data_dir_browse_button = ttk.Button(image_recog_tab, text=\"Select File\", command=lambda: self.select_file(image_recog_tab_data_dir_entry)).place(x=550, y=20)\n\n # Classifier button\n align_data_start_train_button = ttk.Button(image_recog_tab, text=\"Start Recognize\", command=lambda: self.start_image_recognition(image_recog_tab_data_dir_entry, image_recog_tab))\n align_data_start_train_button.place(x=110, y=50, width=425)\n\n tab_control.add(image_recog_tab, text=\" Recognition Image \")",
"def ui():\n win = ControlWindow()\n win.show()",
"def setup_ui(self):\n self.import_layout.addWidget(self.load_c3d_button, 0, 0)\n self.import_layout.addWidget(self.clear_button, 0, 5)\n self.import_layout.addWidget(self.takes_table, 1, 0, 5, 10)\n self.import_layout.addWidget(self.batch_solve_button, 6, 0)\n\n # setup takes table\n column_count = len(self.takes_table_headers)\n self.takes_table.setColumnCount(column_count)\n self.takes_table.setHorizontalHeaderLabels(self.takes_table_headers)\n\n self.set_ui_style()",
"def gui():\n logger.info('Starting Keithley GUI') \n k = KeithleyForceUI()\n k.configure_traits()",
"def launch_data_processing_UI(self):\r\n self.window = QtWidgets.QMainWindow()\r\n # self.ui = CustomApplicationLauncherWindow(current_working_directory)\r\n self.ui = CustomApplicationLauncherWindow(\r\n self.names, self.current_working_directory, self.model_name)\r\n self.ui.setupUi(self.window)\r\n self.window.show()\r\n self.thread.stop() # stop webcam\r\n self.automatic_photos_taker.hide() # hide window\r",
"def _create_batch_tab(self, nb: ttk.Notebook) -> None:\n frame = ttk.Frame(nb)\n nb.add(frame, text=' Batch ', underline=2)",
"def create_tabs(self):\n\n # Tabs\n self.create_setup_tab()\n self.create_part_location_tab()\n self.create_order_tab()\n self.create_challenge_tab()\n self.tab_control.pack(expand=1, fill=\"both\", padx=5, pady=5)",
"def modelPanel(barLayout=bool, docTag=\"string\", defineTemplate=\"string\", parent=\"string\", useTemplate=\"string\", tearOff=bool, label=\"string\", replacePanel=\"string\", unParent=bool, tearOffCopy=\"string\", camera=\"string\", isUnique=bool, createString=bool, needsInit=bool, exists=bool, control=bool, menuBarVisible=bool, init=bool, modelEditor=bool, tearOffRestore=bool, popupMenuProcedure=\"string\", editString=bool, copy=\"string\"):\n pass",
"def show_gui(self):\n self.gui = Browser_GUI(self)",
"def pb_add_callback():\n \n self.dialog_by_model[self.model](1).exec_()\n self.show_table(self.model)",
"def _build_tabs(self, root: Tk) -> None:\r\n tab_control = ttk.Notebook(root)\r\n self.main_tab = LabelFrame(tab_control, labelanchor=NW, fg='black', text='---')\r\n self.log_tab = LabelFrame(tab_control, labelanchor=NW, fg='black', text='LOG')\r\n \r\n tab_control.add(self.main_tab, text=f\"{'Main':^30s}\")\r\n tab_control.add(self.log_tab,text=f\"{'Work log':^30s}\")\r\n tab_control.pack(expand=1, fill='both')",
"def LoadNotebook(self):\n self.tabs = []\n \n self.tab_startup = panel_startup.PanelStartup(parent=self.notebook)\n self.tab_sample = panel_sample.PanelSample(parent=self.notebook)\n self.tab_goniometer = panel_goniometer.PanelGoniometer(parent=self.notebook)\n self.tab_experiment = panel_experiment.PanelExperiment(parent=self.notebook)\n if not gui_utils.fourcircle_mode():\n self.tab_add = panel_add_positions.PanelAddPositions(parent=self.notebook)\n self.tab_try = panel_try_position.PanelTryPosition(parent=self.notebook)\n self.tab_detectors = panel_detectors.PanelDetectors(parent=self.notebook)\n\n\n def AddPage(tab, title, mac_title=\"\", select=False):\n if (gui_utils.is_mac() or gui_utils.is_windows()) and not (mac_title==\"\"):\n title = mac_title\n self.notebook.AddPage(tab, title, select)\n\n AddPage(self.tab_startup, 'Q-Space', 'Q-Space', select=True)\n if not gui_utils.fourcircle_mode():\n AddPage(self.tab_detectors, 'Detectors')\n AddPage(self.tab_goniometer, 'Goniometer')\n AddPage(self.tab_sample, 'Sample')\n if not gui_utils.fourcircle_mode():\n AddPage(self.tab_try, 'Try an\\nOrientation', 'Try Orientation')\n AddPage(self.tab_add, 'Add\\nOrientations', 'Add Orientations')\n AddPage(self.tab_experiment, 'Experiment\\nPlan', 'Experiment Plan' )\n\n self.notebook.Bind(wx.EVT_NOTEBOOK_PAGE_CHANGING, self.onNotebookPageChanging)",
"def main():\n lbls = imageio.v2.imread(Path(\"sample_data/test_labels.tif\"))\n lbls2 = np.zeros_like(lbls)\n lbls2[:, 3:, 2:] = lbls[:, :-3, :-2]\n lbls2 = lbls2 * 20\n\n labels = np.unique(lbls)[1:]\n labels_2 = np.unique(lbls2)[1:]\n\n viewer = napari.Viewer()\n lbls_layer = viewer.add_labels(lbls)\n lbls_layer2 = viewer.add_labels(lbls2)\n\n lbls_layer.features = make_features(labels, roi_id=\"ROI1\", n_features=6)\n lbls_layer2.features = make_features(labels_2, roi_id=\"ROI2\", n_features=6)\n # classifier_widget = ClassifierWidget(viewer)\n\n # viewer.window.add_dock_widget(classifier_widget)\n viewer.show(block=True)",
"def init_ui(self):\n # customize GUI\n self.ok_pb.setText(\"Colin, I love you!\")\n self.cancel_pb.setText(\"Okay, got it\")\n self.okWindow = OKWindow()\n\n # init changelog information\n # make a tab for each date recorded\n #\n changelog = Changelog()\n self.tabWidget = QtGui.QTabWidget(self.centralwidget)\n\n # Reorder the dict from most recent to least\n htmlDict = htmlparser.get_changelog()\n htmlDict = collections.OrderedDict(sorted(htmlDict.items(),\n key=lambda t: t[0]))\n htmlDict = htmlDict.items()\n htmlDict.reverse()\n htmlDict = collections.OrderedDict(htmlDict)\n\n # set the sections to upper to simplify testing\n sectionGlobal = [x.upper() for x in changelog.sectionGlob]\n sectionList = [x.upper() for x in changelog.sectionList]\n for key, items in htmlDict.iteritems():\n label = QtGui.QLabel(self.tabWidget)\n label.setAlignment(QtCore.Qt.AlignLeading|QtCore.Qt.AlignLeft|QtCore.Qt.AlignTop)\n tabToAdd = QtGui.QWidget()\n gridLayout = QtGui.QGridLayout(tabToAdd)\n gridLayout.addWidget(label)\n text = ''\n for k, itms in htmlDict[key].iteritems():\n if (k.upper() in sectionGlobal or k.upper() in sectionList) \\\n and itms != []:\n text += k + '\\n' # add the section name as text\n itms = ['- ' + x for x in itms]\n text += '\\n'.join(itms) # add each point as text\n text += '\\n\\n'\n label.setText(text)\n tabIndex = self.tabWidget.addTab(tabToAdd, key)\n # add grid to the new tab page and place QLabel inside of it\n\n self.tabWidget.setCurrentIndex(0)\n # add tab widget to main\n self.gridLayout.addWidget(self.tabWidget, 1, 0, 1, 3)\n\n # change the all the text\n for f in self.findChildren(QtGui.QLabel):\n formText = str(f.text()).strip()\n if f.objectName() == \"project_l\":\n f.setText(formText.format(proj=consts.PROJECT_NAME_LONG))\n elif f.objectName() == \"version_l\":\n f.setText(formText.format(version=consts.__version__))",
"def __create_tabs(self):\r\n self.tab1 = tk.Frame(self.note)\r\n self.tab2 = tk.Frame(self.note)\r\n self.tab3 = tk.Frame(self.note)\r\n self.note.add(self.tab1, text=\" Lines \")\r\n self.note.add(self.tab2, text=\" Stops \")\r\n self.note.add(self.tab3, text=\" Buses \")\r\n self.note.pack(side=tk.TOP)",
"def create_widgets(self):\n # Cria barra de menus\n self.create_menubar()\n\n # Cria frame de botoes\n self.create_buttons_frame()\n\n # Cria frame para exibicao dos automatos\n self.create_tabbed_frame()\n\n # Cria frame de selecao de automatos para operacoes\n self.create_selection_frame()",
"def construct_notebook(self):\n panel = Panel(self)\n self.notebook = Notebook(panel, style=NB_LEFT)\n self.construct_tabs()\n sizer = BoxSizer(HORIZONTAL)\n sizer.Add(self.notebook, 1, EXPAND)\n panel.SetSizer(sizer)",
"def makeTab(self, name):\n\t\tself.divies.append(JPLDivies('makeTab',name=name))"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Create GUI for align data tab
|
def create_align_tab(self, tab_control):
# Align data tab
align_data_tab = ttk.Frame(tab_control)
align_data_tab_data_dir_label = ttk.Label(align_data_tab, text="Data Dir : ").place(x=20, y=20)
align_data_tab_data_dir_entry = ttk.Entry(align_data_tab, width=70)
align_data_tab_data_dir_entry.place(x=110, y=20)
align_data_tab_data_dir_browse_button = ttk.Button(align_data_tab, text="Select Dir", command=lambda: self.select_dir(align_data_tab_data_dir_entry)).place(x=550, y=20)
# output dir selection
align_data_tab_output_dir_label = ttk.Label(align_data_tab, text="Output Dir : ").place(x=20, y=50)
align_data_tab_output_dir_entry = ttk.Entry(align_data_tab, width=70)
align_data_tab_output_dir_entry.place(x=110, y=50)
align_data_tab_output_dir_browse_button = ttk.Button(align_data_tab, text="Select Dir", command=lambda: self.select_dir(align_data_tab_output_dir_entry)).place(x=550, y=50)
# Text Area
# Horizontal (x) Scroll bar
xscrollbar = Scrollbar(align_data_tab, orient=HORIZONTAL)
xscrollbar.place(x=20, y=320, width=530)
# Vertical (y) Scroll Bar
yscrollbar = Scrollbar(align_data_tab, orient=VERTICAL)
yscrollbar.place(x=550, y=110, height=210)
align_data_textarea = Text(align_data_tab, wrap=NONE, xscrollcommand=xscrollbar.set, yscrollcommand=yscrollbar.set)
align_data_textarea.place(x=20, y=110, width=530, height=210)
xscrollbar.config(command=align_data_textarea.xview)
yscrollbar.config(command=align_data_textarea.yview)
# Align button
align_data_start_train_button = ttk.Button(align_data_tab, text="Start Align",
command=lambda: self.start_align_data(align_data_tab_data_dir_entry, align_data_tab_output_dir_entry, align_data_textarea))
align_data_start_train_button.place(x=110, y=80, width=425)
tab_control.add(align_data_tab, text=" Align Data ")
|
[
"def create_tabs(self):\n\n # Tabs\n self.create_setup_tab()\n self.create_part_location_tab()\n self.create_order_tab()\n self.create_challenge_tab()\n self.tab_control.pack(expand=1, fill=\"both\", padx=5, pady=5)",
"def __create_tabs(self):\r\n self.tab1 = tk.Frame(self.note)\r\n self.tab2 = tk.Frame(self.note)\r\n self.tab3 = tk.Frame(self.note)\r\n self.note.add(self.tab1, text=\" Lines \")\r\n self.note.add(self.tab2, text=\" Stops \")\r\n self.note.add(self.tab3, text=\" Buses \")\r\n self.note.pack(side=tk.TOP)",
"def create_classifier_tab(self, tab_control):\n # Classifier data tab\n classifier_tab = ttk.Frame(tab_control)\n classifier_tab_data_dir_label = ttk.Label(classifier_tab, text=\"Data Dir : \").place(x=20, y=20)\n classifier_tab_data_dir_entry = ttk.Entry(classifier_tab, width=70)\n classifier_tab_data_dir_entry.place(x=110, y=20)\n classifier_tab_data_dir_browse_button = ttk.Button(classifier_tab, text=\"Select Dir\", command=lambda: self.select_dir(classifier_tab_data_dir_entry)).place(x=550, y=20)\n\n # output dir selection\n classifier_tab_model_dir_label = ttk.Label(classifier_tab, text=\"Model Dir : \").place(x=20, y=50)\n classifier_tab_model_dir_entry = ttk.Entry(classifier_tab, width=70)\n classifier_tab_model_dir_entry.place(x=110, y=50)\n classifier_tab_model_dir_browse_button = ttk.Button(classifier_tab, text=\"Select Dir\", command=lambda: self.select_dir(classifier_tab_model_dir_entry)).place(x=550, y=50)\n\n # output dir selection\n classifier_tab_output_dir_label = ttk.Label(classifier_tab, text=\"Output Dir : \").place(x=20, y=80)\n classifier_tab_output_dir_entry = ttk.Entry(classifier_tab, width=70)\n classifier_tab_output_dir_entry.place(x=110, y=80)\n classifier_tab_output_dir_browse_button = ttk.Button(classifier_tab, text=\"Select Dir\", command=lambda: self.select_dir(classifier_tab_output_dir_entry)).place(x=550, y=80)\n\n # Text Area\n # Horizontal (x) Scroll bar\n xscrollbar = Scrollbar(classifier_tab, orient=HORIZONTAL)\n xscrollbar.place(x=20, y=320, width=530)\n\n # Vertical (y) Scroll Bar\n yscrollbar = Scrollbar(classifier_tab, orient=VERTICAL)\n yscrollbar.place(x=550, y=140, height=210)\n\n classifier_tab_textarea = Text(classifier_tab, wrap=NONE, xscrollcommand=xscrollbar.set, yscrollcommand=yscrollbar.set)\n classifier_tab_textarea.place(x=20, y=140, width=530, height=180)\n xscrollbar.config(command=classifier_tab_textarea.xview)\n yscrollbar.config(command=classifier_tab_textarea.yview)\n\n # Classifier button\n align_data_start_train_button = ttk.Button(classifier_tab, text=\"Start generate classifier\",\n command=lambda: self.start_classifier_data(classifier_tab_data_dir_entry, classifier_tab_model_dir_entry, classifier_tab_output_dir_entry, classifier_tab_textarea))\n align_data_start_train_button.place(x=110, y=110, width=425)\n\n tab_control.add(classifier_tab, text=\" Generate Classifier \")",
"def create_train_tab(self, tab_control):\n train_tab = ttk.Frame(tab_control)\n # Data dir selection\n train_tab_data_dir_label = ttk.Label(train_tab, text=\"Data Dir : \").place(x=20, y=20)\n train_tab_data_dir_entry = ttk.Entry(train_tab, width=70)\n train_tab_data_dir_entry.place(x=110, y=20) # have to place in a new line for use insert\n train_tab_data_dir_browse_button = ttk.Button(train_tab, text=\"Select Dir\", command=lambda: self.select_dir(train_tab_data_dir_entry)).place(x=550, y=20)\n\n # Log dir selection\n train_tab_log_dir_label = ttk.Label(train_tab, text=\"Log Dir : \").place(x=20, y=50)\n train_tab_log_dir_entry = ttk.Entry(train_tab, width=70)\n train_tab_log_dir_entry.place(x=110, y=50) # have to place in a new line for use insert\n train_tab_log_dir_browse_button = ttk.Button(train_tab, text=\"Select Dir\", command=lambda: self.select_dir(train_tab_log_dir_entry)).place(x=550, y=50)\n\n # Model output dir selection\n train_tab_model_out_dir_label = ttk.Label(train_tab, text=\"Model Out Dir : \").place(x=20, y=80)\n train_tab_model_out_dir_entry = ttk.Entry(train_tab, width=70)\n train_tab_model_out_dir_entry.place(x=110, y=80) # have to place in a new line for use insert\n train_tab_model_out_dir_browse_button = ttk.Button(train_tab, text=\"Select Dir\", command=lambda: self.select_dir(train_tab_model_out_dir_entry)).place(x=550, y=80)\n\n # Batch size\n train_tab_batch_size_label = ttk.Label(train_tab, text=\"Batch Size : \").place(x=20, y=110)\n train_tab_batch_size_entry = ttk.Entry(train_tab, width=20)\n train_tab_batch_size_entry.place(x=110, y=110)\n\n # Epoch size\n train_tab_epoch_size_label = ttk.Label(train_tab, text=\"Epoch Size : \").place(x=20, y=140)\n train_tab_epoch_size_entry = ttk.Entry(train_tab, width=20)\n train_tab_epoch_size_entry.place(x=110, y=140)\n\n train_tab_start_train_button = ttk.Button(train_tab, text=\"Start Train\", command=lambda: self.start_train_model(train_tab_data_dir_entry,\n train_tab_log_dir_entry,\n train_tab_model_out_dir_entry,\n train_tab_batch_size_entry,\n train_tab_epoch_size_entry))\n train_tab_start_train_button.place(x=constants.GUI_WIDTH - 100, y=constants.GUI_HEIGHT - 75)\n tab_control.add(train_tab, text=\" Train Model \")",
"def _build_tabs(self, root: Tk) -> None:\r\n tab_control = ttk.Notebook(root)\r\n self.main_tab = LabelFrame(tab_control, labelanchor=NW, fg='black', text='---')\r\n self.log_tab = LabelFrame(tab_control, labelanchor=NW, fg='black', text='LOG')\r\n \r\n tab_control.add(self.main_tab, text=f\"{'Main':^30s}\")\r\n tab_control.add(self.log_tab,text=f\"{'Work log':^30s}\")\r\n tab_control.pack(expand=1, fill='both')",
"def view_alignment(self,aln, fontsize=\"9pt\", plot_width=800):\n \n #make sequence and id lists from the aln object\n seqs = [rec.seq for rec in (aln)]\n ids = [rec.id for rec in aln]\n #plus longue seq\n sizes = [len(rec) for rec in seqs]\n #taille=max(sizes)\n taille=min(sizes)\n #résultat :['a','c','-',...]\n text = [i for s in list(seqs) for i in s]\n #résultat :['green','red','white',...]\n colors = self.get_colors(seqs)\n #longueur des chaines (fixe)\n #N = len(seqs[0])\n N=taille\n #Nombre de séquences\n S = len(seqs) \n width = .4\n \n x = numpy.arange(1,N+1)\n y = numpy.arange(0,S,1)\n #creates a 2D grid of coords from the 1D arrays\n xx, yy = numpy.meshgrid(x, y)\n #flattens the arrays/maillage (Affichage de longueur)\n gx = xx.ravel()\n gy = yy.flatten()\n #use recty for rect coords with an offset\n recty = gy+.5\n h= 1/S\n \n #now we can create the ColumnDataSource with all the arrays\n source = ColumnDataSource(dict(x=gx, y=gy, recty=recty, text=text, colors=colors))\n plot_height = len(seqs)*15+50\n x_range = Range1d(0,N+1, bounds='auto')\n if N>100:\n viewlen=100\n else:\n viewlen=N\n #view_range is for the close up view\n view_range = (0,viewlen)\n tools=\"xpan, xwheel_zoom, reset, save\"\n \n \n #entire sequence view (no text, with zoom)\n p = figure(title=None, plot_width= plot_width, plot_height=50,\n x_range=x_range, y_range=(0,S), tools=tools,\n min_border=0, toolbar_location='below')\n rects = Rect(x=\"x\", y=\"recty\", width=1, height=1, fill_color=\"colors\",\n line_color=None, fill_alpha=0.6)\n p.add_glyph(source, rects)\n p.yaxis.visible = False\n p.grid.visible = False \n \n #sequence text view with ability to scroll along x axis\n p1 = figure(title=None, plot_width=plot_width, plot_height=plot_height,\n x_range=view_range, y_range=ids, tools=\"xpan,reset\",\n min_border=0, toolbar_location='below')#, lod_factor=1) \n glyph = Text(x=\"x\", y=\"y\", text=\"text\", text_align='center',text_color=\"black\",\n text_font=\"monospace\",text_font_size=fontsize)\n rects = Rect(x=\"x\", y=\"recty\", width=1, height=1, fill_color=\"colors\",\n line_color=None, fill_alpha=0.4)\n p1.add_glyph(source, glyph)\n p1.add_glyph(source, rects)\n \n p1.grid.visible = False\n p1.xaxis.major_label_text_font_style = \"bold\"\n p1.yaxis.minor_tick_line_width = 0\n p1.yaxis.major_tick_line_width = 0\n \n p = gridplot([[p],[p1]], toolbar_location='below')\n script, div = components(p)\n cdn_js=CDN.js_files[0]\n return p",
"def create_part_location_tab(self):\n part_location_tab = ttk.Frame(self.tab_control)\n\n part_location_tab.grid_columnconfigure(0, weight=1)\n part_location_tab.grid_columnconfigure(1, weight=1)\n part_location_tab.grid_rowconfigure(0, weight=1)\n\n # Left window\n self.left_part_location_frame = ttk.Frame(part_location_tab)\n self.left_part_location_frame.grid(row=0, column=0, sticky=\"nesw\")\n # Right window\n self.right_part_location_frame = ttk.Frame(part_location_tab)\n self.right_part_location_frame.grid(row=0, column=1, sticky=\"nesw\")\n\n # Title of the tab\n self.tab_control.add(\n part_location_tab, text='Part Locations', compound=TOP)\n\n # Description of the tab\n ttk.Label(self.left_part_location_frame,\n text=\"Information on part locations.\",\n font='Arial 17 bold', anchor='w').grid(column=0,\n row=0,\n sticky='w',\n padx=10,\n pady=30)\n\n self.tab1_option0_selected_agv_cb = ttk.Combobox(\n self.left_part_location_frame,\n textvariable=self.tab1_option0_selected_agv_value,\n state='readonly',\n width=5,\n font='Arial 12',\n values=['None', 'agv1', 'agv2', 'agv3', 'agv4'])\n\n self.tab1_option0_selected_agv_cb.grid(column=0, row=1, padx=270, pady=0)\n\n # set the default text\n self.tab1_option0_selected_agv_cb.set('None')\n\n self.tab1_option0_selected_agv_cb.bind(\n '<<ComboboxSelected>>', self.on_agv_selected_callback)\n\n ttk.Label(self.left_part_location_frame,\n text=\"Part location on AGV(s):\",\n font='Arial 12', anchor='w').grid(column=0,\n row=1,\n sticky='w',\n padx=30,\n pady=0)",
"def setup_ui(self):\n self.import_layout.addWidget(self.load_c3d_button, 0, 0)\n self.import_layout.addWidget(self.clear_button, 0, 5)\n self.import_layout.addWidget(self.takes_table, 1, 0, 5, 10)\n self.import_layout.addWidget(self.batch_solve_button, 6, 0)\n\n # setup takes table\n column_count = len(self.takes_table_headers)\n self.takes_table.setColumnCount(column_count)\n self.takes_table.setHorizontalHeaderLabels(self.takes_table_headers)\n\n self.set_ui_style()",
"def add_tab(self):\n if (len(self.tab_list) > 6):\n dialog = ErrorDialog('No more than 6 transforms allowed')\n dialog.size_hint = (0.7,0.6)\n dialog.pos_hint = {'x':0.15,'y':0.2}\n return\n \n pos = self.tab_list.index(self.current_tab)\n content = TransformPanel()\n content.bind(transform=self.recalculate)\n panel = TabbedPanelHeader(text='',content=content)\n panel.background_color = (0.8,0.8,0.5)\n panel.background_down = 'a5lib/uix/tab_down.png'\n panel.background_normal = 'a5lib/uix/tab_up.png'\n self.add_widget(panel)\n for x in range(pos):\n self.shuffle_tab(x,True)\n tab1 = self.tab_list[pos+1]\n tab2 = self.tab_list[pos]\n \n tab1.state = 'normal'\n tab2.state = 'down'\n self.switch_to(self.tab_list[pos])\n # Tab is identity; no recalculation needed.",
"def _layout_distance(self):\n distance_txt = wx.StaticText(self, -1, 'Sample to Detector Distance : ')\n self.distance_tcl = wx.TextCtrl(self, -1,\n size=(_BOX_WIDTH, 20), style=0)\n distance_unit_txt = wx.StaticText(self, -1, 'Unit: ')\n self.distance_unit_tcl = wx.TextCtrl(self, -1,\n size=(_BOX_WIDTH, 20), style=0)\n self.distance_sizer.AddMany([(distance_txt, 0, wx.LEFT | wx.RIGHT, 10),\n (self.distance_tcl, 0, wx.RIGHT, 10),\n (distance_unit_txt, 0, wx.EXPAND),\n (self.distance_unit_tcl, 0, wx.RIGHT, 10)])",
"def initQueryUI(self): \n self.initQueryButtons()\n self.initQueryTextBox()\n self.initResultsTable()\n \n self.tabsVerticalLayout.setStretch(2, 1)",
"def hdictui(arg):\n global tabnum\n global num_tabs\n tabnum = num_tabs = 0\n tab_names = [[], []]\n for i in arg:\n num_tabs += 1\n tab_names[0].append(i['name'].lower())\n tab_names[1].append(i['name'].upper())\n while True:\n # Tab headers.\n wrap_erase()\n if xsize >= 80:\n s = \"Home left a h 4\"\n wrap_addstr(0, 0, s)\n wrap_addstr(0, len(s), \"::\")\n x_pos = len(s) + 2\n for i in range(num_tabs):\n if i == tabnum:\n wrap_addstr(0, x_pos, tab_names[1][i])\n else:\n wrap_addstr(0, x_pos, tab_names[0][i])\n x_pos += len(tab_names[0][i])\n wrap_addstr(0, x_pos, \":\")\n x_pos += 1\n wrap_addstr(0, x_pos, \":6 l d right end\")\n # zxcv\n if have_clipboard:\n wrap_addstr(ysize - 2, 0, \"(z/b) undo : (x/n) redo : (c/m)\" +\n \" Make backup : (v/,) Clear clipboard : (^C) quit\")\n else:\n wrap_addstr(ysize - 2, 0, \"(z/b) undo : (x/n) redo : (c/m)\" +\n \" Make backup : (^C) quit\")\n # Lines.\n wrap_hline(1, 0, ord(\"=\"), xsize)\n wrap_hline(ysize - 3, 0, ord(\"=\"), xsize)\n wrap_refresh()\n else:\n pass #TODO\n # Tab content.\n the_dict = arg[tabnum]\n the_type = the_dict['type']\n if the_type == 'list_choice':\n result = list_choice(2, ysize - 5, the_dict['choices'], True)\n if not isinstance(result, bool):\n # Call custom function with an alias for the result.\n the_dict['function'](the_dict['aliases'][result])\n elif the_type == 'roll_text':\n roll_text(2, ysize - 5, the_dict['text'], True, zxcv_handler)\n else:\n assert False, \"Odd type '{0}' in {1}\".format(the_type, the_dict)",
"def createDataSelectorWidgets (self,parent,parent_layout):;\n \n #print('in createDataSelectionWidgets')\n self._ds_top = top = QWidget(parent);\n parent_layout.addWidget(top);\n self._ds_lo = lotop = QVBoxLayout(top);\n lotop.setContentsMargins(0,0,0,0);\n self._ds_complex = QWidget(top);\n self._ds_complex.setVisible(False);\n lotop.addWidget(self._ds_complex);\n lo = QVBoxLayout(self._ds_complex);\n lo.setContentsMargins(0,0,0,0);\n lab = QLabel(\"complex:\");\n lab.setAlignment(Qt.AlignHCenter);\n lo.addWidget(lab);\n # add complex selector\n lo0 = QHBoxLayout();\n lo0.setContentsMargins(0,0,0,0);\n lo.addLayout(lo0);\n lo1 = QGridLayout()\n lo1.setContentsMargins(0,0,0,0);\n lo1.setHorizontalSpacing(0);\n lo1.setVerticalSpacing(0);\n# lo0.addStretch(1);\n lo0.addLayout(lo1);\n# lo0.addStretch(1);\n bgrp = QButtonGroup(self._ds_complex);\n# tbdesc = { self.AMP:(u\"\\u007Ca\\u007C\",0,0),self.PHASE:(u\"\\u03D5\",0,1),self.REAL:(\"Re\",1,0),self.IMAG:(\"Im\",1,1) };\n# tbdesc = { self.AMP:(\"\\\\u007Ca\\\\u007C\",0,0),self.PHASE:(\"\\\\u0278\",0,1),self.REAL:(\"Re\",1,0),self.IMAG:(\"Im\",1,1) };\n tbdesc = { self.AMP:(\"Amp\",0,0),self.PHASE:(\"Pha\",0,1),self.REAL:(\"Re\",1,0),self.IMAG:(\"Im\",1,1) };\n for label,qa in list(self._qas_complex.items()):\n tbtext,row,col = tbdesc[label];\n tb = QToolButton(self._ds_complex);\n lo1.addWidget(tb,row,col);\n bgrp.addButton(tb);\n tb.setText(tbtext);\n tb.setToolButtonStyle(Qt.ToolButtonTextOnly);\n tb.setSizePolicy(QSizePolicy.MinimumExpanding,QSizePolicy.Minimum);\n tb.setCheckable(True);\n tb.setChecked(label is self.complex_component);\n tb.setMinimumWidth(32);\n tb.clicked[bool].connect(qa.setChecked)\n tb.clicked[bool].connect(self._change_complex)\n qa.triggered[bool].connect(tb.setChecked)\n self._tbs_complex[label] = tb;",
"def _init_tabs(self):\n\n # Loop over number of DUTs and create tmp setup and options for each DUT\n for i in range(self.setup['n_duts']):\n\n tmp_setup = {}\n tmp_options = {}\n\n # Fill setup for i_th DUT\n for s_key in self.setup.keys():\n # Tuples and lists have DUT specific info; loop and assign the respective i_th entry to the tmp setup\n if isinstance(self.setup[s_key], list) or isinstance(self.setup[s_key], tuple):\n tmp_setup[s_key] = self.setup[s_key][i]\n # General info valid for all DUTs\n else:\n tmp_setup[s_key] = self.setup[s_key]\n\n # Fill options for i_th DUT\n for o_key in self.options.keys():\n # Tuples and lists have DUT specific info; loop and assign the respective i_th entry to the tmp options\n if isinstance(self.options[o_key], list) or isinstance(self.options[o_key], tuple):\n tmp_options[o_key] = self.options[o_key][i]\n # General info valid for all DUTs\n else:\n tmp_options[o_key] = self.options[o_key]\n\n # Create widget\n widget = AnalysisWidget(parent=self.tabs, setup=tmp_setup, options=tmp_options, name=self.name,\n tab_list=self.tab_list)\n\n # Remove buttons and progressbar from AnalysisWidget instance; ParallelAnalysisWidget has one for all\n widget.btn_ok.deleteLater()\n widget.btn_rerun.deleteLater()\n widget.p_bar.deleteLater()\n\n # Add to tab widget\n self.tw[self.setup['dut_names'][i]] = widget\n self.tabs.addTab(self.tw[self.setup['dut_names'][i]], self.setup['dut_names'][i])",
"def __init__(self, anchor_positions, *args, **kwargs):\n\n super(AnchorPositionWindow, self).__init__(*args, **kwargs)\n self.setWindowTitle('Anchor Positions')\n\n # Create the variable that will hold the anchor positions\n self.anchor_positions = np.zeros((8,3))\n for i,p in enumerate(anchor_positions):\n self.anchor_positions[i] = p\n \n # Draw the window layout\n layout = QtWidgets.QGridLayout()\n self.setLayout(layout)\n\n self.anchorBox = []\n self.anchorLineEdits = []\n i = 0\n for row in range(2):\n for col in range(4):\n self.anchorBox.append(QtWidgets.QGroupBox('ID{}'.format(i)))\n\n anchorLayout = QtWidgets.QFormLayout()\n self.anchorBox[i].setLayout(anchorLayout)\n\n xline = QtWidgets.QLineEdit(str(self.anchor_positions[i][0]))\n xline.setValidator(QtGui.QDoubleValidator())\n yline = QtWidgets.QLineEdit(str(self.anchor_positions[i][1]))\n yline.setValidator(QtGui.QDoubleValidator())\n zline = QtWidgets.QLineEdit(str(self.anchor_positions[i][2]))\n zline.setValidator(QtGui.QDoubleValidator())\n self.anchorLineEdits.append([xline, yline, zline])\n anchorLayout.addRow('x', xline)\n anchorLayout.addRow('y', yline)\n anchorLayout.addRow('z', zline)\n\n layout.addWidget(self.anchorBox[i], row, col)\n i = i+1\n \n self.ok_button = QtWidgets.QPushButton('OK')\n self.ok_button.clicked.connect(self._ok_button_clicked)\n layout.addWidget(self.ok_button, 2,3)\n\n self.save_button = QtWidgets.QPushButton('Save as file')\n self.save_button.clicked.connect(self._save_button_clicked)\n layout.addWidget(self.save_button, 2,1)\n\n self.load_button = QtWidgets.QPushButton('Load')\n self.load_button.clicked.connect(self._load_button_clicked)\n layout.addWidget(self.load_button, 2,2)",
"def add_gui_section(self):\n self.sections[\"GUI\"] = QtGui.QStandardItem(\"GUI\")\n self.sections[\"GUI\"].setEditable(False)\n gui_section = {\"GapFillFromAlternate\": {\"period_option\": \"days\",\n \"start_date\": \"\", \"end_date\": \"\",\n \"number_days\": \"90\", \"number_months\": \"3\",\n \"auto_complete\": \"yes\", \"min_percent\": \"30\",\n \"overwrite\": \"no\", \"show_plots\": \"no\",\n \"show_all\": \"no\"}}\n for key1 in sorted(list(gui_section.keys())):\n gui_method = QtGui.QStandardItem(key1)\n gui_method.setEditable(False)\n for key2 in sorted(list(gui_section[key1].keys())):\n val = gui_section[key1][key2]\n child0 = QtGui.QStandardItem(key2)\n child0.setEditable(False)\n child1 = QtGui.QStandardItem(val)\n gui_method.appendRow([child0, child1])\n self.sections[\"GUI\"].appendRow(gui_method)\n self.model.insertRow(self.section_headings.index(\"Drivers\"), self.sections[\"GUI\"])\n self.update_tab_text()",
"def _version_tab(ok_cancel_box):\n version_data = get_version()\n\n grid = grid_from_dict(version_data)\n\n hbox = layout_to_hlayout(grid)\n vbox = layout_to_vlayout(hbox)\n\n #---------------------\n version_tab = QWidget()\n version_tab.setLayout(vbox)\n\n return version_tab",
"def set_up_tabs(self):\n _2D_maps_tab = QtGui.QWidget()\n _3D_maps_tab = QtGui.QWidget()\n\n self._2D_maps_tab_placement = QtGui.QGridLayout(_2D_maps_tab)\n self._3D_maps_tab_placement = QtGui.QGridLayout(_3D_maps_tab)\n\n self.tab_widget.addTab(_2D_maps_tab, \"2D Maps\")\n self.tab_widget.addTab(_3D_maps_tab, \"3D Maps\")",
"def construct_tabs(self):\n for key, config_list in self.groups.items():\n page = ConfigPage(self.notebook, config_list)\n self.notebook.AddPage(page, key)\n self.clean_edit_state()"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Create GUI for classifier Tab
|
def create_classifier_tab(self, tab_control):
# Classifier data tab
classifier_tab = ttk.Frame(tab_control)
classifier_tab_data_dir_label = ttk.Label(classifier_tab, text="Data Dir : ").place(x=20, y=20)
classifier_tab_data_dir_entry = ttk.Entry(classifier_tab, width=70)
classifier_tab_data_dir_entry.place(x=110, y=20)
classifier_tab_data_dir_browse_button = ttk.Button(classifier_tab, text="Select Dir", command=lambda: self.select_dir(classifier_tab_data_dir_entry)).place(x=550, y=20)
# output dir selection
classifier_tab_model_dir_label = ttk.Label(classifier_tab, text="Model Dir : ").place(x=20, y=50)
classifier_tab_model_dir_entry = ttk.Entry(classifier_tab, width=70)
classifier_tab_model_dir_entry.place(x=110, y=50)
classifier_tab_model_dir_browse_button = ttk.Button(classifier_tab, text="Select Dir", command=lambda: self.select_dir(classifier_tab_model_dir_entry)).place(x=550, y=50)
# output dir selection
classifier_tab_output_dir_label = ttk.Label(classifier_tab, text="Output Dir : ").place(x=20, y=80)
classifier_tab_output_dir_entry = ttk.Entry(classifier_tab, width=70)
classifier_tab_output_dir_entry.place(x=110, y=80)
classifier_tab_output_dir_browse_button = ttk.Button(classifier_tab, text="Select Dir", command=lambda: self.select_dir(classifier_tab_output_dir_entry)).place(x=550, y=80)
# Text Area
# Horizontal (x) Scroll bar
xscrollbar = Scrollbar(classifier_tab, orient=HORIZONTAL)
xscrollbar.place(x=20, y=320, width=530)
# Vertical (y) Scroll Bar
yscrollbar = Scrollbar(classifier_tab, orient=VERTICAL)
yscrollbar.place(x=550, y=140, height=210)
classifier_tab_textarea = Text(classifier_tab, wrap=NONE, xscrollcommand=xscrollbar.set, yscrollcommand=yscrollbar.set)
classifier_tab_textarea.place(x=20, y=140, width=530, height=180)
xscrollbar.config(command=classifier_tab_textarea.xview)
yscrollbar.config(command=classifier_tab_textarea.yview)
# Classifier button
align_data_start_train_button = ttk.Button(classifier_tab, text="Start generate classifier",
command=lambda: self.start_classifier_data(classifier_tab_data_dir_entry, classifier_tab_model_dir_entry, classifier_tab_output_dir_entry, classifier_tab_textarea))
align_data_start_train_button.place(x=110, y=110, width=425)
tab_control.add(classifier_tab, text=" Generate Classifier ")
|
[
"def create_image_recognition_tab(self, tab_control):\n image_recog_tab = ttk.Frame(tab_control)\n image_recog_tab_data_dir_label = ttk.Label(image_recog_tab, text=\"Image file\").place(x=20, y=20)\n image_recog_tab_data_dir_entry = ttk.Entry(image_recog_tab, width=70)\n image_recog_tab_data_dir_entry.place(x=110, y=20)\n image_recog_tab_data_dir_browse_button = ttk.Button(image_recog_tab, text=\"Select File\", command=lambda: self.select_file(image_recog_tab_data_dir_entry)).place(x=550, y=20)\n\n # Classifier button\n align_data_start_train_button = ttk.Button(image_recog_tab, text=\"Start Recognize\", command=lambda: self.start_image_recognition(image_recog_tab_data_dir_entry, image_recog_tab))\n align_data_start_train_button.place(x=110, y=50, width=425)\n\n tab_control.add(image_recog_tab, text=\" Recognition Image \")",
"def main():\n lbls = imageio.v2.imread(Path(\"sample_data/test_labels.tif\"))\n lbls2 = np.zeros_like(lbls)\n lbls2[:, 3:, 2:] = lbls[:, :-3, :-2]\n lbls2 = lbls2 * 20\n\n labels = np.unique(lbls)[1:]\n labels_2 = np.unique(lbls2)[1:]\n\n viewer = napari.Viewer()\n lbls_layer = viewer.add_labels(lbls)\n lbls_layer2 = viewer.add_labels(lbls2)\n\n lbls_layer.features = make_features(labels, roi_id=\"ROI1\", n_features=6)\n lbls_layer2.features = make_features(labels_2, roi_id=\"ROI2\", n_features=6)\n # classifier_widget = ClassifierWidget(viewer)\n\n # viewer.window.add_dock_widget(classifier_widget)\n viewer.show(block=True)",
"def create_train_tab(self, tab_control):\n train_tab = ttk.Frame(tab_control)\n # Data dir selection\n train_tab_data_dir_label = ttk.Label(train_tab, text=\"Data Dir : \").place(x=20, y=20)\n train_tab_data_dir_entry = ttk.Entry(train_tab, width=70)\n train_tab_data_dir_entry.place(x=110, y=20) # have to place in a new line for use insert\n train_tab_data_dir_browse_button = ttk.Button(train_tab, text=\"Select Dir\", command=lambda: self.select_dir(train_tab_data_dir_entry)).place(x=550, y=20)\n\n # Log dir selection\n train_tab_log_dir_label = ttk.Label(train_tab, text=\"Log Dir : \").place(x=20, y=50)\n train_tab_log_dir_entry = ttk.Entry(train_tab, width=70)\n train_tab_log_dir_entry.place(x=110, y=50) # have to place in a new line for use insert\n train_tab_log_dir_browse_button = ttk.Button(train_tab, text=\"Select Dir\", command=lambda: self.select_dir(train_tab_log_dir_entry)).place(x=550, y=50)\n\n # Model output dir selection\n train_tab_model_out_dir_label = ttk.Label(train_tab, text=\"Model Out Dir : \").place(x=20, y=80)\n train_tab_model_out_dir_entry = ttk.Entry(train_tab, width=70)\n train_tab_model_out_dir_entry.place(x=110, y=80) # have to place in a new line for use insert\n train_tab_model_out_dir_browse_button = ttk.Button(train_tab, text=\"Select Dir\", command=lambda: self.select_dir(train_tab_model_out_dir_entry)).place(x=550, y=80)\n\n # Batch size\n train_tab_batch_size_label = ttk.Label(train_tab, text=\"Batch Size : \").place(x=20, y=110)\n train_tab_batch_size_entry = ttk.Entry(train_tab, width=20)\n train_tab_batch_size_entry.place(x=110, y=110)\n\n # Epoch size\n train_tab_epoch_size_label = ttk.Label(train_tab, text=\"Epoch Size : \").place(x=20, y=140)\n train_tab_epoch_size_entry = ttk.Entry(train_tab, width=20)\n train_tab_epoch_size_entry.place(x=110, y=140)\n\n train_tab_start_train_button = ttk.Button(train_tab, text=\"Start Train\", command=lambda: self.start_train_model(train_tab_data_dir_entry,\n train_tab_log_dir_entry,\n train_tab_model_out_dir_entry,\n train_tab_batch_size_entry,\n train_tab_epoch_size_entry))\n train_tab_start_train_button.place(x=constants.GUI_WIDTH - 100, y=constants.GUI_HEIGHT - 75)\n tab_control.add(train_tab, text=\" Train Model \")",
"def clf_on_click():\n lab = classify(img.resize((8,8)))\n lt.set(f\"Classification:{str(lab)}\")",
"def featuresList(self):\n self.featuresListScreen.setWindowTitle(\"Unique Facial Feature Detection\")\n self.featuresListScreen.resize(575, 400)\n\n featuresLayout = QVBoxLayout()\n featuresBtnLayout = QHBoxLayout()\n\n obtainedFeaturesList = QLabel(self.photoProcessedScreen)\n obtainedFeaturesList.setStyleSheet(\"font: 14pt Century Gothic\")\n obtainedFeaturesList.setText(\"Your unique features!\")\n obtainedFeaturesList.setAlignment(Qt.AlignCenter)\n\n featuresLayout.addWidget(obtainedFeaturesList)\n\n # Features are displayed in outputtingList\n # Buttons are added in outputtingList to maintain order of widgets\n\n self.featuresListScreen.setLayout(featuresLayout)",
"def create_tabs(self):\n\n # Tabs\n self.create_setup_tab()\n self.create_part_location_tab()\n self.create_order_tab()\n self.create_challenge_tab()\n self.tab_control.pack(expand=1, fill=\"both\", padx=5, pady=5)",
"def construct_tabs(self):\n for key, config_list in self.groups.items():\n page = ConfigPage(self.notebook, config_list)\n self.notebook.AddPage(page, key)\n self.clean_edit_state()",
"def LoadNotebook(self):\n self.tabs = []\n \n self.tab_startup = panel_startup.PanelStartup(parent=self.notebook)\n self.tab_sample = panel_sample.PanelSample(parent=self.notebook)\n self.tab_goniometer = panel_goniometer.PanelGoniometer(parent=self.notebook)\n self.tab_experiment = panel_experiment.PanelExperiment(parent=self.notebook)\n if not gui_utils.fourcircle_mode():\n self.tab_add = panel_add_positions.PanelAddPositions(parent=self.notebook)\n self.tab_try = panel_try_position.PanelTryPosition(parent=self.notebook)\n self.tab_detectors = panel_detectors.PanelDetectors(parent=self.notebook)\n\n\n def AddPage(tab, title, mac_title=\"\", select=False):\n if (gui_utils.is_mac() or gui_utils.is_windows()) and not (mac_title==\"\"):\n title = mac_title\n self.notebook.AddPage(tab, title, select)\n\n AddPage(self.tab_startup, 'Q-Space', 'Q-Space', select=True)\n if not gui_utils.fourcircle_mode():\n AddPage(self.tab_detectors, 'Detectors')\n AddPage(self.tab_goniometer, 'Goniometer')\n AddPage(self.tab_sample, 'Sample')\n if not gui_utils.fourcircle_mode():\n AddPage(self.tab_try, 'Try an\\nOrientation', 'Try Orientation')\n AddPage(self.tab_add, 'Add\\nOrientations', 'Add Orientations')\n AddPage(self.tab_experiment, 'Experiment\\nPlan', 'Experiment Plan' )\n\n self.notebook.Bind(wx.EVT_NOTEBOOK_PAGE_CHANGING, self.onNotebookPageChanging)",
"def __create_tabs(self):\r\n self.tab1 = tk.Frame(self.note)\r\n self.tab2 = tk.Frame(self.note)\r\n self.tab3 = tk.Frame(self.note)\r\n self.note.add(self.tab1, text=\" Lines \")\r\n self.note.add(self.tab2, text=\" Stops \")\r\n self.note.add(self.tab3, text=\" Buses \")\r\n self.note.pack(side=tk.TOP)",
"def from_manual(self):\n from tkinter import Tk\n import tsCluster.guiLoader as guiLoader\n root = Tk()\n gui = guiLoader.LoadGroups(root)\n root.mainloop()\n self.__default_constructor__(gui.fileList, gui.nameStruc)",
"def segmentation_gui(self):\n self.segmentation_button.grid_forget()\n self.analysis_button.grid_forget()\n self.back_button.grid(row=0, pady=(2, 2))\n self.title(\"Scaphoid Fracture Segmentation\")\n self.seeds_label.config(text=\"please select the marking\")\n self.output_label.grid(row=1, column=0)\n self.output_input.grid(row=1, column=1)\n self.select_output.grid(row=1, column=2)\n self.file_label.grid(row=2, column=0)\n self.file_input.grid(row=2, column=1)\n self.select_file.grid(row=2, column=2)\n self.seeds_label.grid(row=3, column=0)\n self.seeds_input.grid(row=3, column=1)\n self.select_seeds.grid(row=3, column=2)\n self.segmentation_run.grid(row=4, columnspan=3, sticky=N + S + E + W)",
"def show_gui(self):\n self.gui = Browser_GUI(self)",
"def create_widgets(self):\n # Cria barra de menus\n self.create_menubar()\n\n # Cria frame de botoes\n self.create_buttons_frame()\n\n # Cria frame para exibicao dos automatos\n self.create_tabbed_frame()\n\n # Cria frame de selecao de automatos para operacoes\n self.create_selection_frame()",
"def _create_batch_tab(self, nb: ttk.Notebook) -> None:\n frame = ttk.Frame(nb)\n nb.add(frame, text=' Batch ', underline=2)",
"def _version_tab(ok_cancel_box):\n version_data = get_version()\n\n grid = grid_from_dict(version_data)\n\n hbox = layout_to_hlayout(grid)\n vbox = layout_to_vlayout(hbox)\n\n #---------------------\n version_tab = QWidget()\n version_tab.setLayout(vbox)\n\n return version_tab",
"def create_tabs(self):\n row = 0\n while row < 100:\n self.rowconfigure(row, weight=1)\n self.columnconfigure(row, weight=1)\n row += 1\n\n self.notebook = ttk.Notebook(self, style='Custom.TNotebook')\n self.log = LoggingFrame(parent=self, controller=self)\n\n self.notebook.grid(row=0, column=0, columnspan=100, rowspan=21, sticky='NSWE')\n self.log.grid(row=21, column=0, columnspan=100, rowspan=100, sticky='NSWE')\n\n # Defining the notebook tabs\n self.tabs = {}\n self.tab_map = OrderedDict([\n (InitialFrame, 'Home'),\n (AttackARPFrame, 'ARP Poisoning'),\n (AttackDNSFrame, 'DNS Cache Poisoning'),\n (HelpFrame, 'Help')\n ])\n\n # Add the frames to the application\n for tab in self.tab_map.keys():\n frame_name = self.tab_map[tab]\n frame = tab(parent=self.notebook, controller=self)\n self.notebook.add(frame, text=frame_name)\n self.tabs[tab.__name__] = frame\n\n self.notebook.tab('.!mainapplication.!notebook.!attackdnsframe', state=\"disabled\")",
"def gui():\n logger.info('Starting Keithley GUI') \n k = KeithleyForceUI()\n k.configure_traits()",
"def init_ui(self):\n # customize GUI\n self.ok_pb.setText(\"Colin, I love you!\")\n self.cancel_pb.setText(\"Okay, got it\")\n self.okWindow = OKWindow()\n\n # init changelog information\n # make a tab for each date recorded\n #\n changelog = Changelog()\n self.tabWidget = QtGui.QTabWidget(self.centralwidget)\n\n # Reorder the dict from most recent to least\n htmlDict = htmlparser.get_changelog()\n htmlDict = collections.OrderedDict(sorted(htmlDict.items(),\n key=lambda t: t[0]))\n htmlDict = htmlDict.items()\n htmlDict.reverse()\n htmlDict = collections.OrderedDict(htmlDict)\n\n # set the sections to upper to simplify testing\n sectionGlobal = [x.upper() for x in changelog.sectionGlob]\n sectionList = [x.upper() for x in changelog.sectionList]\n for key, items in htmlDict.iteritems():\n label = QtGui.QLabel(self.tabWidget)\n label.setAlignment(QtCore.Qt.AlignLeading|QtCore.Qt.AlignLeft|QtCore.Qt.AlignTop)\n tabToAdd = QtGui.QWidget()\n gridLayout = QtGui.QGridLayout(tabToAdd)\n gridLayout.addWidget(label)\n text = ''\n for k, itms in htmlDict[key].iteritems():\n if (k.upper() in sectionGlobal or k.upper() in sectionList) \\\n and itms != []:\n text += k + '\\n' # add the section name as text\n itms = ['- ' + x for x in itms]\n text += '\\n'.join(itms) # add each point as text\n text += '\\n\\n'\n label.setText(text)\n tabIndex = self.tabWidget.addTab(tabToAdd, key)\n # add grid to the new tab page and place QLabel inside of it\n\n self.tabWidget.setCurrentIndex(0)\n # add tab widget to main\n self.gridLayout.addWidget(self.tabWidget, 1, 0, 1, 3)\n\n # change the all the text\n for f in self.findChildren(QtGui.QLabel):\n formText = str(f.text()).strip()\n if f.objectName() == \"project_l\":\n f.setText(formText.format(proj=consts.PROJECT_NAME_LONG))\n elif f.objectName() == \"version_l\":\n f.setText(formText.format(version=consts.__version__))",
"def launch_batch(self) -> None:\n print('launching batch extraction gui')\n self.master.title('Python Data Extractor - Batch')\n\n destroy_child_widgets(self.central_widget)\n BatchAppGui(self.central_widget)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Create GUi for image recognition tab
|
def create_image_recognition_tab(self, tab_control):
image_recog_tab = ttk.Frame(tab_control)
image_recog_tab_data_dir_label = ttk.Label(image_recog_tab, text="Image file").place(x=20, y=20)
image_recog_tab_data_dir_entry = ttk.Entry(image_recog_tab, width=70)
image_recog_tab_data_dir_entry.place(x=110, y=20)
image_recog_tab_data_dir_browse_button = ttk.Button(image_recog_tab, text="Select File", command=lambda: self.select_file(image_recog_tab_data_dir_entry)).place(x=550, y=20)
# Classifier button
align_data_start_train_button = ttk.Button(image_recog_tab, text="Start Recognize", command=lambda: self.start_image_recognition(image_recog_tab_data_dir_entry, image_recog_tab))
align_data_start_train_button.place(x=110, y=50, width=425)
tab_control.add(image_recog_tab, text=" Recognition Image ")
|
[
"def main():\n lbls = imageio.v2.imread(Path(\"sample_data/test_labels.tif\"))\n lbls2 = np.zeros_like(lbls)\n lbls2[:, 3:, 2:] = lbls[:, :-3, :-2]\n lbls2 = lbls2 * 20\n\n labels = np.unique(lbls)[1:]\n labels_2 = np.unique(lbls2)[1:]\n\n viewer = napari.Viewer()\n lbls_layer = viewer.add_labels(lbls)\n lbls_layer2 = viewer.add_labels(lbls2)\n\n lbls_layer.features = make_features(labels, roi_id=\"ROI1\", n_features=6)\n lbls_layer2.features = make_features(labels_2, roi_id=\"ROI2\", n_features=6)\n # classifier_widget = ClassifierWidget(viewer)\n\n # viewer.window.add_dock_widget(classifier_widget)\n viewer.show(block=True)",
"def setupUi(self, automatic_photos_taker):\r\n self.automatic_photos_taker = automatic_photos_taker\r\n super().setupUi(self.automatic_photos_taker)\r\n\r\n self.disply_width = 648\r\n self.display_height = 480\r\n\r\n self.status_label.setText('current status: Not running !')\r\n self.process_data_btn.clicked.connect(\r\n self.launch_data_processing_UI)\r\n\r\n for name in self.names:\r\n self.comboBox.addItem(name)\r\n\r\n self.start_btn.clicked.connect(self.takePhotoAutomatically)\r\n self.stop_btn.clicked.connect(self.stopTakingPhotoAutomatically)\r\n\r\n # create the video capture thread\r\n self.thread = VideoThread()\r\n # connect its signal to the update_image slot\r\n self.thread.change_pixmap_signal.connect(self.update_image)\r\n # start the thread\r\n self.thread.start()",
"def photoProcessed(self):\n # set up initial window features\n self.photoProcessedScreen.setWindowTitle(\"Unique Facial Feature Detection\")\n self.photoProcessedScreen.resize(575, 400)\n\n obtainedFeaturesText= QLabel(self.photoProcessedScreen)\n obtainedFeaturesText.setStyleSheet(\"font: 14pt Century Gothic\")\n obtainedFeaturesText.setText(\"Obtained unique features!\")\n obtainedFeaturesText.setGeometry(QRect(30, -10, 500, 200))\n obtainedFeaturesText.setAlignment(Qt.AlignCenter)\n\n global results\n global images\n if saveImage == 1:\n # open cropped image if it exists\n if (str(os.path.isfile(\"./backend/ResizedImages/newCropped.jpeg\")) == True):\n images = Image.open(\"./backend/ResizedImages/newCropped.jpeg\")\n else:\n images = Image.open(path)\n\n # set up button to show unique features\n photoProcessedBtnLayout = QHBoxLayout()\n getFeaturesListBtn = QPushButton(\"Get unique feature's list!\")\n photoProcessedBtnLayout.addWidget(getFeaturesListBtn)\n\n # go to next window if button is clicked\n getFeaturesListBtn.clicked.connect(self.outputtingList)\n\n self.photoProcessedScreen.setLayout(photoProcessedBtnLayout)",
"def make_gui_corporate(self, parent):\n\n # get corporate image\n img = wx.Image(cfg.corporate_image, wx.BITMAP_TYPE_ANY)\n ci_gif = img.ConvertToBitmap()\n\n # create gui objects\n bmp = wx.StaticBitmap(parent, wx.ID_ANY, ci_gif, (0, 0))\n\n # lay out objects\n box = wx.BoxSizer(wx.HORIZONTAL)\n box.Add(bmp, flag=wx.ALIGN_CENTER)\n\n return box",
"def init_ui(self):\n self.setFrameShape(QtWidgets.QFrame.NoFrame)\n\n self.frameLayout = QtWidgets.QVBoxLayout(self)\n self.frameLayout.setObjectName(\"Frame layout\")\n\n self.grview = QGraphicsView()\n self.grview.setRenderHints(self.grview.renderHints() | QPainter.Antialiasing | QPainter.SmoothPixmapTransform)\n self.scene = QGraphicsScene()\n\n # scene.setSceneRect(0, 0, 1500, 459)\n\n self.grview.setScene(self.scene)\n\n noMap = QPixmap('resources/icons/no_map.png')\n self.scene.addPixmap(noMap)\n self.grview.fitInView(self.scene.sceneRect(), Qt.KeepAspectRatio)\n\n self.frameLayout.addWidget(self.grview)",
"def ui():\n win = ControlWindow()\n win.show()",
"def launch_data_processing_UI(self):\r\n self.window = QtWidgets.QMainWindow()\r\n # self.ui = CustomApplicationLauncherWindow(current_working_directory)\r\n self.ui = CustomApplicationLauncherWindow(\r\n self.names, self.current_working_directory, self.model_name)\r\n self.ui.setupUi(self.window)\r\n self.window.show()\r\n self.thread.stop() # stop webcam\r\n self.automatic_photos_taker.hide() # hide window\r",
"def create_picture_gui(self):\n self.screen.fill((255, 255, 255)) # asd\n self.display_author()\n self.display_title()\n # Getting width, height and steps from input boxes.\n w, h, s, _ = self.display_creating_picture_boxes()\n # Checking data validate\n try:\n width, height, steps = gexc.check_creating_data(w, h, s)\n # Checks whether width is int\n except gexc.WidthException:\n self.display_error(\"width\")\n self.create_picture_gui()\n # Checks whether height is int\n except gexc.HeightException:\n self.display_error(\"height\")\n self.create_picture_gui()\n # Checks whether steps is int\n except gexc.StepsException:\n self.display_error(\"steps\")\n self.create_picture_gui()\n # Creating white picture from user's data\n white_picture = ImgInp.create_white_picture(width, height)\n # Makes a simulation\n self.make_simulation(steps, white_picture)",
"def featuresList(self):\n self.featuresListScreen.setWindowTitle(\"Unique Facial Feature Detection\")\n self.featuresListScreen.resize(575, 400)\n\n featuresLayout = QVBoxLayout()\n featuresBtnLayout = QHBoxLayout()\n\n obtainedFeaturesList = QLabel(self.photoProcessedScreen)\n obtainedFeaturesList.setStyleSheet(\"font: 14pt Century Gothic\")\n obtainedFeaturesList.setText(\"Your unique features!\")\n obtainedFeaturesList.setAlignment(Qt.AlignCenter)\n\n featuresLayout.addWidget(obtainedFeaturesList)\n\n # Features are displayed in outputtingList\n # Buttons are added in outputtingList to maintain order of widgets\n\n self.featuresListScreen.setLayout(featuresLayout)",
"def initialise_ui(self):\n \n #Add event boxes to codel color chooser\n self.codelColors = [gtk.EventBox() for color in piedit.colors.all_colors()]\n for (color,(x,y),i) in zip(piedit.colors.all_colors(),\n ((x,y) for x in xrange(7) for y in xrange(3)),\n xrange(len(self.codelColors))): \n event_box = self.codelColors[i]\n event_box.set_events(gtk.gdk.BUTTON_PRESS_MASK)\n event_box.visible = True\n self.gladeui.get_widget(\"codelColorsTable\").attach(\n event_box,\n x,\n x+1,\n y,\n y+1,\n xoptions=gtk.EXPAND|gtk.FILL, \n yoptions=gtk.EXPAND|gtk.FILL, \n xpadding=1, \n ypadding=1)\n event_box.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(color))\n event_box.set_size_request(-1,30)\n event_box.default_color=color\n event_box.connect(\"button_press_event\", self.handlers.on_codelColorEventBox_clicked) \n event_box.show()\n \n #Initialise image \n program_table = self.gladeui.get_widget(\"programTable\")\n program_table.add_events(gtk.gdk.BUTTON_PRESS_MASK)\n program_table.connect(\"button_press_event\", self.handlers.on_programTable_button_press_event)\n self.clear_image(self.width,self.height)",
"def segmentation_gui(self):\n self.segmentation_button.grid_forget()\n self.analysis_button.grid_forget()\n self.back_button.grid(row=0, pady=(2, 2))\n self.title(\"Scaphoid Fracture Segmentation\")\n self.seeds_label.config(text=\"please select the marking\")\n self.output_label.grid(row=1, column=0)\n self.output_input.grid(row=1, column=1)\n self.select_output.grid(row=1, column=2)\n self.file_label.grid(row=2, column=0)\n self.file_input.grid(row=2, column=1)\n self.select_file.grid(row=2, column=2)\n self.seeds_label.grid(row=3, column=0)\n self.seeds_input.grid(row=3, column=1)\n self.select_seeds.grid(row=3, column=2)\n self.segmentation_run.grid(row=4, columnspan=3, sticky=N + S + E + W)",
"def addDisplay(self, outputfilter):\n if not hasattr(outputfilter,'pixmap'):\n return\n grid_item = self.ui.grid.itemAt(0)\n if grid_item is None:\n self.addTabView() \n tabW = self.ui.grid.itemAt(self.ui.grid.count()-1).widget()\n tabW.addTab(ImageLabel(outputfilter),outputfilter.name)\n outputfilter.filter_name_change_sig.connect(tabW.setFilterTabText)\n tabW.setCurrentIndex(tabW.count()-1)",
"def ui_mode():\n # Create a dialog box with the features\n fields = ['id', 'duration', 'codec', 'width', 'height',\n 'bitrate', 'framerate', 'i', 'p', 'b', 'frames',\n 'i_size', 'p_size', 'b_size', 'size', 'o_codec',\n 'o_bitrate', 'o_framerate', 'o_width',\n 'o_height', 'umem']\n layout = [[sg.Text('url'), sg.Input('', key='url')],\n [sg.Text('id'), sg.Input('0Yxo-eU6AjI', key='id')],\n [sg.Text('duration', text_color='red'), sg.Input(326.583, key='duration')],\n [sg.Text('codec'), sg.Input('vp8', key='codec')],\n [sg.Text('width'), sg.Input(640, key='width')],\n [sg.Text('height'), sg.Input(480, key='height')],\n [sg.Text('bitrate'), sg.Input(1055982, key='bitrate')],\n [sg.Text('framerate'), sg.Input(25.03, key='framerate')],\n [sg.Text('i'), sg.Input(102, key='i')],\n [sg.Text('p'), sg.Input(8061, key='p')],\n [sg.Text('b'), sg.Input(0, key='b')],\n [sg.Text('frames'), sg.Input(8163, key='frames')],\n [sg.Text('i_size'), sg.Input(1, key='i_size')],\n [sg.Text('p_size'), sg.Input(41239444, key='p_size')],\n [sg.Text('b_size'), sg.Input(0, key='b_size')],\n [sg.Text('size'), sg.Input(43108248, key='size')],\n [sg.Text('o_codec'), sg.Input(\"fly\", key='o_codec')],\n [sg.Text('o_bitrate'), sg.Input(5000000, key='o_bitrate')],\n [sg.Text('o_framerate'), sg.Input(24, key='o_framerate')],\n [sg.Text('o_width'), sg.Input(480, key='o_width')],\n [sg.Text('o_height'), sg.Input(360, key='o_height')],\n [sg.Text('umem'), sg.Input(215124, key='umem')],\n [sg.Text('Prediction: ', text_color='blue', size=(40, 2), key='_PRED_')],\n [sg.RButton('Predict'), sg.Exit()]]\n window = sg.Window('Enter url and feature values', layout)\n while True:\n event, values = window.Read()\n predictions = str(get_multiple_predictions(values, fields))\n predictions.replace('\"', '')\n if event == 'Predict':\n # change the \"output\" element to be the value of \"input\" element\n window.Element('_PRED_').Update('duration: [' + values['duration'] + ']\\n' +\n 'Prediction: ' + predictions)\n if event is None or event == 'Exit':\n break\n\n window.Close()",
"def __init__(self, baseName, className, rigUiInst, parent=None):\n\n super(ART_AddModule_UI, self).__init__(parent)\n\n # get the directory path of the tools\n settings = QtCore.QSettings(\"Epic Games\", \"ARTv2\")\n self.toolsPath = settings.value(\"toolsPath\")\n self.iconsPath = settings.value(\"iconPath\")\n\n # create class variables\n self.baseName = baseName\n self.className = className\n self.rigUiInst = rigUiInst\n\n # load stylesheet\n styleSheetFile = utils.returnNicePath(self.toolsPath, \"Core/Scripts/Interfaces/StyleSheets/mainScheme.qss\")\n f = open(styleSheetFile, \"r\")\n style = f.read()\n f.close()\n\n self.setStyleSheet(style)\n\n # size policies\n mainSizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed)\n\n # create the main widget\n self.mainWidget = QtWidgets.QWidget()\n self.setCentralWidget(self.mainWidget)\n\n # set qt object name\n self.setObjectName(windowObject)\n self.setWindowTitle(windowTitle)\n\n # create the mainLayout for the rig creator UI\n self.mainLayout = QtWidgets.QHBoxLayout(self.mainWidget)\n self.mainLayout.setContentsMargins(0, 0, 0, 0)\n\n self.setSizePolicy(mainSizePolicy)\n self.setMinimumSize(QtCore.QSize(500, 220))\n self.setMaximumSize(QtCore.QSize(500, 520))\n\n # create the background\n self.frame = QtWidgets.QFrame()\n self.frame.setObjectName(\"mid\")\n self.mainLayout.addWidget(self.frame)\n\n # create the layout for the widgets\n self.column1layout = QtWidgets.QVBoxLayout(self.frame)\n self.mainLayout.addLayout(self.column1layout)\n\n self.column2Layout = QtWidgets.QVBoxLayout()\n self.mainLayout.addLayout(self.column2Layout)\n\n font = QtGui.QFont()\n font.setBold(True)\n\n label = QtWidgets.QLabel(\"Choose Parent Bone\")\n label.setFont(font)\n label.setAlignment(QtCore.Qt.AlignCenter)\n self.column2Layout.addWidget(label)\n\n self.boneSearch = QtWidgets.QLineEdit()\n self.column2Layout.addWidget(self.boneSearch)\n self.boneSearch.setPlaceholderText(\"Search...\")\n self.boneSearch.textChanged.connect(self.searchList)\n\n self.hierarchyTree = QtWidgets.QListWidget()\n self.column2Layout.addWidget(self.hierarchyTree)\n\n # add items to listWidget\n parents = utils.getViableParents()\n for bone in parents:\n self.hierarchyTree.addItem(bone)\n\n if bone == \"root\":\n index = parents.index(bone)\n self.hierarchyTree.setCurrentRow(index)\n\n # create the prefix pair of fields\n self.prefixForm = QtWidgets.QFormLayout()\n self.column1layout.addLayout(self.prefixForm)\n\n self.prefixLabel = QtWidgets.QLabel(\"Prefix: \")\n self.prefixForm.setWidget(0, QtWidgets.QFormLayout.LabelRole, self.prefixLabel)\n\n self.prefix = QtWidgets.QLineEdit()\n self.prefixForm.setWidget(0, QtWidgets.QFormLayout.FieldRole, self.prefix)\n\n # hookup signal/slot connection\n self.prefix.textChanged.connect(self.updatePreview)\n\n # create the suffix pair of fields\n self.suffixForm = QtWidgets.QFormLayout()\n self.column1layout.addLayout(self.suffixForm)\n\n self.suffixLabel = QtWidgets.QLabel(\"Suffix: \")\n self.suffixForm.setWidget(0, QtWidgets.QFormLayout.LabelRole, self.suffixLabel)\n\n self.suffix = QtWidgets.QLineEdit()\n self.suffixForm.setWidget(0, QtWidgets.QFormLayout.FieldRole, self.suffix)\n\n # hookup signal/slot connection\n self.suffix.textChanged.connect(self.updatePreview)\n\n self.previewLabel = QtWidgets.QLabel(\"Module Name: \")\n self.column1layout.addWidget(self.previewLabel)\n\n self.previewName = QtWidgets.QLabel(self.baseName)\n self.previewName.setMinimumSize(QtCore.QSize(255, 25))\n self.previewName.setMaximumSize(QtCore.QSize(255, 25))\n self.previewName.setAlignment(QtCore.Qt.AlignHCenter)\n self.column1layout.addWidget(self.previewName)\n\n # set preview font\n font = QtGui.QFont()\n font.setPointSize(12)\n self.previewName.setFont(font)\n\n spacerItem1 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)\n self.column1layout.addItem(spacerItem1)\n\n # special cases (arms and legs)\n specialCaseModules = [\"ART_Leg_Standard\", \"ART_Arm_Standard\"]\n if className in specialCaseModules:\n # spacer\n groupBox = QtWidgets.QGroupBox(\"\")\n self.column1layout.addWidget(groupBox)\n layout = QtWidgets.QVBoxLayout(groupBox)\n\n self.radioButtonLayout = QtWidgets.QHBoxLayout()\n layout.addLayout(self.radioButtonLayout)\n self.rightRadioBtn = QtWidgets.QRadioButton(\"Right Side\")\n self.leftRadioBtn = QtWidgets.QRadioButton(\"Left Side\")\n self.radioButtonLayout.addWidget(self.rightRadioBtn)\n self.radioButtonLayout.addWidget(self.leftRadioBtn)\n self.leftRadioBtn.setChecked(True)\n\n # spacer\n spacerItem2 = QtWidgets.QSpacerItem(20, 80, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)\n self.column1layout.addItem(spacerItem2)\n\n # create button\n self.createButton = QtWidgets.QPushButton(\"CREATE\")\n self.column1layout.addWidget(self.createButton)\n self.createButton.setMinimumSize(QtCore.QSize(255, 40))\n self.createButton.setMaximumSize(QtCore.QSize(255, 40))\n self.createButton.setSizePolicy(mainSizePolicy)\n self.createButton.setObjectName(\"blueButton\")\n font = QtGui.QFont()\n font.setPointSize(12)\n self.createButton.setFont(font)\n\n # hookup signal/slot on create button\n self.createButton.clicked.connect(self.createModule)\n\n self.hierarchyTree.setFocus()",
"def display(self):\n if self.valid:\n IJShow.runIjandShow(self.image_name)",
"def setup_additional_ui(self):\n\n #set header icon\n header_icon_path = ''\n header_icon_name = 'icon_helga_launcher.png'\n header_icon_path = os.path.join(icons_path, header_icon_name)\n \n #set stylesheet header\n self.wdgt_header_icon.setStyleSheet(\"border-image: url({0});\".format(header_icon_path.replace('\\\\', '/')))\n \n \n #set title\n self.setWindowTitle(self.title)\n #set header label\n self.lbl_header_text.setText(self.title)\n\n #setup dcc buttons\n self.setup_dcc_buttons()\n\n #setup_mvc\n self.setup_mvc()",
"def create_gui(geometry=None,callback=None,\n opts_choice=None,opts_range=None,opts_color=None,\n initial_values=None,layout=None,\n height=400,width=400, background='gray',\n orthographic=False, camera_position=[0,0,-10],\n view=(10,-10,-10,10),fov=50,\n add_objects=True, add_labels=True,\n show_object_info=False,\n otype_column=None, jslink=True):\n ## intialise options\n init_vals = {} if initial_values is None else initial_values\n \n opts_choice = {} if opts_choice is None else opts_choice\n all_options = {label:init_vals[label] if label in init_vals else options[0] \n for label, options in opts_choice.items()}\n opts_range = {} if opts_range is None else opts_range\n all_options.update({label:init_vals[label] if label in init_vals else options[0] \n for label, options in opts_range.items()})\n opts_color = {} if opts_color is None else opts_color\n all_options.update({label:init_vals[label] if label in init_vals else init \n for label, init in opts_color.items()})\n \n if len(all_options) != len(opts_choice)+len(opts_range)+len(opts_color):\n raise ValueError('options in opts_choice, opts_slide, and opts_color are not unique')\n \n ## intialise layout\n layout = [] if layout is None else layout\n layout_dict = OrderedDict(layout)\n if len(layout_dict) != len(layout):\n raise ValueError('layout tab names are not unique')\n\n ## initialise renderer\n if geometry is None:\n gcollect = pjs.models.GeometricCollection()\n else:\n gcollect = geometry\n scene = pjs.views.create_js_scene_view(gcollect,\n add_objects=add_objects,add_labels=add_labels, jslink=jslink)\n camera, renderer = pjs.views.create_jsrenderer(scene,\n orthographic=orthographic, camera_position=camera_position,\n view=view,fov=fov,\n height=height,width=width, background=background)\n \n ## create minimal callback \n if callback is None:\n def callback(geometry, options):\n return\n \n ## initialise geometry in renderer \n with renderer.hold_trait_notifications():\n callback(gcollect, all_options)\n \n ## Create controls and callbacks\n controls = {}\n \n # a check box for showing labels\n if add_labels: \n toggle=widgets.Checkbox(\n value=False,\n description='View Label:')\n def handle_toggle(change):\n for obj in gcollect.idobjects:\n obj.label_visible = change.new\n toggle.observe(handle_toggle,names='value')\n controls['View Label'] = toggle\n \n # zoom sliders for orthographic\n if orthographic:\n top,bottom,left,right = view\n axiszoom = widgets.FloatSlider(\n value=0,\n min=-10,\n max=10,\n step=0.1,\n description='zoom',\n continuous_update=True,)\n def handle_axiszoom(change): \n if change.new>1:\n zoom = 1./change.new\n elif change.new<-1:\n zoom = -change.new\n else:\n zoom = 1\n with renderer.hold_trait_notifications():\n camera.left = zoom * left\n camera.right = zoom * right\n camera.top = zoom * top\n camera.bottom = zoom * bottom\n axiszoom.observe(handle_axiszoom,names='value')\n \n controls['Orthographic Zoom'] = axiszoom\n \n # add additional options\n \n dd_min=4 # min amount of options before switch to toggle buttons\n for label in opts_choice:\n options = opts_choice[label]\n initial = init_vals[label] if label in init_vals else options[0]\n assert initial in list(options), \"initial value {0} for {1} not in range: {2}\".format(\n initial, label, list(options))\n if (len(options)==2 and True in options and False in options \n and isinstance(options[0],bool) and isinstance(options[1],bool)):\n ddown = widgets.Checkbox(value=initial,\n description=label)\n elif len(options)< dd_min:\n ddown = widgets.ToggleButtons(options=list(options),\n description=label,value=initial) \n else:\n ddown = widgets.Dropdown(options=list(options),\n description=label,value=initial)\n handle = _create_callback(renderer,ddown,callback, \n gcollect,all_options)\n ddown.observe(handle, names='value')\n \n controls[label] = ddown\n \n for label in opts_range:\n options = opts_range[label]\n initial = init_vals[label] if label in init_vals else options[0]\n assert initial in list(options), \"initial value {0} for {1} not in range: {2}\".format(\n initial, label, list(options))\n slider = widgets.SelectionSlider(description=label,\n value=initial,options=list(options), \n continuous_update=False)\n handle = _create_callback(renderer,slider,callback, \n gcollect,all_options)\n slider.observe(handle, names='value')\n\n controls[label] = slider\n\n for label in opts_color:\n option = init_vals[label] if label in init_vals else opts_color[label]\n color = widgets.ColorPicker(description=label,\n value=option, concise=False)\n handle = _create_callback(renderer, color,callback, \n gcollect,all_options)\n color.observe(handle, names='value')\n \n controls[label] = slider\n \n # add mouse hover information box\n # TODO doesn't work for orthographic https://github.com/jovyan/pythreejs/issues/101\n if not orthographic and show_object_info: \n # create information box\n click_picker = tjs.Picker(root=scene.children[0], event='mousemove')\n infobox = widgets.HTMLMath()\n def change_info(change):\n if click_picker.object:\n infobox.value = 'Object Coordinate: ({1:.3f}, {2:.3f}, {3:.3f})<br>{0}'.format(\n click_picker.object.other_info, *click_picker.object.position)\n else:\n infobox.value = ''\n click_picker.observe(change_info, names=['object'])\n renderer.controls = renderer.controls + [click_picker]\n renderer = widgets.HBox([renderer,infobox])\n \n if not controls:\n return (renderer,gcollect,\n all_options.viewitems() if hasattr(all_options,'viewitems')\n else all_options.items()) # python 2/3 compatability \n\n ## layout tabs and controls \n tabs = OrderedDict() \n for tab_name, clist in layout_dict.items():\n vbox_list = []\n \n for cname in clist:\n if isinstance(cname,list):\n hbox_list = [controls.pop(subcname) for subcname in cname]\n vbox_list.append(widgets.HBox(hbox_list))\n else:\n vbox_list.append(controls.pop(cname))\n tabs[tab_name] = widgets.VBox(vbox_list)\n \n if 'Orthographic Zoom' in controls:\n tabs.setdefault('View', widgets.Box() )\n tabs['View'] = widgets.VBox([tabs['View'],\n controls.pop('Orthographic Zoom')])\n \n if 'View Label' in controls:\n tabs.setdefault('View', widgets.Box() )\n tabs['View'] = widgets.VBox([tabs['View'],\n controls.pop('View Label')])\n \n # deal with remaining controls\n if controls:\n vbox_list = []\n for cname in natural_sort(controls):\n vbox_list.append(controls.pop(cname))\n tabs.setdefault('Other', widgets.Box() )\n tabs['Other'] = widgets.VBox([tabs['Other'],\n widgets.VBox(vbox_list)])\n \n options = widgets.Tab(children=tuple(tabs.values()))\n for i, name in enumerate(tabs):\n options.set_title(i, name)\n \n return (widgets.VBox([options, renderer]),gcollect,\n all_options.viewitems() if hasattr(all_options,'viewitems')\n else all_options.items()) # python 2/3 compatability",
"def graphic_window(self):",
"def draw_dialog():\n Launcher.create_main_window()\n Launcher.create_labels()\n Launcher.create_images()\n Launcher.create_buttons()"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Select directory and set the directory absolute path to entry
|
def select_dir(self, entry: Entry):
entry.delete(0, END)
filename = filedialog.askdirectory()
entry.insert(0, filename)
|
[
"def choose_dir(self):\n self.output_dir.set(filedialog.askdirectory())",
"def ask_dir(self):\n\t\targs ['directory'] = askdirectory(**self.dir_opt) \n\t\tself.dir_text.set(args ['directory'])",
"def setDirectory(*args, **kwargs):\n \n pass",
"def set_dirname(self, dirname):\n self.dirname = os.path.abspath(os.path.expanduser(dirname))",
"def set_default_directory(self, suggestion):\n if os.path.exists(suggestion):\n if not os.path.isdir(suggestion):\n suggestion = os.path.dirname(suggestion)\n self.mainwindow.default_directory = self.default_directory = suggestion",
"def on_pbOutputDirectory_click(self):\n output_dir = open_file_dialog('directory')\n self.lblDataDir.setText(f'{output_dir}')",
"def set_dirtext(self):\n self.tree_dir.setText(self.get_dirtext(self.tree_widget.currentItem()))",
"def ask_directory():\n path = askdirectory()\n folder_selected = os.path.abspath(path) \n return folder_selected",
"def set_directory_url(self):\n\n self.filelike = False\n if not self.dirpath or \\\n (self.dirpath and self.dirpath[-1] != self.lastpath):\n self.dirpath.append(self.lastpath)\n self.validfilename = 'index.html'",
"def browse_output_directory(self) -> None:\n filename = filedialog.askdirectory(initialdir=self.ROOT_DIR, title=\"Select directory which will hold the\"\n \"results from the processing\")\n self.set_input(filename, self.output_entry)",
"def _browseModulePath(self):\n\t\tselectedDir = str(QtGui.QFileDialog.getExistingDirectory(self,\"Browse\"))\n\t\tif selectedDir:\n\t\t\twritObj = utils.ReadWriteCustomPathsToDisk()\n\t\t\tif not writObj._entryExist(selectedDir):\n\t\t\t\twritObj.updateXml()\n\t\t\tself.addPathEdit.setText(selectedDir)\n\t\t\tself.lookInsideEdit.setText(os.path.split(selectedDir)[-1])\n\t\t\tself.pathAdded = selectedDir",
"def path_button_clicked(self):\n open_dialog = QFileDialog()\n if not self.path_text.text():\n button_path = expanduser(\"~\")\n else:\n button_path = self.path_text.text()\n\n temp_path = open_dialog.getExistingDirectory(self, \"Package directory:\", button_path)\n\n if temp_path:\n self.path_text.setText(temp_path)",
"def browse_glacier_directory(self):\n filename = filedialog.askdirectory(initialdir=self.ROOT_DIR, title=\"Select directory which has the TIF\"\n \"images for processing..\")\n self.set_input(filename, self.input_entry)",
"def browse_for_dir(self, event=None):\n\n # Start in the directory containing the current file, or the\n # current working directory if no files are currently open\n if self._files:\n initialdir = os.path.dirname(self._selected_file.get())\n else:\n initialdir = self._browse_dir\n\n new_dir = askdirectory(parent=self,\n title=\"Select Folder\",\n initialdir=initialdir)\n\n if new_dir:\n # Note that self.open_dir() will normalize the pathname\n self.open_dir(new_dir)\n\n elif not self._files:\n # Close the application if no files were previously open\n self.close_window()",
"def choose_src(self, event):\n dialog = wx.DirDialog(self.panel, \n message='Select the Source directory',\n style=wx.DD_DEFAULT_STYLE | wx.DD_NEW_DIR_BUTTON)\n if dialog.ShowModal() == wx.ID_OK:\n self.src_text.SetValue(dialog.GetPath())\n self.Config.source = self.src_text.GetValue()\n\n self.DirtyState = True\n self.UpdateUI()",
"def post_set_ms_dir(self, value, change_userdefine, raiseerror, *opts):\n \n self.__setitem__('curr_dir', value, change_userdefine=change_userdefine)",
"def cd(self, *p):\n if self.directory:\n return dpath(self.directory, os.path.join(self, *p))\n else:\n return dpath(os.path.join(self, *p), **self.connection)",
"def select_file_path(tk_file_loc_var, initial_directory=os.getcwd()):\r\n selected_path = askopenfilename(initialdir=initial_directory, filetypes=[('XML Files', '*.xml'),('All files', '*')])\r\n tk_file_loc_var.set(selected_path)",
"def choose_file(self):\n dirname = self.get_default_directory(self.filename.text())\n filename = getOpenFileName(self, 'Open File', dirname)\n if os.path.exists(filename): # avoids problems if <Cancel> was selected\n dirname = os.path.dirname(filename)\n self.filename.setText(str(filename))\n self.set_default_directory(dirname)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get Bamboo plan key.
|
def plan_key(self):
return self.__plan_key
|
[
"def encode_plan_key(self, job_id, state):\n return \"%s@%s\" % (state, job_id)",
"def _get_key(sample, project):\n return sample + \".\" + project",
"def runningclub_key(runningclub_name):\n#----------------------------------------------------------------------\n keyname = '.userpw.{}'.format(runningclub_name)\n thisrckey = db.Key.from_path('SubApp', '.userpw', 'RunningClub', keyname)\n return thisrckey",
"def service_plan_id(self) -> pulumi.Output[str]:\n return pulumi.get(self, \"service_plan_id\")",
"def lesson_key(lessonplan_name = DEFAULT_LESSONPLAN_NAME):\n return ndb.Key('Lesson', lessonplan_name)",
"def get_apikey(self):\n return self.apikeys[self.apikey_index]",
"def contact_key(self, contact_id) -> str:\n return self.cursor.execute(\"SELECT SecretKey \"\n \"FROM contacts \"\n \"WHERE contactID = ?\",\n (contact_id,)).fetchone()",
"def get_plan(self, job_id):\n return _execute_rest_request(url=f\"{self.prefix}/{job_id}/plan\")[\"plan\"]",
"def service_plan_id(self) -> pulumi.Input[str]:\n return pulumi.get(self, \"service_plan_id\")",
"def api_key_id(self) -> pulumi.Output[str]:\n return pulumi.get(self, \"api_key_id\")",
"def sp_key(self) -> pulumi.Output[str]:\n return pulumi.get(self, \"sp_key\")",
"def get_next_available_key(self) -> str:\n\n last_key = self._get_last_project_key()\n assert last_key.startswith(self.initials)\n key_number = int(last_key[len(self.initials) :])\n key_number += 1\n next_available_key = f\"{self.initials}{key_number:05d}\"\n return next_available_key",
"def get_key(self):\n\t\tprint(\"---get public pvt key pair---\")\n\t\tkey = RSA.generate(2048)\n\t\treturn key",
"def get_apikey(self, target, required=True):\n endpoint = self._parse_project(target)[1]\n try:\n return self.apikeys[endpoint]\n except KeyError:\n if not required:\n return None\n msg = \"Could not find API key. Please run 'shub login' first.\"\n if endpoint != 'default':\n msg = \"Could not find API key for endpoint %s.\" % endpoint\n raise ClickException(msg)",
"def getTaskKey(self, task_id):\n return",
"def api_key_id(self) -> Optional[pulumi.Input[str]]:\n return pulumi.get(self, \"api_key_id\")",
"def get_codegen_key(self):\n return None",
"def GetId(apig,usageplan_name: str):\n\t\t\t\tusageplan_list = AWS.APIGateway.UsagePlan.List(apig)\n\n\t\t\t\tusageplan_id = ''\n\t\t\t\tfor usp in usageplan_list:\n\t\t\t\t\tif usp['name'] == usageplan_name:\n\t\t\t\t\t\tusageplan_id = usp['id']\n\t\t\t\treturn usageplan_id",
"def key(self):\n return self.param_info.key"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get extra values to compound the url.
|
def url_extra_values(self):
return self.__url_extra_values
|
[
"def get_url_params(self, url_path):\n return self.url_rule.extract_params(url_path)",
"def _GetUrlParams(self, query=None):\n params = sum([c_w_c._GetUrlParams() for c_w_c in self.reactants], [])\n params.extend(self.aq_params._GetUrlParams())\n\n if query is not None:\n for arrow in constants.POSSIBLE_REACTION_ARROWS:\n tmp_query = query.replace(arrow, '=>')\n params.append('query=%s' % urllib.parse.quote(tmp_query))\n\n return params",
"def flat_extra(self, kwargs=None):\n if kwargs is None:\n kwargs = {}\n return reduce(lambda x, y: dict(x, **y), self.extras + [kwargs.get(\"extra\", {})])",
"def get_arguments(self):\n return dict(self.request.rel_url.query)",
"def extract_params(self, url_path):\n return self.regex.fullmatch(url_path).groupdict()",
"def combineArgs(self, url, kwargs):\n\n # parse the existing URL\n parsed_url = list(urlparse(url))\n # get the existing query string\n qs = parsed_url[4]\n # parse the query into a dict\n d = parse_qs(qs, 1)\n # update with stuff from kwargs\n for k, v in kwargs.items():\n if isinstance(v, six.text_type):\n v = v.encode(URL_ENCODING)\n d[k] = [v] # put in a list to be consistent with parse_qs\n # parse_qs behaves a little unexpectedly -- all query string args\n # are represented as lists. I think the reason is so that you get\n # consistent behavior for things like http://myurl?a=1&a=2&a=3\n # For this case parse_qs returns d['a'] = ['1','2','3']\n # However, that means that http://myurl?a=1 comes back as d['a']=['1']\n # unmunge some of parse_qs's weirdness\n dnew = {}\n for k, v in d.items():\n if v and len(v) == 1:\n dnew[k] = v[0]\n else:\n dnew[k] = v\n return dnew",
"def extra_info(self) -> Dict:\n return self._extra_info",
"def get_url_info(url):\n\tdat = _select_fancy('urls', ['url', 'post_id', 'file_path'], 'url = :ur', {'ur':url})\n\tif dat: #!cover\n\t\tif dat['file_path'] == 'False':\n\t\t\tdat['file_path'] = False\n\t\tif dat['file_path'] == 'None':\n\t\t\tdat['file_path'] = None\n\treturn dat",
"def as_url_fields(url, prefix=''):\n up = urlparse(url)\n d = {}\n if len(prefix) > 0:\n prefix = \"{}_\".format(prefix)\n d[prefix+'host'] = up.hostname\n d[prefix+'has_query'] = len(up.query) > 0\n if up.port:\n d[prefix+'port'] = up.port\n elif up.scheme == 'https':\n d[prefix+'port'] = 443\n elif up.scheme == 'http':\n d[prefix+'port'] = 80\n d[prefix+'scheme'] = up.scheme\n d[prefix+'path'] = up.path\n return d",
"def _add_extra_http_data(environ, args):\n extra = {}\n extra.update(args)\n if 'REMOTE_USER' in environ:\n extra['userName'] = environ['REMOTE_USER']\n if 'REMOTE_ADDR' in environ:\n extra['clientIp'] = environ['REMOTE_ADDR']\n if 'SERVER_ADDR' in environ:\n extra['serverIp'] = environ['SERVER_ADDR']\n if environ.get('REQUEST_METHOD') == 'POST':\n m = re.match(r\"/([^/]+)/(git-upload-pack|git-receive-pack)\",\n environ['PATH_INFO'])\n if m:\n extra['repo'] = m.group(1)\n extra['command'] = m.group(2)\n else:\n m = re.match(\"service=(.*)\", environ.get('QUERY_STRING', ''))\n if m:\n extra['command'] = m.group(1)\n m = re.match(r\"/([^/]+)/(info/refs|HEAD)\", environ.get('PATH_INFO', ''))\n if m:\n extra['repo'] = m.group(1)\n return extra",
"def url_plus_query(self, url, query=None):\n if query is None:\n query = {}\n parts = url.split('?', 1)\n oldargs = {}\n if len(parts) > 1:\n for arg in parts[1].split('&'):\n k,v = [unquote_plus(s) for s in arg.split('=',1)]\n oldargs[k] = v\n\n return \"%s?%s\" % (parts[0], self.query_string(query, oldargs))",
"def get_url_extension(self):",
"def extra_args(self):\n return deepcopy(self._extra_args)",
"def get_reverse_kwargs(self):\n return [self.path_url_kwarg]",
"def parse_url_params_for_body(self) -> (str, str):\n query_params = []\n path_params = []\n\n param_map = {\n \"query\": query_params,\n \"path\": path_params\n }\n for key, value in self.url_params.items():\n param_map[value[0]].append(f\"'{key}': {value[1]}\")\n\n query_str = \"{}\"\n path_str = \"{}\"\n\n if query_params:\n query_str = \"{\" + \", \".join(query_params) + \"}\"\n\n if path_params:\n path_str = \"{\" + \", \".join(path_params) + \"}\"\n\n return query_str, path_str",
"def params_url(self):\n return {\"address\": self.adress.replace(\" \", \"+\"),\n \"key\": self.GOOGLE_KEY}",
"def _get_url_param(self, category):\n res = get_nested(ATTR_CONFIG, category)\n\n if type(res) == dict and 'default' in res:\n return res[\"default\"] # for the root value\n else:\n return res",
"def _get_extra_info(self, payload, **options):\n\n return None",
"def get_pagination_vars(self):\n data = self.filter_data.copy()\n data = {k: v for k, v in data.items() if v and k not in self.url_kwargs}\n if data:\n return \"&\" + urlencode(data)\n return \"\""
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get the url mask to trigger builds.
|
def trigger_plan_url_mask(self):
return self.__trigger_plan_url_mask
|
[
"def artifact_url_mask(self):\n return self.__artifact_url_mask",
"def query_plan_url_mask(self):\n return self.__query_plan_url_mask",
"def latest_queue_url_mask(self):\n return self.__latest_queue_url_mask",
"def plan_results_url_mask(self):\n return self.__plan_results_url_mask",
"def mask_cmd(self):\r\n return self.findParam(('maskgroup', 'cmdmask')).getValue()",
"def getMaskFunction(self):\n return self.mask",
"def get_flag_url(self):\n return self.flag_url",
"def stop_plan_url_mask(self):\n return self.__stop_plan_url_mask",
"def netmask(self) -> Optional[str]:\n return pulumi.get(self, \"netmask\")",
"def network_mask(self):\n ret = self._get_attr(\"networkMask\")\n return ret",
"def _url_http_format(self):\n return self.__url_root + self.__url_suffix_repo",
"def get_ipmask(self):\n return self._fields['ipmask']",
"def hostmask(self):\n hostmask = (1 << (self._module.width - self._prefixlen)) - 1\n return IPAddress(hostmask, self._module.version)",
"def get_masks(target):\n path = STYLE_MASK_PATH if target else CONTENT_MASK_PATH\n masks = [f for f in os.listdir(path) if is_jpg_mask(f)]\n return masks",
"def _default_masks_root(self) -> str:\n concept_hash = '{}_rad{:.3}' \\\n .format('-'.join(sorted(self.keypoint_names)), self.pt_radius)\n masks_basename = \"{img_base}_{concept_hash}\".format(\n img_base=os.path.basename(self.dataset_root),\n concept_hash=concept_hash)\n masks_dirname = os.path.join(\n os.path.dirname(os.path.dirname(self.dataset_root)),\n \"masks\"\n )\n return os.path.join(masks_dirname, masks_basename)",
"def _hostmask_int(self):\n return (1 << (self._module.width - self._prefixlen)) - 1",
"def mask(self):\r\n arg_str = p2e._base._util._convert_args_to_string(\"get.object.mask\", self._object._eco_id)\r\n val = p2e._app.Request(arg_str)\r\n mask_index = p2e._base._util._convert_str_to_type(val, int)\r\n return p2e.model._masks[mask_index]",
"def get_mask(op_weights):\n return op_weights[\"mask\"]",
"def url_map(self) -> str:\n return pulumi.get(self, \"url_map\")"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get the url mask to stop the current running plan.
|
def stop_plan_url_mask(self):
return self.__stop_plan_url_mask
|
[
"def query_plan_url_mask(self):\n return self.__query_plan_url_mask",
"def trigger_plan_url_mask(self):\n return self.__trigger_plan_url_mask",
"def plan_results_url_mask(self):\n return self.__plan_results_url_mask",
"def latest_queue_url_mask(self):\n return self.__latest_queue_url_mask",
"def via_stop_layer(self):\n return list(self.via_layers)[-1]",
"def netmask(self) -> Optional[str]:\n return pulumi.get(self, \"netmask\")",
"def get_ipmask(self):\n return self._fields['ipmask']",
"def getMaskFunction(self):\n return self.mask",
"def artifact_url_mask(self):\n return self.__artifact_url_mask",
"def network_mask(self):\n ret = self._get_attr(\"networkMask\")\n return ret",
"def mask_cmd(self):\r\n return self.findParam(('maskgroup', 'cmdmask')).getValue()",
"def stop_server(self):\n response = requests.post(self._build_url(\"stop\"))\n return response",
"def cancel_reminder_url(self):\n return f\"//{Site.objects.get_current()}\" + reverse(\n \"reminders_cancel\",\n kwargs={\"pk\": self.pk, \"key\": self.get_generate_salted_hmac()},\n )",
"def mask(self):\r\n arg_str = p2e._base._util._convert_args_to_string(\"get.object.mask\", self._object._eco_id)\r\n val = p2e._app.Request(arg_str)\r\n mask_index = p2e._base._util._convert_str_to_type(val, int)\r\n return p2e.model._masks[mask_index]",
"def volume_scrub_stop(self, name=None):\n return self.request( \"volume-scrub-stop\", {\n 'name': [ name, 'name', [ basestring, 'None' ], False ],\n }, {\n } )",
"def get_flag_url(self):\n return self.flag_url",
"def get_mask_id(self):\n return self.sp.piece_to_id(self._mask)",
"def ifmask(ifname):\n return Ip(_ifctl(ifname, 0x891b)[20:24]) # SIOCGIFNETMASK",
"def getPolicyMask(self):\n return self.policy_mask"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get plan results url mask.
|
def plan_results_url_mask(self):
return self.__plan_results_url_mask
|
[
"def query_plan_url_mask(self):\n return self.__query_plan_url_mask",
"def trigger_plan_url_mask(self):\n return self.__trigger_plan_url_mask",
"def stop_plan_url_mask(self):\n return self.__stop_plan_url_mask",
"def artifact_url_mask(self):\n return self.__artifact_url_mask",
"def result_url(self):\n return self._result_url",
"def flag_url(self, flag_pk): \n self.c.execute(\"SELECT url FROM flags WHERE id=%s\", (flag_pk,))\n return self.c.fetchone()[0]",
"def get_show_url(self, name):",
"def url_map(self) -> str:\n return pulumi.get(self, \"url_map\")",
"def latest_queue_url_mask(self):\n return self.__latest_queue_url_mask",
"def results_url(self) -> str:\n return pulumi.get(self, \"results_url\")",
"def get_flag_url(self):\n return self.flag_url",
"def get_project_url(self):",
"def url(self):\n return api.selector +'?'+ urlencode(self.queries)",
"def get_full_url_sans_port(self):\n\n rval = self.get_full_domain()\n if self.dirpath:\n newpath = \"\".join([ x+'/' for x in self.dirpath])\n rval = \"\".join((rval, self.URLSEP, newpath))\n\n if rval[-1] != self.URLSEP:\n rval += self.URLSEP\n\n if self.filelike:\n rval = \"\".join((rval, self.filename))\n\n return self.make_valid_url(rval)",
"def public_records_url(self):\n # Not every site wants the Learner Records feature, so we allow opting out.\n if not is_learner_records_enabled():\n return None\n root = helpers.get_value('CREDENTIALS_PUBLIC_SERVICE_URL', settings.CREDENTIALS_PUBLIC_SERVICE_URL)\n return urljoin(root, '/records/')",
"def get_url_with_ip(self):\n url = \"https://www.virustotal.com/api/v3/ip_addresses/\"\n url += self.ipAddress\n return url",
"def _get_all_url(cls) -> str:",
"def get_plants_grid_urls_letter_results_monrovia(letter, start):\n url_base = 'http://www.monrovia.com/plant-catalog/plants/'\n page, dom = get_letter_search_results_monrovia(letter, start)\n urls = []\n print(letter, start)\n plants = dom.find('.plants-grid').find('.list-plant')\n for plant in plants:\n if plant.find('a') is not None:\n name = plant.find(\n 'a').text.replace(' ', '_').lower()\n link = plant.find('a').get('href')\n info = link.replace(url_base, '')\n data = dict(name=name, link=link, info=info)\n urls.append(data)\n ppr(urls)\n return urls",
"def planpath_baselink(self):\n\n if self.path_blade.header.frame_id == '':\n rospy.logerr(\"%s - cutsurface planning step cannot find filtered data\", self.name)\n return 1\n\n return 2"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get the query url mask.
|
def query_plan_url_mask(self):
return self.__query_plan_url_mask
|
[
"def query_url(self):\n return self._query_url",
"def plan_results_url_mask(self):\n return self.__plan_results_url_mask",
"def getParamMask(self):\n return _core.CGPopt_getParamMask(self)",
"def get_ipmask(self):\n return self._fields['ipmask']",
"def latest_queue_url_mask(self):\n return self.__latest_queue_url_mask",
"def mask_cmd(self):\r\n return self.findParam(('maskgroup', 'cmdmask')).getValue()",
"def trigger_plan_url_mask(self):\n return self.__trigger_plan_url_mask",
"def getParamMask(self):\n return _core.CGPbase_getParamMask(self)",
"def artifact_url_mask(self):\n return self.__artifact_url_mask",
"def getParamMask(self):\n return _core.CGPkronSum_getParamMask(self)",
"def getMaskFunction(self):\n return self.mask",
"def get_mask(op_weights):\n return op_weights[\"mask\"]",
"def path_qs(self):\n path = self.path\n qs = self.environ.get('QUERY_STRING')\n if qs:\n path += '?' + qs\n return path",
"def basic_query_url(self):\n return \"/?query=\"+self.value",
"def mask(self):\r\n arg_str = p2e._base._util._convert_args_to_string(\"get.object.mask\", self._object._eco_id)\r\n val = p2e._app.Request(arg_str)\r\n mask_index = p2e._base._util._convert_str_to_type(val, int)\r\n return p2e.model._masks[mask_index]",
"def network_mask(self):\n ret = self._get_attr(\"networkMask\")\n return ret",
"def _GetQueryURL(self, path):\n return \"http://{0}/{1}/{2}\".format(\n self._query_ip, self._query_version, path)",
"def _GetUrlParams(self, query=None):\n params = sum([c_w_c._GetUrlParams() for c_w_c in self.reactants], [])\n params.extend(self.aq_params._GetUrlParams())\n\n if query is not None:\n for arrow in constants.POSSIBLE_REACTION_ARROWS:\n tmp_query = query.replace(arrow, '=>')\n params.append('query=%s' % urllib.parse.quote(tmp_query))\n\n return params",
"def _encode_query(items: dict, *, mask=False) -> str:\n pairs = []\n for key in sorted(items.keys()):\n value = _MASK if mask and key in _MASKED_PARAMS else items[key]\n item = \"{}={}\".format(key, _quote(value))\n # Ensure 'url' goes last per CLI spec\n if key == \"url\":\n pairs.append(item)\n else:\n pairs.insert(0, item)\n return \"&\".join(pairs)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get latest queue url mask.
|
def latest_queue_url_mask(self):
return self.__latest_queue_url_mask
|
[
"def queue_url(self) -> pulumi.Output[str]:\n return pulumi.get(self, \"queue_url\")",
"def query_plan_url_mask(self):\n return self.__query_plan_url_mask",
"def artifact_url_mask(self):\n return self.__artifact_url_mask",
"def getQueueURL():\n q = SQS.get_queue_url(QueueName='RestaurantRequest').get(QUEUE_URL)\n logger.debug(\"Queue URL is %s\", QUEUE_URL)\n return q",
"def trigger_plan_url_mask(self):\n return self.__trigger_plan_url_mask",
"def get_task_queue_host():\n # modules.get_hostname sometimes fails with unknown internal error.\n # Cache its result in a memcache to avoid calling it too often.\n cache_key = 'task_queue_host:%s:%s' % (_task_queue_module, get_app_version())\n value = gae_memcache.get(cache_key)\n if not value:\n value = modules.get_hostname(module=_task_queue_module)\n gae_memcache.set(cache_key, value)\n return value",
"def get_queue(self):\n if self.queue is not None:\n return self.queue\n from timon.state import TMonQueue\n state = self.get_state()\n self.queue = queue = state.get_queue()\n #print(\"IQ\", queue)\n return self.queue",
"def get_queue(self, task_name):",
"def popUrl(self):\r\n url = None\r\n score = 0\r\n try:\r\n if self.qtype == 'q':\r\n url = self.__Queue.pop()\r\n elif self.qtype == 'p':\r\n url, score = self.__Queue.pop(withscores=True)\r\n except Exception as error:\r\n log.info('redisScheduler.RedisScheduler.popUrl ERROR(reason: %s)', error)\r\n\r\n return pUrl(url, score), None",
"def queue_time_out_url(self):\n return self._queue_time_out_url",
"def get_current_mask(self):\n return self.masks[self.curr_mask_index]",
"def plan_results_url_mask(self):\n return self.__plan_results_url_mask",
"def get_queue(self, queue: str, *, vhost: str = None):\n vhost = vhost if vhost is not None else self.vhost\n endpoint = self.build_url(\"/queues/{vhost}/{queue}\", vhost=vhost, queue=queue)\n return self.request('get', endpoint)",
"def queue(self):\n return self._get(\"me/player/queue\")",
"def _HotQueue__redis(self):\n return self.queue._HotQueue__redis",
"def get(self, queue_name):\n if queue_name not in self._queues.keys():\n raise NoSuchQueue(\"Queue {0} does not exist\".format(queue_name))\n\n try:\n address = self._queues[queue_name].pop(0)\n except IndexError:\n raise EmptyQueue(\"Queue {0} is empty\".format(queue_name))\n\n self._used_ips.add(address)\n\n return address",
"def parse_queue_urls(self, data):\n\n # In this case we return directly as the data that is\n # pushed exactly match this structure\n return data",
"def get_route_spec_queue(self):\n return self.q_route_spec",
"def queue(self):\n return self._cmd_queue"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get artifact url mask.
|
def artifact_url_mask(self):
return self.__artifact_url_mask
|
[
"def query_plan_url_mask(self):\n return self.__query_plan_url_mask",
"def latest_queue_url_mask(self):\n return self.__latest_queue_url_mask",
"def artifact_urls(self):\n data = self._api.get_api_data()\n artifacts_node = data['artifacts']\n retval = []\n\n for node in artifacts_node:\n url = urllib_parse.urljoin(\n self._api.url, \"artifact/\" + node['fileName'])\n retval.append(url)\n\n return retval",
"def _url_http_format(self):\n return self.__url_root + self.__url_suffix_repo",
"def _url_folder_format(self):\n return self.__url_root + self.__url_suffix_repo",
"def trigger_plan_url_mask(self):\n return self.__trigger_plan_url_mask",
"def getMaskTransparency():\n\n return _maskTransparency",
"def plan_results_url_mask(self):\n return self.__plan_results_url_mask",
"def get_url(self):\n return self._asset.get_url()",
"def get_masks(target):\n path = STYLE_MASK_PATH if target else CONTENT_MASK_PATH\n masks = [f for f in os.listdir(path) if is_jpg_mask(f)]\n return masks",
"def getIconUrl(self):",
"def getMaskFunction(self):\n return self.mask",
"def GetMaskImage(self) -> \"itkImageUS3 const *\":\n return _itkHistogramThresholdImageFilterPython.itkHistogramThresholdImageFilterIUS3IUS3_GetMaskImage(self)",
"def mask_cmd(self):\r\n return self.findParam(('maskgroup', 'cmdmask')).getValue()",
"def url_repo_http(self):\n return self._url_http_format.format(**self._git)",
"def GetMaskImage(self) -> \"itkImageUS3 const *\":\n return _itkHistogramThresholdImageFilterPython.itkHistogramThresholdImageFilterIF3IUS3_GetMaskImage(self)",
"def get_external_url():",
"def get_flag_url(self):\n return self.flag_url",
"def network_mask(self):\n ret = self._get_attr(\"networkMask\")\n return ret"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Trigger a build using Bamboo API.
|
def trigger_plan_build(self, bamboo_server=None, plan_key=None, req_values=None):
if not bamboo_server and not self.bamboo_server:
return {'content': "No Bamboo server supplied!"}
if not plan_key:
return {'content': "Incorrect input provided!"}
# Execute all stages by default if no options received
request_payload = {'stage&executeAllStages': [True]}
if req_values:
# req_values[0] = True/False
request_payload['stage&executeAllStages'] = [req_values[0]]
# Example
# req_value[1] = {'bamboo.driver': "xyz", bamboo.test': "xyz_1"}
# API supports a list as values
for key, value in req_values[1].items():
# Use custom revision when triggering build
if key.lower() == 'custom.revision':
request_payload["bamboo.customRevision"] = [value]
continue
request_payload["bamboo.{key}".format(key=key)] = [value]
url = "{url}{plan_key}.json".format(url=self.trigger_plan_url_mask.format(bamboo_server), plan_key=plan_key)
if self.verbose:
print("URL used to trigger build: '{url}'".format(url=url))
try:
response = requests.request('POST',
url=url,
auth=requests.auth.HTTPBasicAuth(self.account.username, self.account.password),
headers=self.headers,
data=json.dumps(request_payload),
timeout=30,
allow_redirects=False)
except (requests.RequestException, requests.ConnectionError, requests.HTTPError,
requests.ConnectTimeout, requests.Timeout) as err:
raise ValueError(
"Error when requesting URL: '{url}'{line_sep}{err}".format(url=url, line_sep=os.linesep, err=err)
)
except Exception as err:
raise Exception(
"Unknown error when requesting URL: '{url}'{line_sep}{err}".format(
url=url, line_sep=os.linesep, err=err
)
)
# Check HTTP response code
if response.status_code != 200:
return self.pack_response_to_client(
response=False, status_code=response.status_code, content=response.json(), url=url
)
try:
# Get the JSON reply from the web page
response.encoding = "utf-8"
response_json = response.json()
except ValueError as err:
raise ValueError("Error decoding JSON: {err}".format(err=err))
except Exception as err:
raise Exception("Unknown error: {err}".format(err=err))
# Send response to client
return self.pack_response_to_client(
response=True, status_code=response.status_code, content=response_json, url=url
)
|
[
"def RunBuildCmd(wspath, prj, bc):\n # TODO: Continue coding from here\n pass",
"def trigger_build(repository, payload_data):\n access_token = os.environ.get('QUAYIO_ACCESSTOKEN')\n quayio_apiurl = 'https://quay.io/api/v1/repository'\n\n if not access_token:\n raise RuntimeError(\"QUAYIO_ACCESSTOKEN environment variable is required\")\n\n command = ('curl -sS -XPOST', '-H \"Content-Type: application/json\"',\n '-H \"Authorization: Bearer {}\"'.format(access_token), '-d @-',\n \"{api}/{repository}/build/\".format(api=quayio_apiurl.strip('/'),\n repository=repository.strip('/')))\n\n result = shell_out(' '.join(command), payload_data)\n\n if result.failed:\n print result.output\n sys.exit(1)\n\n print_build_result(result.output)",
"def _trigger_build(self):\n if not self._dry_run():\n _gh_api.gh_http_post_request( \\\n '{}/repos/{}/dispatches'.format(self._config['GitHub']['service_url'],\n self._build_repo_full_name()),\n auth=self._config.auth(),\n params={'accept': 'application/vnd.github.v3+json'},\n json={'event_type': 'trigger-action'})\n self._log.info('Build triggered on \"%s\"', self._build_repo_full_name())\n else:\n self._log.info('Build triggered on \"%s\" (DRY RUN)', self._build_repo_full_name())",
"def build(ctx):\n ctx.run(BUILD_COMMAND)",
"def do_build_request(self, method, job_id, build_id, subcommand, **kwargs):\n base_url = random.choice(self.parent.config['frontends'])\n path = 'jobs/%s/builds' % job_id\n if build_id is not None:\n path = '%s/%s' % (path, build_id)\n if subcommand is not None:\n path = '%s/%s' % (path, subcommand)\n return self._do_request(base_url,\n method,\n path,\n **kwargs)",
"def build(args):\n descriptions = {\n 'success': \"Build succeeded.\",\n 'failure': \"Build failed.\",\n 'error': \"There was an error building.\",\n 'pending': \"Build results pending.\"}\n set_status(args, 'build', descriptions)",
"def test_build_hook(self):\n url = '/v1/apps'\n response = self.client.post(url, HTTP_AUTHORIZATION='token {}'.format(self.token))\n self.assertEqual(response.status_code, 201)\n app_id = response.data['id']\n build = {'username': 'autotest', 'app': app_id}\n url = '/v1/hooks/builds'.format(**locals())\n body = {'receive_user': 'autotest',\n 'receive_repo': app_id,\n 'image': '{app_id}:v2'.format(**locals())}\n # post the build without an auth token\n response = self.client.post(url, json.dumps(body), content_type='application/json')\n self.assertEqual(response.status_code, 401)\n # post the build with the builder auth key\n response = self.client.post(url, json.dumps(body), content_type='application/json',\n HTTP_X_DEIS_BUILDER_AUTH=settings.BUILDER_KEY)\n self.assertEqual(response.status_code, 200)\n self.assertIn('release', response.data)\n self.assertIn('version', response.data['release'])\n self.assertIn('domains', response.data)",
"def execute(self):\n if self.disabled:\n self.ci.trace(1, \"Build operation disabled\")\n return\n\n self.ci.trace(1, \"Executing build command: '\" + self.cmd + \"'..\")\n if not self.log_file:\n self.log_file = self.ci.tempnam(\"build\")\n self.t0 = self.t1 = self.ci.gettime()\n if self.wdir:\n cwd = os.getcwd()\n os.chdir(self.wdir)\n self.ci.trace(1, \" setting work directory: chdir \" + self.wdir)\n else:\n cwd = None\n\n ret = self.ci.exec_cmd(self.cmd,\n out_fname=self.log_file,\n filter_func=self._parse_output)\n\n if cwd is not None:\n os.chdir(cwd)\n\n if ret.error():\n self.have_err = True\n self.warn_err.append(BuildMsgItem(\"Error\", self.line_cnt,\n str(ret), \"\", 0))\n\n self.t1 = self.ci.gettime()",
"def process_jenkins_build(self):\n self.logger.info(\"Starting to process_jenkins_build\")\n\n title = self._cfg['title']\n if title == 'ss4gating':\n env = \"INT\"\n else:\n env = \"PROD\"\n\n last_build_url = self._cfg['jenkins_url']\n\n if self._cfg.influx_host:\n influx_host = self._cfg.influx_host\n else:\n influx_host = influx_config.INFLUXDBIP\n\n if self._cfg.influx_port:\n influx_port = self._cfg.influx_port\n else:\n influx_port = influx_config.PORT\n\n influx_client = influx_dbmanager.get_influx_client(influx_host,\n influx_port,\n influx_config.USERNAME,\n influx_config.PASSWORD,\n influx_config.DATABASENAME)\n try:\n data = http_requests.get(\n last_build_url +\n '/api/json?depth=1',\n auth=(\n self._cfg['jenkins_username'],\n self._cfg['jenkins_password']))\n except BaseException:\n self.logger.exception(\n 'Unknown error occurred while fetching job details in \\'process_jenkins_build\\'')\n return\n if data:\n # Fetch job details\n job_number = data.json()['number']\n joburl = data.json()['url']\n datetime_obj = datetime.datetime.fromtimestamp(\n data.json()['timestamp'] / 1000.0)\n timestamp = str(datetime_obj)\n jobresult = data.json()['result']\n self.logger.info(\n 'Latest job:(' +\n str(job_number) +\n ',' +\n joburl +\n ',' +\n timestamp +\n ',' +\n jobresult +\n ')')\n self.logger.info(\"details does not exists\")\n set_bot_cfg(self._cfg)\n set_logger(self.logger)\n parse_logs_result = parselogs(\n self._job_name, str(job_number), str(job_number))\n self.logger.info('the result for parse log results is %s' % parse_logs_result)\n global errors\n errors = soft_assert_errors()\n if title == 'meeting_launch_duration':\n meeting_launch_time = cilogparser2_gating.get_launch_time(joburl, auth=(self._cfg['jenkins_username'],\n self._cfg['jenkins_password']))\n self.logger.info(\"The meeting launch time is {}\".format(meeting_launch_time))\n if meeting_launch_time:\n if meeting_launch_time in range(4):\n category = 1\n elif meeting_launch_time in range(4, 10):\n category = 2\n elif meeting_launch_time > 10:\n category = 3\n try:\n if self._influx_write:\n self.logger.info(\"Inserting job result for passed case\")\n if not influx_dbmanager.write_meeting_data(influx_client, title, meeting_launch_time, category):\n self.logger.exception(\"Data for the successful test {} not written\"\n \" into the influx database\".format(title))\n except BaseException as e:\n self.logger.exception(\"Hit exception while to write to influx\", e)\n spark_util.post_spark_message(BOT_CRASH_NOTIFICATION_ROOM, e, self._cfg['bearer_token'])\n else:\n self.logger.info(\"Influx write is false. No data written to the database\")\n\n if parse_logs_result and parse_logs_result[3] == 0 and parse_logs_result[9] == 0:\n job_msg_result = 'SUCCESS'\n elif parse_logs_result and parse_logs_result[3] == 0 and parse_logs_result[9] > 0:\n job_msg_result = 'SUCCESS with Retries'\n elif jobresult == 'ABORTED':\n job_msg_result = 'ABORTED'\n elif parse_logs_result and jobresult == 'FAILURE':\n job_msg_result = 'FAILURE'\n elif not parse_logs_result:\n job_msg_result = 'UNDETERMINED'\n self.logger.info(\"The job result is {}\".format(job_msg_result))\n\n if parse_logs_result and len(parse_logs_result[8].keys()) == 1 and 'afterSuite' in parse_logs_result[\n 8].keys():\n job_msg_result = 'SUCCESS'\n # Post in Spark room if there is a failure\n if job_msg_result != 'SUCCESS' and jobresult != 'ABORTED':\n report_dict = self.process_failed_success_with_retries_build(\n datetime_obj, job_msg_result, parse_logs_result, job_number, joburl, env, influx_client)\n elif job_msg_result != 'SUCCESS' and jobresult == 'ABORTED':\n self.process_aborted_build(job_number, joburl, title, influx_client)\n elif job_msg_result == 'SUCCESS':\n self.process_success_build(job_number, joburl, title, influx_client, parse_logs_result[2])\n else:\n job_msg_result = 'UNDETERMINED'\n undetermined_msg = 'The build {} has failed/aborted/not anlayzed/ could not' \\\n ' find the report for this run'.format(last_build_url)\n if job_msg_result == 'UNDETERMINED':\n spark_util.post_spark_message(self._cfg['spark_room'],\n undetermined_msg,\n self._cfg['bearer_token'])",
"async def post_projectversion_toggle_ci(request):\n projectversion_id = request.match_info[\"projectversion_id\"]\n try:\n projectversion_id = int(projectversion_id)\n except (ValueError, TypeError):\n return web.Response(text=\"Incorrect value for projectversion_id\", status=400)\n\n projectversion = (\n request.cirrina.db_session.query(ProjectVersion)\n .filter(ProjectVersion.id == projectversion_id) # pylint: disable=no-member\n .first()\n )\n\n if not projectversion:\n return web.Response(\n text=\"Projectversion#{projectversion_id} not found\".format(\n projectversion_id=projectversion_id\n ),\n status=400,\n )\n\n projectversion.ci_builds_enabled = not projectversion.ci_builds_enabled\n request.cirrina.db_session.commit() # pylint: disable=no-member\n\n result = \"enabled\" if projectversion.ci_builds_enabled else \"disabled\"\n\n logger.info(\n \"continuous integration builds %s on ProjectVersion '%s/%s'\",\n result,\n projectversion.project.name,\n projectversion.name,\n )\n\n return web.Response(text=\"Ci builds are now {}.\".format(result), status=200)",
"def main():\n \n jobInfo = jenkinsBase(jenkinsUrl)\n dbConn,cursor = mysqlConnect()\n \n updateProjectIndB(jobInfo, dbConn, cursor)\n buildsInfo(jobInfo, dbConn, cursor)",
"def sendchange(branch, revision, username, master, products):\n if isinstance(products, basestring):\n products = [products]\n cmd = [\n 'buildbot',\n 'sendchange',\n get_buildbot_username_param(),\n username,\n '--master',\n master,\n '--branch',\n branch,\n '-p',\n 'products:%s' % ','.join(products),\n '-p',\n 'script_repo_revision:%s' % revision,\n 'release_or_beta'\n ]\n logging.info(\"Executing: %s\" % cmd)\n run_cmd(cmd)",
"def build(self):\n\n build_dir = os.path.join(self.path, 'build')\n\n self.logger.info('Build started...')\n\n self.run_command('rm -rf %s' % self.path)\n self.run_command('git clone %s %s' % (GIT, self.path))\n self.run_command('mkdir -p %s' % build_dir)\n self.run_command('cmake ..', build_dir)\n self.run_command('make procam -j4', build_dir)",
"def run_build(steps, images):\n credentials, _ = google.auth.default()\n build_body = {\n 'steps': steps,\n 'timeout': str(6 * 3600) + 's',\n 'options': {\n 'machineType': 'N1_HIGHCPU_32'\n },\n 'images': images\n }\n cloudbuild = build('cloudbuild',\n 'v1',\n credentials=credentials,\n cache_discovery=False)\n build_info = cloudbuild.projects().builds().create(projectId=BASE_PROJECT,\n body=build_body).execute()\n build_id = build_info['metadata']['build']['id']\n logging.info('Build ID: %s', build_id)\n logging.info('Logs: %s',\n build_base_images.get_logs_url(build_id, BASE_PROJECT))",
"def wait(build_id):\n api = Heroku()\n\n while True:\n if api.check_build_status(build_id):\n break\n sleep(3)",
"def trigger_doc_build(self, config):\n api_token = None\n rtd_creds = config.get_config_item(READTHEDOCS_CREDS)\n if rtd_creds:\n api_token = rtd_creds['readthedocs_rdr_api_token']\n docs = ReadTheDocsHandler(api_token)\n\n try:\n if self.deploy_type == 'prod':\n docs.update_project_to_release(self.args.git_target)\n _logger.info(f'ReadTheDocs latest version default branch/tag updated to {self.args.git_target}')\n\n build_id = docs.build_the_docs(self.docs_version)\n _logger.info(f'Started documentation build for version {self.docs_version} (build ID: {build_id})')\n except (ValueError, RuntimeError) as e:\n _logger.error(f'Failed to trigger readthedocs documentation build for version {self.docs_version}. {e}')",
"def get_buildURL(self):\n return 'http://build.dimagi.com:250/viewLog.html?buildTypeId=bt%s&buildNumber=%s' % \\\n (self.project.project_id, self.build_number)",
"def upload_build():\n\n if not os.path.exists('./auth'):\n print ('WARNING: Unable to upload build. auth file not found. '\n 'Set your credentials in auth file (username,password)')\n return\n\n fname = bpath('build.zip')\n user, password = open('./auth').read().strip().split(',')\n result = commands.getoutput('curl -u %s:%s -X PUT -F file=@%s %s' % (user, password, fname, PHONEGAP_API_URL))\n\n if not '\"error\":{}' in result:\n print result\n else:\n print 'Build uploaded'",
"def test_build_hook_procfile(self):\n url = '/v1/apps'\n response = self.client.post(url, HTTP_AUTHORIZATION='token {}'.format(self.token))\n self.assertEqual(response.status_code, 201)\n app_id = response.data['id']\n build = {'username': 'autotest', 'app': app_id}\n url = '/v1/hooks/builds'.format(**locals())\n PROCFILE = {'web': 'node server.js', 'worker': 'node worker.js'}\n SHA = 'ecdff91c57a0b9ab82e89634df87e293d259a3aa'\n body = {'receive_user': 'autotest',\n 'receive_repo': app_id,\n 'image': '{app_id}:v2'.format(**locals()),\n 'sha': SHA,\n 'procfile': PROCFILE}\n # post the build without an auth token\n response = self.client.post(url, json.dumps(body), content_type='application/json')\n self.assertEqual(response.status_code, 401)\n # post the build with the builder auth key\n response = self.client.post(url, json.dumps(body), content_type='application/json',\n HTTP_X_DEIS_BUILDER_AUTH=settings.BUILDER_KEY)\n self.assertEqual(response.status_code, 200)\n self.assertIn('release', response.data)\n self.assertIn('version', response.data['release'])\n self.assertIn('domains', response.data)\n # make sure build fields were populated\n url = '/v1/apps/{app_id}/builds'.format(**locals())\n response = self.client.get(url, HTTP_AUTHORIZATION='token {}'.format(self.token))\n self.assertEqual(response.status_code, 200)\n self.assertIn('results', response.data)\n build = response.data['results'][0]\n self.assertEqual(build['sha'], SHA)\n self.assertEqual(build['procfile'], PROCFILE)\n # test listing/retrieving container info\n url = \"/v1/apps/{app_id}/containers/web\".format(**locals())\n response = self.client.get(url, HTTP_AUTHORIZATION='token {}'.format(self.token))\n self.assertEqual(response.status_code, 200)\n self.assertEqual(len(response.data['results']), 1)\n container = response.data['results'][0]\n self.assertEqual(container['type'], 'web')\n self.assertEqual(container['num'], 1)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Query a plan build using Bamboo API.
|
def query_plan(self, bamboo_server=None, plan_key=None, query_type=None):
if not bamboo_server and not self.bamboo_server:
return {'content': "No Bamboo server supplied!"}
if not plan_key or not query_type:
return {'content': "Incorrect input provided!"}
self.bamboo_server = bamboo_server
self.plan_key = plan_key
url = self.compound_url(query_type)
if self.verbose:
print("URL used in query: '{url}'".format(url=url))
try:
response = requests.request('GET',
url=url,
auth=requests.auth.HTTPBasicAuth(self.account.username, self.account.password),
headers=self.headers,
timeout=30,
allow_redirects=False)
except (requests.RequestException, requests.ConnectionError, requests.HTTPError,
requests.ConnectTimeout, requests.Timeout) as err:
raise ValueError(
"Error when requesting URL: '{url}'{line_sep}{err}".format(url=url, line_sep=os.linesep, err=err)
)
except Exception as err:
raise Exception(
"Unknown error when requesting URL: '{url}'{line_sep}{err}".format(
url=url, line_sep=os.linesep, err=err
)
)
# Check HTTP response code
if response.status_code != 200:
return self.pack_response_to_client(
response=False, status_code=response.status_code, content=response.json(), url=url
)
try:
# Get the JSON reply from the web page
response.encoding = "utf-8"
response_json = response.json()
except ValueError as err:
raise ValueError("Error decoding JSON: {err}".format(err=err))
except Exception as err:
raise Exception("Unknown error: {err}".format(err=err))
# Send response to client
return self.pack_response_to_client(
response=True, status_code=response.status_code, content=response_json, url=url
)
|
[
"def stop_build(self, bamboo_server=None, plan_key=None, query_type=None):\n\n if not bamboo_server and not self.bamboo_server:\n return {'content': \"No Bamboo server supplied!\"}\n\n if not plan_key:\n return {'content': \"No Bamboo plan key provided!\"}\n\n self.bamboo_server = bamboo_server\n self.plan_key = plan_key\n\n url = self.compound_url(query_type)\n\n if self.verbose:\n print(\"URL used to stop plan: '{url}'\".format(url=url))\n\n try:\n response = requests.request('POST',\n url=url,\n auth=requests.auth.HTTPBasicAuth(self.account.username, self.account.password),\n headers=self.headers,\n timeout=30,\n allow_redirects=True)\n except (requests.RequestException, requests.ConnectionError, requests.HTTPError,\n requests.ConnectTimeout, requests.Timeout) as err:\n raise ValueError(\n \"Error when requesting URL: '{url}'{line_sep}{err}\".format(url=url, line_sep=os.linesep, err=err)\n )\n except Exception as err:\n raise Exception(\n \"Unknown error when requesting URL: '{url}'{line_sep}{err}\".format(\n url=url, line_sep=os.linesep, err=err\n )\n )\n\n # Check HTTP response code\n if response.status_code != 200:\n return self.pack_response_to_client(\n response=False, status_code=response.status_code, content=response.json(), url=url\n )\n\n # Send response to client\n try:\n response.encoding = \"utf-8\"\n response_json = response.json()\n except Exception as err:\n if self.verbose:\n print(\"Unknown error when setting encoding to 'utf-8': {err}\".format(err=err))\n\n response_json = \"\"\n\n return self.pack_response_to_client(\n response=True, status_code=response.status_code, content=response_json, url=url\n )",
"def trigger_plan_build(self, bamboo_server=None, plan_key=None, req_values=None):\n\n if not bamboo_server and not self.bamboo_server:\n return {'content': \"No Bamboo server supplied!\"}\n\n if not plan_key:\n return {'content': \"Incorrect input provided!\"}\n\n # Execute all stages by default if no options received\n request_payload = {'stage&executeAllStages': [True]}\n if req_values:\n # req_values[0] = True/False\n request_payload['stage&executeAllStages'] = [req_values[0]]\n\n # Example\n # req_value[1] = {'bamboo.driver': \"xyz\", bamboo.test': \"xyz_1\"}\n # API supports a list as values\n for key, value in req_values[1].items():\n # Use custom revision when triggering build\n if key.lower() == 'custom.revision':\n request_payload[\"bamboo.customRevision\"] = [value]\n continue\n\n request_payload[\"bamboo.{key}\".format(key=key)] = [value]\n\n url = \"{url}{plan_key}.json\".format(url=self.trigger_plan_url_mask.format(bamboo_server), plan_key=plan_key)\n if self.verbose:\n print(\"URL used to trigger build: '{url}'\".format(url=url))\n try:\n response = requests.request('POST',\n url=url,\n auth=requests.auth.HTTPBasicAuth(self.account.username, self.account.password),\n headers=self.headers,\n data=json.dumps(request_payload),\n timeout=30,\n allow_redirects=False)\n except (requests.RequestException, requests.ConnectionError, requests.HTTPError,\n requests.ConnectTimeout, requests.Timeout) as err:\n raise ValueError(\n \"Error when requesting URL: '{url}'{line_sep}{err}\".format(url=url, line_sep=os.linesep, err=err)\n )\n except Exception as err:\n raise Exception(\n \"Unknown error when requesting URL: '{url}'{line_sep}{err}\".format(\n url=url, line_sep=os.linesep, err=err\n )\n )\n\n # Check HTTP response code\n if response.status_code != 200:\n return self.pack_response_to_client(\n response=False, status_code=response.status_code, content=response.json(), url=url\n )\n\n try:\n # Get the JSON reply from the web page\n response.encoding = \"utf-8\"\n response_json = response.json()\n except ValueError as err:\n raise ValueError(\"Error decoding JSON: {err}\".format(err=err))\n except Exception as err:\n raise Exception(\"Unknown error: {err}\".format(err=err))\n\n # Send response to client\n return self.pack_response_to_client(\n response=True, status_code=response.status_code, content=response_json, url=url\n )",
"def test_get_plan_by_id(self):\n response = self.client.open(\n '/phuthien007/test/1.0.0/api/plans/{plan_id}'.format(plan_id=789),\n method='GET')\n self.assert200(response,\n 'Response body is : ' + response.data.decode('utf-8'))",
"def test_get_all_plans(self):\n query_string = [('key_word', 'key_word_example'),\n ('page_num', 1.2),\n ('records_per_page', 1.2)]\n response = self.client.open(\n '/phuthien007/test/1.0.0/api/plans',\n method='GET',\n query_string=query_string)\n self.assert200(response,\n 'Response body is : ' + response.data.decode('utf-8'))",
"def plan_details(request, plan_id):\n header = get_api_header()\n resp = r.get(_url_plans(_base_url(request)),\n headers=header, params={'id': plan_id},verify=False)\n if resp.status_code != 200:\n return {}\n else:\n result = json.loads(resp.content)\n if result[u'count'] == 0:\n return {}\n else:\n return result[u'results'][0]",
"def get_plan(self, job_id):\n return _execute_rest_request(url=f\"{self.prefix}/{job_id}/plan\")[\"plan\"]",
"def Get(self, request):\n if request.test_plan_id == '0':\n # For ID 0, return an empty test plan object to use as a template in UI.\n test_plan = ndb_models.TestPlan(id=0, name='')\n else:\n test_plan = mtt_messages.ConvertToKey(\n ndb_models.TestPlan, request.test_plan_id).get()\n if not test_plan:\n raise endpoints.NotFoundException(\n 'No test plan with ID %s' % request.test_plan_id)\n return mtt_messages.Convert(test_plan, mtt_messages.TestPlan)",
"def test_basic_query():\n rally = Rally(server=RALLY, user=RALLY_USER, password=RALLY_PSWD)\n response = rally.get('Project', fetch=False, limit=10)\n assert response.status_code == 200\n assert response.errors == []\n assert response.warnings == []\n assert response.resultCount > 0",
"def plan(options, config):\n if options.time is None or options.time == 'now':\n dt = datetime.now()\n else:\n dt = parse(options.time)\n url = config['url'] + '/plan'\n params = {\n 'fromPlace': options.from_location,\n 'toPlace': options.to_location,\n 'time': str(dt.time()),\n 'date': str(dt.date()),\n 'arriveBy': False,\n 'showIntermediateStops': False,\n 'maxWalkDistance': 750,\n 'mode': 'TRANSIT,WALK',\n }\n r = requests.get(url, params=params,\n auth=(config['username'], config['password']))\n r.raise_for_status()\n result = r.json()\n print_result(result)",
"def get_execution_plan(self):",
"def get_manage_scheduled_plans_by_filter(self, **kwargs):\n\n all_params = ['filter', 'page', 'limit', 'sort']\n all_params.append('callback')\n\n params = locals()\n for key, val in iteritems(params['kwargs']):\n if key not in all_params:\n raise TypeError(\n \"Got an unexpected keyword argument '%s'\"\n \" to method get_manage_scheduled_plans_by_filter\" % key\n )\n params[key] = val\n del params['kwargs']\n\n\n resource_path = '/beta/manageScheduledPlans/search'.replace('{format}', 'json')\n path_params = {}\n\n query_params = {}\n if 'filter' in params:\n query_params['filter'] = params['filter']\n if 'page' in params:\n query_params['page'] = params['page']\n if 'limit' in params:\n query_params['limit'] = params['limit']\n if 'sort' in params:\n query_params['sort'] = params['sort']\n\n header_params = {}\n\n form_params = []\n local_var_files = {}\n\n body_params = None\n\n # HTTP header `Accept`\n header_params['Accept'] = self.api_client.\\\n select_header_accept(['application/json'])\n if not header_params['Accept']:\n del header_params['Accept']\n\n # HTTP header `Content-Type`\n header_params['Content-Type'] = self.api_client.\\\n select_header_content_type([])\n\n # Authentication setting\n auth_settings = ['api_key']\n\n response = self.api_client.call_api(resource_path, 'GET',\n path_params,\n query_params,\n header_params,\n body=body_params,\n post_params=form_params,\n files=local_var_files,\n response_type='list[ManageScheduledPlans]',\n auth_settings=auth_settings,\n callback=params.get('callback'))\n return response",
"def list(self, **kwargs):\n def handle(response):\n if response.status_code == 204:\n return []\n return response.json()\n return self.request(\"get\", \"/plans\", handle_response=handle, params=kwargs)",
"def get_build(cloudbuild, image_project, build_id):\n return cloudbuild.projects().builds().get(projectId=image_project,\n id=build_id).execute()",
"def test_jenkins_test_plans(self, test_plan_name: str):\n tp.TestPlanDispatcher().dispatch_test_plan_for_pull_request(test_plan_name, self.info.number)",
"def do_show_plan(args):\n # Expand the query template.\n ns = setup_namespace(args.json_params)\n q = query_template.expand_file(args.qt_filename, ns)\n # Get the Redshift connection.\n conn = get_connection(args)\n cs = conn.cursor()\n # Set the query_group.\n conn_args = get_conn_args(args)\n query_group = _pick_query_group(args, conn_args)\n if query_group:\n cs.execute(\"SET query_group TO '%s';\" % (query_group,))\n logger.info(\"SET query_group TO '%s';\" % (query_group,))\n # Set the search_path.\n search_path = conn_args.get(\"search_path\")\n if search_path is not None:\n cs.execute(\"SET search_path TO %s;\" % (search_path,))\n logger.info(\"SET search_path TO %s;\" % (search_path,))\n # Run the explain.\n cs.execute(\"explain \"+q)\n # Write the plan to stdout.\n while 1:\n row = cs.fetchone()\n if row is None:\n break\n print row[0]",
"def query_base_benchmark_results(\n commit: str, verbose: bool = False\n) -> BenchmarkQueryResults:\n build_id = get_git_total_commit_count(commit, verbose)\n payload = {\"projectId\": IREE_PROJECT_ID, \"buildId\": build_id}\n return get_from_dashboard(\n f\"{IREE_DASHBOARD_URL}/getBuild\", payload, verbose=verbose\n )",
"def GetV2BuildByBuilderAndBuildNumber(project,\n bucket,\n builder_name,\n build_number,\n fields=None):\n builder = BuilderID(project=project, bucket=bucket, builder=builder_name)\n request = GetBuildRequest(\n builder=builder, build_number=build_number, fields=fields)\n status_code, content, response_headers = FinditHttpClient().Post(\n _BUILDBUCKET_V2_GET_BUILD_ENDPOINT,\n request.SerializeToString(),\n headers={'Content-Type': 'application/prpc; encoding=binary'})\n if status_code == 200 and response_headers.get('X-Prpc-Grpc-Code') == GRPC_OK:\n result = Build()\n result.ParseFromString(content)\n return result\n logging.warning('Unexpected prpc code: %s',\n response_headers.get('X-Prpc-Grpc-Code'))\n return None",
"def get(\n self, resource_group_name, plan_name, custom_headers=None, raw=False, **operation_config):\n # Construct URL\n url = self.get.metadata['url']\n path_format_arguments = {\n 'subscriptionId': self._serialize.url(\"self.config.subscription_id\", self.config.subscription_id, 'str'),\n 'resourceGroupName': self._serialize.url(\"resource_group_name\", resource_group_name, 'str', max_length=90, min_length=1),\n 'planName': self._serialize.url(\"plan_name\", plan_name, 'str', pattern=r'^[a-zA-Z0-9]')\n }\n url = self._client.format_url(url, **path_format_arguments)\n\n # Construct parameters\n query_parameters = {}\n query_parameters['api-version'] = self._serialize.query(\"self.api_version\", self.api_version, 'str')\n\n # Construct headers\n header_parameters = {}\n header_parameters['Accept'] = 'application/json'\n if self.config.generate_client_request_id:\n header_parameters['x-ms-client-request-id'] = str(uuid.uuid1())\n if custom_headers:\n header_parameters.update(custom_headers)\n if self.config.accept_language is not None:\n header_parameters['accept-language'] = self._serialize.header(\"self.config.accept_language\", self.config.accept_language, 'str')\n\n # Construct and send request\n request = self._client.get(url, query_parameters, header_parameters)\n response = self._client.send(request, stream=False, **operation_config)\n\n if response.status_code not in [200]:\n raise models.CodespacesPlanErrorResponseException(self._deserialize, response)\n\n deserialized = None\n\n if response.status_code == 200:\n deserialized = self._deserialize('CodespacesPlan', response)\n\n if raw:\n client_raw_response = ClientRawResponse(deserialized, response)\n return client_raw_response\n\n return deserialized",
"def raw_query(request: Request, sql, client, timer, stats=None):\n from snuba.clickhouse.native import NativeDriverReader\n\n project_ids = to_list(request.extensions['project']['project'])\n project_id = project_ids[0] if project_ids else 0 # TODO rate limit on every project in the list?\n stats = stats or {}\n grl, gcl, prl, pcl, use_cache, use_deduper, uc_max = state.get_configs([\n ('global_per_second_limit', None),\n ('global_concurrent_limit', 1000),\n ('project_per_second_limit', 1000),\n ('project_concurrent_limit', 1000),\n ('use_cache', 0),\n ('use_deduper', 1),\n ('uncompressed_cache_max_cols', 5),\n ])\n\n # Specific projects can have their rate limits overridden\n prl, pcl = state.get_configs([\n ('project_per_second_limit_{}'.format(project_id), prl),\n ('project_concurrent_limit_{}'.format(project_id), pcl),\n ])\n\n all_confs = state.get_all_configs()\n query_settings = {\n k.split('/', 1)[1]: v\n for k, v in all_confs.items()\n if k.startswith('query_settings/')\n }\n\n # Experiment, if we are going to grab more than X columns worth of data,\n # don't use uncompressed_cache in clickhouse, or result cache in snuba.\n if len(all_referenced_columns(request.query.get_body())) > uc_max:\n query_settings['use_uncompressed_cache'] = 0\n use_cache = 0\n\n timer.mark('get_configs')\n\n query_id = md5(force_bytes(sql)).hexdigest()\n with state.deduper(query_id if use_deduper else None) as is_dupe:\n timer.mark('dedupe_wait')\n\n result = state.get_result(query_id) if use_cache else None\n timer.mark('cache_get')\n\n stats.update({\n 'is_duplicate': is_dupe,\n 'query_id': query_id,\n 'use_cache': bool(use_cache),\n 'cache_hit': bool(result)}\n ),\n\n if result:\n status = 200\n else:\n with state.rate_limit('global', grl, gcl) as (g_allowed, g_rate, g_concurr):\n metrics.gauge('query.global_concurrent', g_concurr)\n stats.update({'global_rate': g_rate, 'global_concurrent': g_concurr})\n\n with state.rate_limit(project_id, prl, pcl) as (p_allowed, p_rate, p_concurr):\n stats.update({'project_rate': p_rate, 'project_concurrent': p_concurr})\n timer.mark('rate_limit')\n\n if g_allowed and p_allowed:\n\n # Experiment, reduce max threads by 1 for each extra concurrent query\n # that a project has running beyond the first one\n if 'max_threads' in query_settings and p_concurr > 1:\n maxt = query_settings['max_threads']\n query_settings['max_threads'] = max(1, maxt - p_concurr + 1)\n\n # Force query to use the first shard replica, which\n # should have synchronously received any cluster writes\n # before this query is run.\n consistent = request.extensions['performance'].get('consistent', False)\n stats['consistent'] = consistent\n if consistent:\n query_settings['load_balancing'] = 'in_order'\n query_settings['max_threads'] = 1\n\n try:\n result = NativeDriverReader(client).execute(\n sql,\n query_settings,\n # All queries should already be deduplicated at this point\n # But the query_id will let us know if they aren't\n query_id=query_id if use_deduper else None,\n with_totals=request.query.get_body().get('totals', False),\n )\n status = 200\n\n logger.debug(sql)\n timer.mark('execute')\n stats.update({\n 'result_rows': len(result['data']),\n 'result_cols': len(result['meta']),\n })\n\n if use_cache:\n state.set_result(query_id, result)\n timer.mark('cache_set')\n\n except BaseException as ex:\n error = str(ex)\n status = 500\n logger.exception(\"Error running query: %s\\n%s\", sql, error)\n if isinstance(ex, ClickHouseError):\n result = {'error': {\n 'type': 'clickhouse',\n 'code': ex.code,\n 'message': error,\n }}\n else:\n result = {'error': {\n 'type': 'unknown',\n 'message': error,\n }}\n\n else:\n status = 429\n Reason = namedtuple('reason', 'scope name val limit')\n reasons = [\n Reason('global', 'concurrent', g_concurr, gcl),\n Reason('global', 'per-second', g_rate, grl),\n Reason('project', 'concurrent', p_concurr, pcl),\n Reason('project', 'per-second', p_rate, prl)\n ]\n reason = next((r for r in reasons if r.limit is not None and r.val > r.limit), None)\n result = {'error': {\n 'type': 'ratelimit',\n 'message': 'rate limit exceeded',\n 'detail': reason and '{r.scope} {r.name} of {r.val:.0f} exceeds limit of {r.limit:.0f}'.format(r=reason)\n }}\n\n stats.update(query_settings)\n\n if settings.RECORD_QUERIES:\n # send to redis\n state.record_query({\n 'request': request.body,\n 'sql': sql,\n 'timing': timer,\n 'stats': stats,\n 'status': status,\n })\n\n # send to datadog\n tags = [\n 'status:{}'.format(status),\n 'referrer:{}'.format(stats.get('referrer', 'none')),\n 'final:{}'.format(stats.get('final', False))\n ]\n mark_tags = [\n 'final:{}'.format(stats.get('final', False))\n ]\n timer.send_metrics_to(metrics, tags=tags, mark_tags=mark_tags)\n\n result['timing'] = timer\n\n if settings.STATS_IN_RESPONSE or request.extensions['performance'].get('debug', False):\n result['stats'] = stats\n result['sql'] = sql\n\n return (result, status)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Download artifacts from Bamboo plan.
|
def get_artifact(self, bamboo_server=None, plan_key=None, query_type=None, job_name=None, artifact_name=None,
url_extra_values=None, destination_file=None):
if not bamboo_server and not self.bamboo_server:
return {'content': "No Bamboo server supplied!"}
if not plan_key or not query_type or not job_name or not artifact_name or not destination_file:
return {'content': "Incorrect input provided!"}
self.bamboo_server = bamboo_server
self.plan_key = plan_key
self.job_name = job_name
self.artifact_name = artifact_name
if url_extra_values:
self.url_extra_values = url_extra_values
url = self.compound_url(query_type)
if self.verbose:
print("URL used to download artifact: '{url}'".format(url=url))
try:
response = requests.request('GET',
url=url,
auth=requests.auth.HTTPBasicAuth(self.account.username, self.account.password),
headers=self.headers,
timeout=60,
allow_redirects=False)
except (requests.RequestException, requests.ConnectionError, requests.HTTPError,
requests.ConnectTimeout, requests.Timeout) as err:
raise ValueError(
"Error when requesting URL: '{url}'{line_sep}{err}".format(url=url, line_sep=os.linesep, err=err)
)
except Exception as err:
raise Exception(
"Unknown error when requesting URL: '{url}'{line_sep}{err}".format(
url=url, line_sep=os.linesep, err=err
)
)
# Check HTTP response code
if response.status_code != 200:
return self.pack_response_to_client(
response=False, status_code=response.status_code, content=response.json(), url=url
)
try:
get_file = requests.get(url)
with open(destination_file, 'wb') as f:
f.write(get_file.content)
except ValueError as err:
raise ValueError("Error when downloading artifact: {err}".format(err=err))
except Exception as err:
raise Exception("Unknown error when downloading artifact: {err}".format(err=err))
# Send response to client
return self.pack_response_to_client(
response=True, status_code=response.status_code, content=None, url=url
)
|
[
"def download(self, nexus_hostname, target_dir):\n url = self.get_url(nexus_hostname)\n target_file = os.path.join(target_dir, self.filename)\n print(\"Will try to download from: %s and save as %s\" % (url, target_file))\n curl_args = ['curl', '-sSLA', 'fabric-deploy', url, '-o', target_file]\n\n status, stdout, stderr = local2(curl_args)\n return status, stdout, stderr",
"def download_project_files():\n log_path = os.getcwd() + \"/log/\"\n output = subprocess.getstatusoutput(\"cd AIstudio_Download && python ./aistudio_client.py\")\n with open(log_path + \"download.log\", \"a\") as flog:\n flog.write(\"%s\" % (output[1]))",
"def _download( self ):\n self._system.download_file(\"https://github.com/mastbaum/avalanche/tarball/\" + self._tar_name)",
"def download_build(source, user, passwd, last_date, filename, outdir):\n\n print \"Downloading build file: {}\".format(filename)\n url = source + last_date + '/' + filename\n print \"Url: {}\".format(url)\n r = requests.get(url, stream=True, auth=(user, passwd))\n with open(outdir + '/' + filename, 'wb') as f:\n for chunk in r.iter_content(chunk_size=16384):\n if chunk:\n f.write(chunk)\n f.flush()",
"def download(\n pipeline,\n revision,\n outdir,\n compress,\n force,\n tower,\n download_configuration,\n container_system,\n container_library,\n container_cache_utilisation,\n container_cache_index,\n parallel_downloads,\n):\n from nf_core.download import DownloadWorkflow\n\n dl = DownloadWorkflow(\n pipeline,\n revision,\n outdir,\n compress,\n force,\n tower,\n download_configuration,\n container_system,\n container_library,\n container_cache_utilisation,\n container_cache_index,\n parallel_downloads,\n )\n dl.download_workflow()",
"def download_job():\n\n metadata = FileMetaData()\n scraper = FileScraper()\n db_controller = DBController()\n\n try:\n metadata.file_url, metadata.date = scraper.get_file_metadata()\n except Exception as err:\n logger.error(f\"Could not get file metadata: {err}\")\n\n if db_controller.check_file_update(metadata):\n try:\n scraper.download_file(metadata)\n logger.info(\n f\"Download file from {metadata.file_url} on {metadata.date}\")\n except Exception as err:\n logger.error(f\"Could not download file: {err}\")\n\n db_controller.close_db()",
"def download(all):\n print(\"Downloading\")",
"def download(self):\n url = 'https://github.com/drphilmarshall/OM10/raw/master/data/qso_mock.fits'\n self.catalog = url.split('/')[-1]\n if self.vb: print('OM10: Looking for local catalog {:s}'.format(self.catalog))\n if not os.path.isfile(self.catalog):\n urllib.request.urlretrieve(url, self.catalog)\n if self.vb: print('OM10: Downloaded catalog: {:s}'.format(self.catalog))\n else:\n if self.vb: print('OM10: File already exists, no need to download.')\n return",
"def download_url():",
"def download_stock_data(self):\n if not os.path.exists(self.output_path):\n os.makedirs(self.output_path)\n print(\"Output Directory created\", self.output_path)\n\n print(\"[INFO] Path to company data:\", self.output_path)\n print(\"[INFO] Starting download \" + re.sub(r'apikey=[A-Za-z0-9]+&', 'apikey=my_api_key&', self.url))\n request.urlretrieve(self.url, self.file_path)\n print(\"[INFO] Finish download data\")",
"def fetch_artifacts(client, out_dir, target, pattern, build_id):\n if not os.path.exists(out_dir):\n os.makedirs(out_dir)\n\n # Build a list of needed artifacts\n artifacts = list_artifacts(\n client=client,\n regex=pattern,\n buildId=build_id,\n target=target)\n\n for artifact in artifacts:\n fetch_artifact(\n client=client,\n build_id=build_id,\n target=target,\n resource_id=artifact,\n dest=os.path.join(out_dir, artifact))",
"def _wget_download(self):\n print(\"Info : Starting to download with wget %s ...\" %\n (self._data_requirement_file[\"src\"]))\n # Try it few times to avoid truncated data\n attempts = 0\n while attempts < 3:\n # Download with standard weblink\n try:\n wget.download(\n self._data_requirement_file[\"src\"], out=self._dst_path)\n print(\" \")\n attempts = 999\n except urllib.error.ContentTooShortError:\n attempts = attempts + 1\n print(\"Warning : Truncated data, retry %d ...\" % (attempts))\n pass",
"def stop_build(self, bamboo_server=None, plan_key=None, query_type=None):\n\n if not bamboo_server and not self.bamboo_server:\n return {'content': \"No Bamboo server supplied!\"}\n\n if not plan_key:\n return {'content': \"No Bamboo plan key provided!\"}\n\n self.bamboo_server = bamboo_server\n self.plan_key = plan_key\n\n url = self.compound_url(query_type)\n\n if self.verbose:\n print(\"URL used to stop plan: '{url}'\".format(url=url))\n\n try:\n response = requests.request('POST',\n url=url,\n auth=requests.auth.HTTPBasicAuth(self.account.username, self.account.password),\n headers=self.headers,\n timeout=30,\n allow_redirects=True)\n except (requests.RequestException, requests.ConnectionError, requests.HTTPError,\n requests.ConnectTimeout, requests.Timeout) as err:\n raise ValueError(\n \"Error when requesting URL: '{url}'{line_sep}{err}\".format(url=url, line_sep=os.linesep, err=err)\n )\n except Exception as err:\n raise Exception(\n \"Unknown error when requesting URL: '{url}'{line_sep}{err}\".format(\n url=url, line_sep=os.linesep, err=err\n )\n )\n\n # Check HTTP response code\n if response.status_code != 200:\n return self.pack_response_to_client(\n response=False, status_code=response.status_code, content=response.json(), url=url\n )\n\n # Send response to client\n try:\n response.encoding = \"utf-8\"\n response_json = response.json()\n except Exception as err:\n if self.verbose:\n print(\"Unknown error when setting encoding to 'utf-8': {err}\".format(err=err))\n\n response_json = \"\"\n\n return self.pack_response_to_client(\n response=True, status_code=response.status_code, content=response_json, url=url\n )",
"def inception_v3_download():",
"def test_downloading(self):\n #from os.path import join, abspath, dirname\n #deam_rel_root = dirname(dirname(abspath(__file__)))\n #repo_handler = RepositoryHandler(join(deam_rel_root, 'testing'))\n # repo_handler.execute(False)\n self.assertEqual(True)",
"def download_workflow(self):\n\n # Get workflow details\n try:\n self.prompt_pipeline_name()\n self.pipeline, self.wf_revisions, self.wf_branches = nf_core.utils.get_repo_releases_branches(\n self.pipeline, self.wfs\n )\n self.prompt_revision()\n self.get_revision_hash()\n # Inclusion of configs is unnecessary for Tower.\n if not self.tower and self.include_configs is None:\n self.prompt_config_inclusion()\n # If a remote cache is specified, it is safe to assume images should be downloaded.\n if not self.container_cache_utilisation == \"remote\":\n self.prompt_container_download()\n else:\n self.container_system = \"singularity\"\n self.prompt_singularity_cachedir_creation()\n self.prompt_singularity_cachedir_utilization()\n self.prompt_singularity_cachedir_remote()\n # Nothing meaningful to compress here.\n if not self.tower:\n self.prompt_compression_type()\n except AssertionError as e:\n raise DownloadError(e) from e\n\n summary_log = [\n f\"Pipeline revision: '{', '.join(self.revision) if len(self.revision) < 5 else self.revision[0]+',['+str(len(self.revision)-2)+' more revisions],'+self.revision[-1]}'\",\n f\"Use containers: '{self.container_system}'\",\n ]\n if self.container_system:\n summary_log.append(f\"Container library: '{', '.join(self.container_library)}'\")\n if self.container_system == \"singularity\" and os.environ.get(\"NXF_SINGULARITY_CACHEDIR\") is not None:\n summary_log.append(f\"Using [blue]$NXF_SINGULARITY_CACHEDIR[/]': {os.environ['NXF_SINGULARITY_CACHEDIR']}'\")\n if self.containers_remote:\n summary_log.append(\n f\"Successfully read {len(self.containers_remote)} containers from the remote '$NXF_SINGULARITY_CACHEDIR' contents.\"\n )\n\n # Set an output filename now that we have the outdir\n if self.tower:\n self.output_filename = f\"{self.outdir}.git\"\n summary_log.append(f\"Output file: '{self.output_filename}'\")\n elif self.compress_type is not None:\n self.output_filename = f\"{self.outdir}.{self.compress_type}\"\n summary_log.append(f\"Output file: '{self.output_filename}'\")\n else:\n summary_log.append(f\"Output directory: '{self.outdir}'\")\n\n if not self.tower:\n # Only show entry, if option was prompted.\n summary_log.append(f\"Include default institutional configuration: '{self.include_configs}'\")\n else:\n summary_log.append(f\"Enabled for seqeralabs® Nextflow Tower: '{self.tower}'\")\n\n # Check that the outdir doesn't already exist\n if os.path.exists(self.outdir):\n if not self.force:\n raise DownloadError(\n f\"Output directory '{self.outdir}' already exists (use [red]--force[/] to overwrite)\"\n )\n log.warning(f\"Deleting existing output directory: '{self.outdir}'\")\n shutil.rmtree(self.outdir)\n\n # Check that compressed output file doesn't already exist\n if self.output_filename and os.path.exists(self.output_filename):\n if not self.force:\n raise DownloadError(\n f\"Output file '{self.output_filename}' already exists (use [red]--force[/] to overwrite)\"\n )\n log.warning(f\"Deleting existing output file: '{self.output_filename}'\")\n os.remove(self.output_filename)\n\n # Summary log\n log.info(\"Saving '{}'\\n {}\".format(self.pipeline, \"\\n \".join(summary_log)))\n\n # Perform the actual download\n if self.tower:\n self.download_workflow_tower()\n else:\n self.download_workflow_static()",
"def __download_file(self):\n\n self.__logger.info('start download as %s', self.__args.output)\n\n video_file = open(self.__args.output, \"wb\")\n curl = pycurl.Curl()\n curl.setopt(pycurl.URL, self.__video_url)\n curl.setopt(pycurl.WRITEDATA, video_file)\n curl.setopt(curl.NOPROGRESS, False)\n curl.setopt(curl.XFERINFOFUNCTION, Streamcloud.__progress)\n curl.perform()\n curl.close()\n video_file.close()\n\n self.__logger.info('finish download as %s', self.__args.output)",
"def _download_datasets():\n def filepath(*args):\n return abspath(join(dirname(__file__), *args))\n for name in DATASETS_TO_DOWNLOAD:\n data = Dataset(name)\n url = data.url\n filename = filepath(data.filename)\n print(\"retrieving data {0} -> {1}\".format(url, filename))\n urlretrieve(url, filename)\n with open(filepath('listing.txt'), 'w') as f:\n f.write('\\n'.join(DATASETS_TO_DOWNLOAD) + '\\n')",
"def download( self ):\n urls = [ self.root_url ]\n\n while len( urls ) > 0:\n url = urls.pop()\n if self.is_raw_file( url ):\n print( \"is raw {}\".format( url ) )\n self.download_raw_file( url )\n elif self.is_folder( url ):\n for f in self.parse_folder( url ):\n if f.startswith( \"https://\" ) or f.startswith( \"http://\" ):\n urls.append( f )\n else: urls.append( \"https://github.com%s\" % f )\n else:\n self.download_raw_file( url )"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Stop a running plan from Bamboo using Bamboo API.
|
def stop_build(self, bamboo_server=None, plan_key=None, query_type=None):
if not bamboo_server and not self.bamboo_server:
return {'content': "No Bamboo server supplied!"}
if not plan_key:
return {'content': "No Bamboo plan key provided!"}
self.bamboo_server = bamboo_server
self.plan_key = plan_key
url = self.compound_url(query_type)
if self.verbose:
print("URL used to stop plan: '{url}'".format(url=url))
try:
response = requests.request('POST',
url=url,
auth=requests.auth.HTTPBasicAuth(self.account.username, self.account.password),
headers=self.headers,
timeout=30,
allow_redirects=True)
except (requests.RequestException, requests.ConnectionError, requests.HTTPError,
requests.ConnectTimeout, requests.Timeout) as err:
raise ValueError(
"Error when requesting URL: '{url}'{line_sep}{err}".format(url=url, line_sep=os.linesep, err=err)
)
except Exception as err:
raise Exception(
"Unknown error when requesting URL: '{url}'{line_sep}{err}".format(
url=url, line_sep=os.linesep, err=err
)
)
# Check HTTP response code
if response.status_code != 200:
return self.pack_response_to_client(
response=False, status_code=response.status_code, content=response.json(), url=url
)
# Send response to client
try:
response.encoding = "utf-8"
response_json = response.json()
except Exception as err:
if self.verbose:
print("Unknown error when setting encoding to 'utf-8': {err}".format(err=err))
response_json = ""
return self.pack_response_to_client(
response=True, status_code=response.status_code, content=response_json, url=url
)
|
[
"def StopBlp(self, request, context):\n context.code(beta_interfaces.StatusCode.UNIMPLEMENTED)",
"def stop(self):\n self.logger.debug('Server - td-agent-bit - stop call.')\n self.change_service_status(\"stop\")",
"def test_stop_running_job(self, db_session: Session) -> None:\n pass # TODO implement",
"def stop(self, instance: RuntimeInstance.Params, env: RuntimeEnvironment.Params, **kwargs):",
"def stop_instance(self, zone: str, resource_id: str, project_id: str) -> None:\n response = (\n self.get_conn()\n .instances()\n .stop(project=project_id, zone=zone, instance=resource_id)\n .execute(num_retries=self.num_retries)\n )\n try:\n operation_name = response[\"name\"]\n except KeyError:\n raise AirflowException(f\"Wrong response '{response}' returned - it should contain 'name' field\")\n self._wait_for_operation_to_complete(project_id=project_id, operation_name=operation_name, zone=zone)",
"def stop(self, source_id):\n return self.request.post('stop', dict(id=source_id))",
"def stop(self):\n if self.send('/stop', 'post') is None:\n self.delete()",
"def stop():\n driver.quit()\n result = status",
"def test_stop_run(self):\n pass",
"def stop_transport_process(self, process_num):",
"def test_del_plan_by_id(self):\n response = self.client.open(\n '/phuthien007/test/1.0.0/api/plans/{plan_id}'.format(plan_id=789),\n method='DELETE')\n self.assert200(response,\n 'Response body is : ' + response.data.decode('utf-8'))",
"def stop(queue: str, project: str):\n _stop_worker_pool(queue, project)",
"async def stop(self):\n self._init_events()\n if not self._should_stop.is_set():\n logger.info(\"Stopping opa runner\")\n self._should_stop.set()\n self._terminate_opa()\n await asyncio.sleep(1) # wait for opa process to go down\n\n if self._run_task is not None:\n await self._run_task\n self._run_task = None",
"def stop(self):\n self.tasks.stop()",
"def stop(self):\n Multipass.stop(self.name)",
"def cmd_stop_traffic(self, options, extra_vars):\n \n # uses the inventory created in ~/vars/f5aws/env/<env name> created by `init`\n inventory = '%s/%s/inventory/hosts' % (self.settings['env_path'], options.env_name)\n self.run_playbooks(['stop_traffic.yml'], inventory, options, extra_vars)\n print 'Stopped jmeter client.'",
"def stop(self):\n self.dispatch(Request.stop())",
"def stop_server(self):\n response = requests.post(self._build_url(\"stop\"))\n return response",
"def StopSlave(self, request, context):\n context.code(beta_interfaces.StatusCode.UNIMPLEMENTED)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Metodo que genera la matriz de rotacion para aplicar el pulso. Esta matriza es nx3x3, ya que es una matriz 3x3 para cada sitio. input
|
def generar_matriz_R(self, tp):
# modulo del campo en el plano xy
B1 = np.array([self.Bx, self.By])
B1 = np.linalg.norm(B1, axis=0)
# tres componentes de la direccion de rotacion. Cada U es un array de
# n elementos, uno por cada sitio. Uz son ceros porque el campo en z
# NO excita los spines.
Ux = self.Bx/B1
Uy = self.By/B1
Uz = np.zeros_like(Ux)
angulo = B1*tp
# array de ceros y unos de tamano nx1
zeros = np.zeros_like(Ux)
ones = np.ones_like(Ux)
# para definir la matriz uso la formula de Rodrigues:
# https://en.wikipedia.org/wiki/Rotation_matrix#Rotation_matrix_from_axis_and_angle
U_matrix = np.array([[ zeros, -Uz , Uy ],
[ Uz , zeros, -Ux ],
[-Uy , Ux , zeros]]
)
Uxy, Uxz, Uyz = [Ux*Uy, Ux*Uz, Uy*Uz]
U2_matrix = np.array([[Ux*Ux, Uxy , Uxz ],
[Uxy , Uy*Uy, Uyz ],
[Uxz , Uyz , Uz*Uz]]
)
I = np.array([[ones, zeros, zeros], [zeros, ones, zeros], [zeros, zeros, ones]])
R = np.cos(angulo) * I + np.sin(angulo) * U_matrix + (1-np.cos(angulo)) * U2_matrix
# convierto en array nx3x3
R = np.moveaxis(R,2,0)
return R
|
[
"def getRotationMatrix( self):",
"def rotation_matrix(self) -> Tensor:\n return self.extrinsics[..., :3, :3]",
"def rotar(matriz, NAXIS1, NAXIS2, angulo):\n\n matriz = NDData(matriz)\n if (angulo > 360 or angulo < 1):\n print \"<Error: Imagen no rotada, angulo no permitido>\"\n return matriz\n # ------ PARA 0 NO ES NECESARIO ROTAR ------ #\n if (angulo == 0 or angulo ==360):\n return matriz\n \n # ------ PARA 90, 180 y 270 ES UNA SIMPLE TRASLACION DE PUNTOS ------ #\n \n if (angulo == 90):\n matriz_final = np.zeros((NAXIS2,NAXIS1))\n matriz_final = NDData(matriz_final)\n for i in range(NAXIS1):\n for j in range(NAXIS2):\n matriz_final.data[NAXIS2 - j -1][i] = matriz.data[i][j]\n return matriz_final\n\n if (angulo == 180):\n matriz_final = np.zeros((NAXIS1,NAXIS2))\n matriz_final = NDData(matriz_final)\n for i in range(NAXIS1):\n for j in range(NAXIS2):\n matriz_final.data[NAXIS1 - i - 1][NAXIS2 - j -1] = matriz.data[i][j]\n return matriz_final\n\n if (angulo == 270):\n matriz_final = np.zeros((NAXIS2,NAXIS1))\n matriz_final = NDData(matriz_final)\n for i in range(NAXIS1):\n for j in range(NAXIS2):\n matriz_final.data[j][i] = matriz.data[i][j]\n return matriz_final\n\n else:\n \n coseno = math.cos((angulo*math.pi)/180)\n seno = math.sin((angulo*math.pi)/180)\n \n punto_central_x = int(round(NAXIS1/2))\n punto_central_y = int(round(NAXIS2/2))\n \n \n # --- Para rotar sobre el centro de la imagen, hay que hacer una pequena traslacion --- #\n # --- Conociendo la distancia del origen al centro de la imagen es suficiente --- #\n distancia_centro = int(round(info_imagen.distancia(0,0,punto_central_x,punto_central_y))) - 1\n \n # --- PUNTO MAS NEGATIVO EN X Y EN Y ---------------------- #\n # --- ESTO ES PARA DEJAR TODAS LAS POSICIONES POSITIVAS --- #\n vec = [0,0,NAXIS1,NAXIS2,NAXIS1,0,0,NAXIS2]\n fila_mas_negativa = columna_mas_negativa = 0\n fila_mas_positiva = columna_mas_positiva = 0\n\n for i in range(7):\n alfa = (vec[i]-distancia_centro)*coseno - (vec[i+1]-distancia_centro)*seno\n beta = (vec[i]-distancia_centro)*seno + (vec[i+1]-distancia_centro)*coseno\n\n if (alfa < fila_mas_negativa):\n fila_mas_negativa = int(math.ceil(alfa))\n if (alfa > fila_mas_positiva):\n fila_mas_positiva = int(math.ceil(alfa))\n if (beta < columna_mas_negativa):\n columna_mas_negativa = int(math.ceil(beta))\n if (beta > columna_mas_positiva):\n columna_mas_positiva = int(math.ceil(beta))\n\n distancia_1 = fila_mas_positiva + abs(fila_mas_negativa)\n distancia_2 = columna_mas_positiva + abs(columna_mas_negativa)\n matriz_final = np.zeros((distancia_1+1,distancia_2+1))\n matriz_final = NDData(matriz_final)\n\n for x in range(NAXIS1):\n for y in range(NAXIS2):\n \n # ---- a X e Y hay que restarle y luego sumarle la traslacion -- #\n a = ((x-distancia_centro)*coseno - (y-distancia_centro)*seno ) + abs(fila_mas_negativa)\n b = ((x-distancia_centro)*seno + (y-distancia_centro)*coseno ) + abs(columna_mas_negativa)\n\n bandera_decimal_a = 100\n bandera_decimal_b = 100\n\n if( a - int(a) != 0):\n bandera_decimal_a = 101\n if( b - int(b) != 0):\n bandera_decimal_b = 110\n \n #Ya que en python no existe switch, se hace artesanalmente\n suma_banderas = bandera_decimal_a + bandera_decimal_b\n \n while(1):\n \n porcentaje_columna_derecha = porcentaje_columna_izquierda = 0\n porcentaje_fila_abajo = porcentaje_fila_arriba = 0\n \n porcentaje_fila_arriba = abs(abs(a) - int(abs(a)))\n porcentaje_fila_abajo = 1 - porcentaje_fila_arriba\n porcentaje_columna_derecha = abs(abs(b) - int(abs(b)))\n porcentaje_columna_izquierda = 1 - porcentaje_columna_derecha\n\n \n #Solo A es decimal\n if(suma_banderas == 201):\n matriz_final.data[int(a)][b] += porcentaje_fila_abajo*matriz.data[x][y]\n matriz_final.data[math.ceil(a)][b] += porcentaje_fila_arriba*matriz.data[x][y]\n break\n \n #Solo B es decimal\n if(suma_banderas == 210):\n matriz_final.data[a][int(b)] += porcentaje_columna_izquierda*matriz.data[x][y]\n matriz_final.data[a][math.ceil(b)] += porcentaje_columna_derecha*matriz.data[x][y]\n break\n\n #Ambos son decimales\n if(suma_banderas == 211):\n matriz_final.data[int(a)][int(b)] += porcentaje_fila_abajo*porcentaje_columna_izquierda*matriz.data[x][y]\n matriz_final.data[math.ceil(a)][math.ceil(b)] += porcentaje_fila_arriba*porcentaje_columna_derecha*matriz.data[x][y]\n matriz_final.data[int(a)][math.ceil(b)] += porcentaje_fila_abajo*porcentaje_columna_derecha*matriz.data[x][y]\n matriz_final.data[math.ceil(a)][int(b)] += porcentaje_fila_arriba*porcentaje_columna_izquierda*matriz.data[x][y]\n break\n \n #Ambos son enteros\n if(suma_banderas == 200):\n matriz_final.data[a][b] = matriz.data[x][y]\n break\n \n return matriz_final",
"def _extract_rotation_matrix(self, mod):\n r = np.matrix(\n [\n [mod.rot_xu.item(), mod.rot_xv.item(), mod.rot_xw.item()],\n [mod.rot_yu.item(), mod.rot_yv.item(), mod.rot_yw.item()],\n [mod.rot_zu.item(), mod.rot_zv.item(), mod.rot_zw.item()],\n ]\n )\n return r",
"def rotation_matrix(self):\n return np.array([self.axis_u, self.axis_v, self.axis_w])",
"def rotate(self,R,xmultivars):\r\n\tn = len(xmultivars)\r\n\tnn = len(xmultivars[0])\r\n\tymultivars = []\r\n\tfor i in range(n): ymultivars.append([])\r\n\tfor i in range(nn):\r\n\t x0 = n*[0.] ##### It's an entry !!!!!!!, n is the number of variables !!\r\n\t for j in range(n): x0[j] = xmultivars[j][i]\r\n\t x0 = numpy.array(x0)\r\n\t #print x0\r\n\t #print R\r\n\t #u0 = numpy.array(numpy.matrixmultiply(R,x0))\r\n\t u0 = numpy.array(numpy.matrixmultiply(R,x0)) #!!!!!!!!!!!!!!!!!!!!!!!!!?/\r\n\t #print u0\r\n\t for j in range(n):\r\n # TODO: change from lxplus to Mac \r\n\t\tymultivars[j].append(u0[0][j])\r\n\t\t#print ymultivars[j][-1]\r\n\treturn ymultivars",
"def eulersToRotationMatrix(e1,e2,e3):\n\tcphi = math.cos(e1)\n\tsphi = math.sin(e1)\n\tctheta = math.cos(e2)\n\tstheta = math.sin(e2)\n\tcpsi = math.cos(e3)\n\tspsi = math.sin(e3)\n\n\tm11 = cphi*ctheta*cpsi-sphi*spsi\n\tm21 = -cphi*ctheta*spsi-sphi*cpsi\n\tm31 = cphi*stheta\n\tm12 = sphi*ctheta*cpsi+cphi*spsi\n\tm22 = -sphi*ctheta*spsi+cphi*cpsi\n\tm32 = sphi*stheta\n\tm13 = -stheta*cpsi\n\tm23 = stheta*spsi\n\tm33 = ctheta\n\n\treturn [[m11,m12,m13],[m21,m22,m23],[m31,m32,m33]]",
"def rotation_matrix(u):\n c = 0.0\n s = 1.0\n # u has to be a versor in the l2-norm\n u = u / np.linalg.norm(u)\n x = u[0]\n y = u[1]\n z = u[2]\n C = 1. - c\n R = np.array([\n [(x * x * C + c), (x * y * C - z * s), (x * z * C + y * s)],\n [(y * x * C + z * s), (y * y * C + c), (y * z * C - x * s)],\n [(z * x * C - y * s), (z * y * C + x * s), (z * z * C + c)]])\n return R",
"def transformation_matrix(self, s1, s2, s3, t1, t2 ,t3):\n\n s1 = np.array(s1)\n s2 = np.array(s2)\n s3 = np.array(s3)\n t1 = np.array(t1)\n t2 = np.array(t2)\n t3 = np.array(t3)\n\n Q = np.array([\n [t2[0] - t1[0], t2[1] - t1[1], t2[2] - t1[2]],\n [t3[0] - t1[0], t3[1] - t1[1], t3[2] - t1[2]]\n ])\n\n P = np.array([\n [s2[0] - s1[0], s2[1] - s1[1]],\n [s3[0] - s1[0], s3[1] - s1[1]]\n ])\n\n\n try:\n # Invert the P matrix\n Pinv = inv(P)\n\n # Build the dot product\n T = np.dot(Pinv, Q)\n\n # Offset\n V0 = np.subtract(t2,np.transpose(s2[0:2]).dot(T))\n except Exception as e:\n l.error(\"An error occured during the transformation with error: \" + str(e))\n return -1, -1\n\n return T, V0",
"def rotator_to_matrix(rotator: Rotator):\n return rotation_to_matrix([rotator.pitch, rotator.yaw, rotator.roll])",
"def getTranslationMatrix(t):\n mat = np.zeros((4,4))\n mat[0, 0] = 1\n mat[1, 1] = 1\n mat[2, 2] = 1\n mat[3, 0] = t[0]\n mat[3, 1] = t[1]\n mat[3, 2] = t[2]\n mat[3, 3] = 1\n return mat",
"def rotation_matrix(delta):\n return np.array([[np.cos(delta), -np.sin(delta)],[np.sin(delta), np.cos(delta)]])",
"def get_rotationMatrix(self):\n rot_mat = quat2mat(self.quat)\n try:\n [U, s, V] = np.linalg.svd(rot_mat)\n return np.dot(U, V)\n except:\n return np.eye(3)",
"def matrix_from_angles(rot):\n rank = len(rot.shape)\n # Swap the two last dimensions\n perm = torch.cat([torch.arange(start=0, end=rank-1), torch.tensor([rank]), torch.tensor([rank - 1])], dim=0)\n return from_euler(-rot).permute(tuple(perm.numpy()))",
"def rotation_matrices(self):\n matrices = []\n for r in self.rotations:\n matrices.append(cv2.Rodrigues(r))\n return matrices",
"def getMatrix(self, action: 'SoGetMatrixAction') -> \"void\":\n return _coin.SoRotation_getMatrix(self, action)",
"def _rotation_matrix(psi,theta,phi, R):\n cospsi = cos(psi)\n sinpsi = sin(psi)\n costheta = cos(theta)\n sintheta = sin(theta)\n cosphi = cos(phi)\n sinphi = sin(phi)\n\n sinphi_sinpsi = sinphi * sinpsi\n sinphi_cospsi = sinphi * cospsi \n\n cosphi_sinpsi = cosphi * sinpsi\n cosphi_cospsi = cosphi * cospsi\n \n R[0,0] = costheta * cosphi_cospsi - sinphi_sinpsi\n R[0,1] = - costheta * cosphi_sinpsi - sinphi_cospsi\n R[0,2] = cosphi * sintheta\n R[1,0] = costheta * sinphi_cospsi + cosphi_sinpsi\n R[1,1] = cosphi_cospsi - costheta * sinphi_sinpsi\n R[1,2] = sintheta * sinphi\n R[2,0] = - cospsi * sintheta\n R[2,1] = sintheta*sinpsi\n R[2,2] = costheta",
"def rot6d_to_rotmat_spin(x):\n x = x.view(-1,3,2)\n a1 = x[:, :, 0]\n a2 = x[:, :, 1]\n b1 = F.normalize(a1)\n b2 = F.normalize(a2 - torch.einsum('bi,bi->b', b1, a2).unsqueeze(-1) * b1)\n\n # inp = a2 - torch.einsum('bi,bi->b', b1, a2).unsqueeze(-1) * b1\n # denom = inp.pow(2).sum(dim=1).sqrt().unsqueeze(-1) + 1e-8\n # b2 = inp / denom\n\n b3 = torch.cross(b1, b2)\n return torch.stack((b1, b2, b3), dim=-1)",
"def rotation_matrix(angles, out): \n if len(angles) != 3:\n raise ValueError(\"Invalid input data shape\")\n _rotation_matrix(angles[0],angles[1],angles[2], out)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Displays the scatterplot of repeatedly applying function to the elements of inputs. X axis = input Y axis = function(input)
|
def show_scatter_plot(inputs, function, x_label, y_label):
inps = list(inputs)
plot.scatter(inps, [function(x) for x in inps])
plot.xlabel(x_label)
plot.ylabel(y_label)
plot.show()
|
[
"def show_scatterplot(self, *args, **kwargs):\n raise NotImplementedError()",
"def plot_results(my_func, my_points, min_x=-30, max_x=30, min_y=-30, max_y=30, nbx=100, nby=100, title=\"Title\"):\n X = np.linspace(min_x, max_x, num=nbx)\n Y = np.linspace(min_y, max_y, num=nby)\n Z=np.zeros((nbx,nby),dtype=np.double)\n for i in range(nbx):\n for j in range(nby):\n Z[i][j]=my_func([X[i],Y[j]])\n fig,ax=plt.subplots(figsize=(5,5))\n ax.set_xlim(min_x,max_x)\n ax.set_ylim(min_y,max_y)\n ax.imshow(Z, cmap='hot', interpolation='nearest',extent=(min_x,max_x,min_y,max_y))\n \n #print(\"Points: \"+str(my_points))\n x=[]\n y=[]\n for p in my_points:\n x.append(p[0])\n y.append(p[1])\n\n ax.plot(x,y,\".\")\n ax.set_title(title)\n plt.show()",
"def notebook_scatter(self,**kwargs):\n \n cols_x = self.data.columns\n cols_y = [self.data.columns[1],self.data.columns[0],*self.data.columns[2:]]\n\n @interact(\n x = cols_x,\n y = cols_y,\n hue = [self.dataset.target,*self.dataset.features,None],\n size = [None,*self.data.columns]\n )\n def show(x,y,hue,size):\n self.show_scatter(x,y,hue,size,**kwargs)",
"def function_graph(self):\n x = value_range()\n y = self.a * x ** 2 + self.b * x + self.c\n plt.plot(x, y)\n plt.show()",
"def plot_pairwise_feature_scatter(feature_sequence):\n nfeatures = np.shape(feature_sequence)[1]\n if nfeatures%2:\n f_s = np.insert(feature_sequence, nfeatures-1, feature_sequence[:,nfeatures-2], axis=1) #if uneven number of features, insert second-to-last feature before last feature like [0,1,2,3,3,4]\n nfeatures += 1 \n print(\"new shape\", np.shape(f_s))\n else:\n f_s = feature_sequence\n _,axarr = pyplot.subplots(1,nfeatures//2)\n if nfeatures == 2:\n axarr = [axarr]\n for i in range(nfeatures//2):\n f1 = f_s[:,i*2]\n f2 = f_s[:,i*2+1]\n #rangel = [[np.floor(np.min(f1)),np.ceil(np.max(f1))],[np.floor(np.min(f2)),np.ceil(np.max(f2))]]\n _ = axarr[i].scatter(f1,f2,s=2)\n #axarr[i].set_xticklabels(np.concatenate((np.array([0]),np.linspace(rangel[0][0], rangel[0][1], num=5))))\n #axarr[i].set_yticklabels(np.concatenate((np.array([0]),np.linspace(rangel[1][0], rangel[1][1], num=5))))\n #for (ii, jj), z in np.ndenumerate(histlist[-1]):\n # axarr[i].text(jj, ii, int(z), ha='center', va='center',color=\"red\")\n #f.subplots_adjust(right=0.8)\n #cbar_ax = f.add_axes([0.85, 0.15, 0.05, 0.7])\n #f.colorbar(axc, cax=cbar_ax)",
"def plot_fancy_activations():\n\n function_names = [\n SELU_FUNCTION_NAME, ELU_FUNCTION_NAME, RELU_FUNCTION_NAME\n ]\n function_names_verbose = ['SeLU', 'eLU', 'Leaky ReLU']\n input_values = numpy.linspace(-3, 3, num=1000, dtype=float)\n\n _, axes_object = pyplot.subplots(\n 1, 1, figsize=(FIGURE_WIDTH_INCHES, FIGURE_HEIGHT_INCHES)\n )\n axes_object.plot(\n input_values, numpy.zeros(input_values.shape),\n linewidth=2, linestyle='dashed', color=GREY_COLOUR\n )\n\n function_colours = [GREEN_COLOUR, ORANGE_COLOUR, PURPLE_COLOUR]\n\n for i in range(len(function_names)):\n these_output_values = _do_activation(\n input_values=input_values, function_name=function_names[i],\n slope_param=0.2\n )\n axes_object.plot(\n input_values, these_output_values, linewidth=4, linestyle='solid',\n color=function_colours[i], label=function_names_verbose[i]\n )\n\n axes_object.legend(loc='upper left')\n axes_object.set_xlabel('Input (before activation)')\n axes_object.set_ylabel('Output (after activation)')\n pyplot.show()",
"def plot(self): \n # Forwards plot\n self.__plot_vals(self.xin, self.yin, self.__eval_forward)",
"def display_2D_scatter_plot(dataset, title, xlabel, ylabel, labels = None):\n \n plt.figure()\n plt.scatter(dataset[:,0], dataset[:,1], c = labels)\n plt.suptitle(title)\n plt.xlabel(xlabel)\n plt.ylabel(ylabel)\n plt.show()",
"def visualization_2d(self, x, y):\n z = self.trainer.session.run(self.z, feed_dict={self.X: x.reshape((-1, self.input_shape[0], self.input_shape[1]))})\n assert z.shape[1] == 2, 'reduced_dim, i.e., dimension of z, must be 2 for this display to work'\n plt.figure(figsize=(10, 8)) \n plt.scatter(z[:, 0], z[:, 1], c=np.argmax(y, axis=1))\n plt.colorbar()\n plt.grid()",
"def plot2Variables(functions):\n\tprint('---------Plotting---------')\n\tinitialPoint=float(input('Insert a lower bound for plot:'))\n\tfinalPoint=float(input('Insert a upper bound for plot:'))\n\tp1=plot_implicit(functions[0],('x1', initialPoint, finalPoint),adaptive=False,title='Plot of functions',show=False)\n\tp2=plot_implicit(functions[1],('x1', initialPoint, finalPoint),adaptive=False,show=False)\n\tp1.extend(p2)\n\tp1[1].line_color='r'\n\tp1.show()",
"def onclick(event):\n global ix, iy\n ix, iy = int(event.xdata), int(event.ydata)\n # print(ix, iy)\n plt.scatter([ix], [iy], s = 2, c='r')\n plt.draw()\n global coords\n coords.append((iy, ix))",
"def plot_basic_activations():\n\n function_names = [\n SIGMOID_FUNCTION_NAME, TANH_FUNCTION_NAME, RELU_FUNCTION_NAME\n ]\n function_names_verbose = ['Sigmoid', 'tanh', 'ReLU']\n input_values = numpy.linspace(-3, 3, num=1000, dtype=float)\n\n _, axes_object = pyplot.subplots(\n 1, 1, figsize=(FIGURE_WIDTH_INCHES, FIGURE_HEIGHT_INCHES)\n )\n axes_object.plot(\n input_values, numpy.zeros(input_values.shape),\n linewidth=2, linestyle='dashed', color=GREY_COLOUR\n )\n\n function_colours = [GREEN_COLOUR, ORANGE_COLOUR, PURPLE_COLOUR]\n\n for i in range(len(function_names)):\n these_output_values = _do_activation(\n input_values=input_values, function_name=function_names[i],\n slope_param=0.\n )\n axes_object.plot(\n input_values, these_output_values, linewidth=4, linestyle='solid',\n color=function_colours[i], label=function_names_verbose[i]\n )\n\n axes_object.legend(loc='upper left')\n axes_object.set_xlabel('Input (before activation)')\n axes_object.set_ylabel('Output (after activation)')\n pyplot.show()",
"def visualize(X, Y):\n plt.plot(X, Y, \"bx\")\n plt.show()",
"def graph_scatter(arr, color='green', title='Scatter Plot of Given Points', x_label='X', y_label='Y'):\n plt.style.use('ggplot')\n\n x, y = [], []\n for point in arr:\n x.append(point[0])\n y.append(point[1])\n\n fig = plt.figure()\n axes = fig.add_axes([0,0,1,1])\n axes.scatter(x, y, color=color)\n axes.set_xlabel(x_label)\n axes.set_ylabel(y_label)\n axes.set_title(title)\n plt.show()",
"def create_plots(begin, end, stride):\r\n \r\n # generate x coordinates for plot points\r\n x_coords = []\r\n current_x = begin\r\n while current_x < end:\r\n x_coords.append(current_x)\r\n current_x += stride\r\n \r\n # compute list of (x, y) coordinates for each function\r\n double_plot = [(x_val, double(x_val)) for x_val in x_coords]\r\n square_plot = [(x_val, square(x_val)) for x_val in x_coords]\r\n exp_plot = [(x_val, exp(x_val)) for x_val in x_coords]\r\n \r\n # plot the list of points\r\n simpleplot.plot_lines(\"Plots of three functions\", 600, 400, \"x\", \"f(x)\",\r\n [double_plot, square_plot, exp_plot], \r\n True, [\"double\", \"square\", \"exp\"])",
"def C_animated_plot(model, X, y, Xtest, ytest):\n for index,c in enumerate(C):\n plt.ion()\n\n plt.scatter(X[:, 0], X[:, 1], marker='o',cmap=plt.cm.coolwarm, facecolors='none', edgecolors=color_list(y.tolist()), label='Truth Training')\n plt.title(\"C: \" + str(c))\n plt.legend()\n plt.pause(2.0)\n #plt.cla()\n\n plt.scatter(X[:, 0], X[:, 1], marker='+', cmap=plt.cm.coolwarm, c=color_list(model[index][1].tolist()), label='Prediction Training')\n plt.title(\"C: \" + str(c))\n plt.legend()\n plt.pause(2.0)\n #plt.cla()\n\n plt.scatter(Xtest[:, 0], Xtest[:, 1], marker='s',cmap=plt.cm.coolwarm, facecolors='none', edgecolors=color_list(ytest.tolist()), label='Truth Testing')\n plt.title(\"C: \" + str(c))\n plt.pause(2.0)\n plt.legend()\n #plt.cla()\n\n plt.scatter(Xtest[:, 0], Xtest[:, 1], marker='+', cmap=plt.cm.coolwarm, c=color_list(model[index][3].tolist()), label='Prediction Testing')\n plt.title(\"C: \" + str(c))\n plt.legend()\n plt.pause(5.0)\n plt.cla()\n\n plt.draw()",
"def plot_learning(self):\n plt.figure(figsize=(10,7))\n plt.plot([i for i in range(len(self.fitness_list))], self.fitness_list)\n plt.ylabel(\"Fitness\")\n plt.xlabel(\"Iteration\")\n plt.title('Cost function over iterations')\n plt.show()",
"def create_scatter_plot(self):\n xy = self.get_x_and_y_as_dict()\n x = xy[\"x\"]\n y = xy[\"y\"]\n plt.scatter(x, y)\n plt.xlabel(\"x\")\n plt.ylabel(\"y\")\n plt.title(\"Scatter plot of x and y values\")\n plt.savefig(f\"{self.save_directory}/task_2_scatter_plot.png\")",
"def scatterplots_to_screen(col1, col2):\r\n create_scatter(col1, col2)\r\n print(\"Correlation: \" + str(calculate_pearsons_corr(col1, col2)))\r\n return"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
(numpy.array, int, int) > numpy.array Creates a 4D, readonly view of some 2D numpy array as a 2D array of 2D patches. There are (arr_height x arr_width) patches and each patch is of size (patch_h, patch_w)
|
def patch_view(arr, patch_h, patch_w):
assert len(arr.shape) == 2
# Numpy stride code examples (magic):
# https://stackoverflow.com/questions/16774148/
# https://github.com/keras-team/keras/issues/2983
# New height and width are now going to be in terms of
# number of overlapping patches we can fit into arr
new_h, new_w = np.array(arr.shape) - np.array([patch_h, patch_w]) + 1
return np.lib.stride_tricks.as_strided(
np.ascontiguousarray(arr),
shape=(new_h, new_w, patch_h, patch_w),
strides=arr.strides + arr.strides,
writeable=False
)
|
[
"def make_array_2d(arr):\n if arr.ndim == 1:\n arr.shape = (arr.shape[0], 1)",
"def split_image_into_overlapping_patches(image_array, patch_size, padding_size=2):\n \n xmax, ymax, _ = image_array.shape\n x_remainder = xmax % patch_size\n y_remainder = ymax % patch_size\n \n # modulo here is to avoid extending of patch_size instead of 0\n x_extend = (patch_size - x_remainder) % patch_size\n y_extend = (patch_size - y_remainder) % patch_size\n \n # make sure the image is divisible into regular patches\n extended_image = np.pad(image_array, ((0, x_extend), (0, y_extend), (0, 0)), 'edge')\n \n # add padding around the image to simplify computations\n padded_image = pad_patch(extended_image, padding_size, channel_last=True)\n \n xmax, ymax, _ = padded_image.shape\n patches = []\n \n x_lefts = range(padding_size, xmax - padding_size, patch_size)\n y_tops = range(padding_size, ymax - padding_size, patch_size)\n \n for x in x_lefts:\n for y in y_tops:\n x_left = x - padding_size\n y_top = y - padding_size\n x_right = x + patch_size + padding_size\n y_bottom = y + patch_size + padding_size\n patch = padded_image[x_left:x_right, y_top:y_bottom, :]\n patches.append(patch)\n \n return np.array(patches), padded_image.shape",
"def extract_patches(img, patch_size=(3, 3), stride=(1, 1)):\n assert type(patch_size) in [int, tuple], 'patch size should be int or tuple int'\n assert type(stride) in [int, tuple], 'stride size should be int or tuple int'\n if type(stride) is int:\n stride = (stride, stride)\n if type(patch_size) is int:\n patch_size = (patch_size, patch_size)\n patches = img.unfold(2, patch_size[0], stride[0]).unfold(3, patch_size[1], stride[1]) \n patches = patches.contiguous().view(img.shape[0], img.shape[1], -1, patch_size[0], patch_size[1])\n patches = patches.transpose(1, 2)\n return patches",
"def _extract_3d_patches(arr, patch_radius):\n if isinstance(patch_radius, int):\n patch_radius = np.ones(3, dtype=int) * patch_radius\n if len(patch_radius) != 3:\n raise ValueError(\"patch_radius should have length 3\")\n else:\n patch_radius = np.asarray(patch_radius, dtype=int)\n patch_size = 2 * patch_radius + 1\n\n dim = arr.shape[-1]\n\n all_patches = []\n\n # loop around and find the 3D patch for each direction\n for i in range(patch_radius[0], arr.shape[0] -\n patch_radius[0], 1):\n for j in range(patch_radius[1], arr.shape[1] -\n patch_radius[1], 1):\n for k in range(patch_radius[2], arr.shape[2] -\n patch_radius[2], 1):\n\n ix1 = i - patch_radius[0]\n ix2 = i + patch_radius[0] + 1\n jx1 = j - patch_radius[1]\n jx2 = j + patch_radius[1] + 1\n kx1 = k - patch_radius[2]\n kx2 = k + patch_radius[2] + 1\n\n X = arr[ix1:ix2, jx1:jx2,\n kx1:kx2].reshape(np.prod(patch_size), dim)\n all_patches.append(X)\n\n return np.array(all_patches).T",
"def reshape_as_image(arr):\n return np.swapaxes(np.swapaxes(arr, 0, 2), 0, 1)",
"def gridwise_sample(imgarray, patchsize, rs):\r\n patchidx = []\r\n nrows, ncols, nbands = imgarray.shape\r\n patchsamples = np.zeros(shape=(0, patchsize, patchsize, nbands),\r\n dtype=imgarray.dtype)\r\n for i in range(round(nrows / patchsize)):\r\n for j in range(round(ncols / patchsize)):\r\n if i+1 <= int(nrows / patchsize) and j+1 <= int(ncols / patchsize):\r\n tocat = imgarray[i * patchsize:(i + 1) * patchsize,\r\n j * patchsize:(j + 1) * patchsize, :]\r\n tocat = np.expand_dims(tocat, axis=0) / rs\r\n patchsamples = np.concatenate((patchsamples, tocat), axis=0)\r\n patchidx.append([i, j])\r\n elif i+1 <= int(nrows / patchsize) and j+1 >= int(ncols / patchsize):\r\n tocat = imgarray[i * patchsize:(i + 1) * patchsize, -patchsize:, :]\r\n tocat = np.expand_dims(tocat, axis=0) / rs\r\n patchsamples = np.concatenate((patchsamples, tocat), axis=0)\r\n patchidx.append([i, j])\r\n elif i+1 >= int(nrows / patchsize) and j+1 <= int(ncols / patchsize):\r\n tocat = imgarray[-patchsize:, j * patchsize:(j + 1) * patchsize, :]\r\n tocat = np.expand_dims(tocat, axis=0) / rs\r\n patchsamples = np.concatenate((patchsamples, tocat), axis=0)\r\n patchidx.append([i, j])\r\n elif i+1 >= int(nrows / patchsize) and j+1 >= int(ncols / patchsize):\r\n tocat = imgarray[-patchsize:, -patchsize:, :]\r\n tocat = np.expand_dims(tocat, axis=0) / rs\r\n patchsamples = np.concatenate((patchsamples, tocat), axis=0)\r\n patchidx.append([i, j])\r\n\r\n return patchsamples, patchidx",
"def _2d(a):\n\tif len(a.shape) == 1:\n\t\ta.shape = (len(a), 1)\n\treturn a",
"def rebuild_array(wrapper, shape, dtype, order, strides, offset):\r\n arr = np.asarray(BufferWrapperArray(wrapper, shape, dtype, order, strides, offset))\r\n return arr",
"def extract_patches_3d(image, coords, patch_len):\n \n n_patches = coords.shape[0]\n ch = image.shape[2] # no. of colour channels\n \n patches = np.zeros((n_patches, patch_len, patch_len, ch))\n for i in range(n_patches):\n x, y = coords[i]\n patches[i] = image[x:x+patch_len, y:y+patch_len,:]\n \n return patches",
"def tile_image(image: np.ndarray, patch_size: Tuple, patch_stride=None) -> Tuple:\n points = _calculate_tiles(image.shape, patch_size, patch_stride)\n\n # return a list of patches\n patches = []\n\n for i in range(len(points)):\n start_point = points[i]\n end_point = (start_point[0] + patch_size[0], start_point[1] + patch_size[1])\n patch = image[start_point[0]:end_point[0], start_point[1]:end_point[1]]\n patches.append(patch)\n\n return patches, points",
"def array2d(self, surface, copydata=False):\n imagedata = surface.impl.getImageData(0, 0, surface.width, surface.height)\n if not copydata:\n return PyImageMatrixInteger(imagedata)\n else:\n return PyImageInteger(imagedata)",
"def array3d_to_pixmap(array: np.ndarray) -> QPixmap:\n assert array.ndim == 3\n height, width, color_bytes = array.shape\n return QPixmap.fromImage(QImage(array.data, width, height, color_bytes * width, QImage.Format_BGR888))",
"def _get_orthrectified_from_array_flat(self, ortho_bounds, row_array, col_array, value_array):\n\n raise NotImplementedError",
"def create_patches_test_data(imgs, patch_size, stride, padding):\n # Extract patches from input images\n img_patches = [img_crop(imgs[i], patch_size, patch_size, stride, padding) for i in range(len(imgs))]\n\n # Linearize list of patches, code from tf_aerial_images.py\n img_patches = np.asarray([img_patches[i][j] for i in range(len(img_patches)) for j in range(len(img_patches[i]))])\n\n return img_patches",
"def create_from_array(cls,\n array: Union[np.ndarray, DataArray],\n tiling_scheme: TilingScheme,\n level_image_id_factory: LevelImageIdFactory = None,\n **kwargs) -> 'ImagePyramid':\n tile_size = tiling_scheme.tile_size\n num_levels = tiling_scheme.num_levels\n level_images: List[Optional[TiledImage]] = [None] * num_levels\n z_index_max = num_levels - 1\n for i in range(0, num_levels):\n z_index = z_index_max - i\n image_id = level_image_id_factory(z_index) if level_image_id_factory else None\n level_images[z_index] = FastNdarrayDownsamplingImage(array,\n tile_size,\n i,\n image_id=image_id, **kwargs)\n return ImagePyramid(tiling_scheme, level_images)",
"def slice_array(array_3d, grid, i, view, origin='upper'):\n\n if origin not in ('upper', 'lower'):\n logging.warning('Unrecognized origin \"%s\" (using \"upper\")' % origin)\n origin = 'upper'\n\n # assumes BIPED coordinate system (DICOM C.7.6.2.1.1):\n # x-axis: increasing to patient's left side\n # y-axis: increasing to posterior\n # z-axis: increasing to superior\n\n # imshow and pcolor expect [i,j] -> [row,column]\n x, y, z = grid\n\n # sagittal image: {bottom, left} -> {inferior, anterior}\n if view in sagittal_aliases:\n\n if i >= array_3d.shape[0]:\n logging.warning('index %s is out-of-bounds' % i)\n i = -1\n\n array_2d = array_3d[i,:,:].T\n axis_X = y\n axis_Y = z\n\n # coronal image: {bottom, left} -> {inferior, patient's right}\n elif view in coronal_aliases:\n\n if i >= array_3d.shape[1]:\n logging.warning('index %s is out-of-bounds' % i)\n i = -1\n\n array_2d = array_3d[:,i,:].T\n axis_X = x\n axis_Y = z\n\n # transverse image: {bottom, left} -> {posterior, patient's right}\n # note that the y-axis must be reversed when plotting\n elif view in transverse_aliases:\n\n if i >= array_3d.shape[2]:\n logging.warning('index %s is out-of-bounds' % i)\n i = -1\n\n array_2d = array_3d[:,:,i].T\n axis_X = x\n axis_Y = y\n\n if origin == 'upper':\n array_2d = np.flipud(array_2d)\n axis_Y = axis_Y[::-1]\n\n # convert bin-centers to bin-edges for pcolor\n axis_X = np.append(axis_X, axis_X[-1] + np.diff(axis_X)[-1])\n axis_Y = np.append(axis_Y, axis_Y[-1] + np.diff(axis_Y)[-1])\n\n return axis_X, axis_Y, array_2d",
"def extract_patches(image, size=11):\n n, m, c = image.shape\n n = n - size + 1\n m = m - size + 1\n\n dimensions = size**2 * c\n patches = np.zeros((dimensions, n*m))\n\n for i in range(n*m):\n col = i % m\n row = i // m\n patches[:, i] = np.reshape(image[row:row+size, col:col+size, :], dimensions, \"F\")\n\n return patches",
"def image_array(self):\n \n # Retrieve all of the hex digits in the list.\n # NOTE: ? digits are interpreted as having a value of 0.\n digits = self.digits()\n imgarray = [0 if digit == -1 else digit for digit in digits]\n \n # Each line in a bytes file contains 40 digits. The last line of the\n # file, however, may contain less than 40 digits. In order to create\n # a non-jagged 2D array, we need to reduce the number of pixels to the\n # largest multiple of 40.\n lines = len(imgarray) // 40\n imgarray = imgarray[:lines*40]\n \n # Reshape the array of pixels into a 2D array containing 40 columns\n # and a number of rows equivalent to the number of rows in the file\n # (potentially minus 1 row).\n imgarray = np.reshape(imgarray, (lines, 40)) \n \n # Turn the list into a numpy array.\n imgarray = np.array(imgarray)\n \n return imgarray",
"def patch_batch_prepare(image, length_stride_list, width_stride_list, patch_size):\n min_x, min_y = 0, 0\n minibatch_patches = []\n img_width, img_length = image.shape\n\n for stride_y in length_stride_list + [0]:\n for stride_x in width_stride_list + [-(img_width - patch_size)]:\n patch = image[min_x:min_x + patch_size, min_y:min_y + patch_size]\n minibatch_patches.append(np.expand_dims(patch, axis=2))\n min_x += stride_x\n min_y += stride_y\n \n return minibatch_patches"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
(int > numpy.array) Creates a 2Dboolean mask of a circle with radius radius. Returns a 2D, square array with side length size 2radius + 1
|
def circular_mask(radius):
diameter = 2*radius + 1
center_x = center_y = radius
x, y = np.indices((diameter, diameter))
distances = ((center_x - x) ** 2 + (center_y - y) ** 2) ** 0.5
return (distances <= radius)
|
[
"def create_2d_circle_kernel(radius):\n return np.array([ np.sqrt( x * x + y * y ) <= float(radius) for y in xrange(-radius, radius+1) for x in xrange(-radius, radius+1)], dtype=np.float32).reshape( radius*2+1, radius*2+1 )",
"def gen_radial_mask(shape, center, radius, mask=True,\n xy_scale=None, r_scale=None):\n r = gen_radius_array(shape, center, xy_scale=xy_scale, r_scale=r_scale)\n out = (r >= radius[0]) & (r <= radius[1])\n return out if mask else np.logical_not(out)",
"def circular_kernel(radius):\n\n width = 2*radius + 1\n kernel = np.zeros((width, width), np.uint8)\n for i in range(0, width):\n for j in range(0, width):\n if (i - radius) ** 2 + (j - radius) ** 2 <= radius**2:\n kernel[i][j] = int(1)\n return kernel",
"def create_circle_mask(self, cells, i):\n xx, yy = np.mgrid[:(cells*2)+1, : (cells*2)+1]\n qsr_mask = (xx - float(cells))** 2 + (yy - float(cells))** 2\n #print qsr_mask\n qsr_mask[qsr_mask > cells**2] = (cells**2)+1\n #print \"max: \", qsr_mask.max()\n #print qsr_mask\n\n label = self.sorted_params[i][0]\n binary_circle_mask = (qsr_mask <=cells**2)*100\n #donut = np.logical_and(circle < (6400 + 60), circle > (6400 - 60)) ???\n\n #This removes the center of the mask if i>0\n self.binary_masks[label] = self.remove_center_of_mask(i, binary_circle_mask)",
"def image_mask(CS_mask,radius = 15):\n from numpy import indices\n w,h = shape(CS_mask)\n x_indices,y_indices = indices((w,h))\n SAXS_mask = sqrt((y_indices-(h-1)/2)**2+(x_indices-(w-1)/2)**2) < radius\n Border_mask = (y_indices<2) | (y_indices>(h-3)) | \\\n (x_indices<2) | (x_indices>(w-3))\n CS_mask *= ~(SAXS_mask | Border_mask)\n return CS_mask",
"def find_rotated_mask(shape,Rx,Ry,angle,xc,yc):\n arr = np.empty((shape[0],shape[1]), dtype = bool)\n #now fill the array with distance away from center\n for i in range(arr.shape[0]):\n for j in range(arr.shape[1]):\n xpos, ypos = pos(j,i,xc,yc,angle)\n if (xpos/Rx)**2 + (ypos/Ry)**2 < 1:\n arr[i,j] = True\n else:\n arr[i,j] = False\n\n return arr",
"def in_circle(radius):\n return lambda z: z.real ** 2 + z.imag ** 2 < radius ** 2",
"def circle_mask(shape, sharpness = 40):\n assert shape[1] == shape[2], \"circle_mask received a bad shape: \" + shape\n\n diameter = shape[1]\n x = np.linspace(-1, 1, diameter)\n y = np.linspace(-1, 1, diameter)\n xx, yy = np.meshgrid(x, y, sparse=True)\n z = (xx**2 + yy**2) ** sharpness\n\n mask = 1 - np.clip(z, -1, 1)\n mask = np.expand_dims(mask, axis=0)\n mask = np.broadcast_to(mask, shape)\n mask = torch.tensor(mask, dtype=torch.float)\n return mask",
"def extract_neighborhood(x, y, arr, radius):\n if x < radius or y < radius or x>=480-radius or y>=640-radius:\n return np.ones((radius*2+1,radius*2+1)).ravel()\n return arr[(x - radius) : (x + radius + 1), (y - radius) : (y + radius + 1)].ravel()",
"def fill_small_radius_holes(mask, max_radius):\n mask = mask.astype(bool)\n outside = ndimage.binary_propagation(numpy.zeros_like(mask), mask=~mask, border_value=1)\n holes = ~(mask | outside)\n large_hole_centers = ndimage.binary_erosion(holes, iterations=max_radius+1)\n large_holes = ndimage.binary_propagation(large_hole_centers, mask=holes)\n small_holes = holes ^ large_holes\n return mask | small_holes",
"def circle(x, y, r, width, height, channels=1):\n img = np.zeros( (height, width, channels), dtype=np.float32 )\n (X,Y) = np.meshgrid(range(width), range(height))\n img[np.sqrt((X-x)**2 + (Y-y)**2) < r] = 1.0\n return img",
"def get_in_radius_pixels(point: tuple, radius: int) -> np.ndarray:\n # Construct the array of pixels which may be effected\n x_val, y_val = np.mgrid[-radius: radius + 1: 1, -radius: radius + 1: 1]\n # The mask will be used to filter out the pixels further than\n # the radius around the center.\n mask = x_val * x_val + y_val * y_val <= radius * radius\n # Construct an array of DiameterXDiameter pixels\n in_radius_ar = np.vstack((x_val.flatten(), y_val.flatten())).T.reshape(\n (radius * 2 + 1, radius * 2 + 1, 2))\n # Return the pixels within radius distance, plus an offset so we test\n # the relevant location rather than center of the screen\n return in_radius_ar[mask] + np.array(point)",
"def mask_eccentric(x, y, center_x, center_y, e1, e2, r):\n x_, y_ = param_util.transform_e1e2_product_average(x, y, e1, e2, center_x, center_y)\n r_ab = (x_**2 + y_**2) / r ** 2\n mask = np.empty_like(r_ab, dtype='int')\n mask[r_ab > 1] = 0\n mask[r_ab <= 1] = 1\n return mask",
"def remove_small_radius_objects(mask, max_radius):\n eroded = ndimage.binary_erosion(mask, iterations=max_radius)\n return ndimage.binary_propagation(eroded, mask=mask)",
"def generate_binary_elipsoid(ndradius=[1, 1, 1]):\n ndradius = np.asarray(ndradius).astype(np.double)\n shape = ((ndradius * 2) + 1).astype(np.uint)\n logger.debug(\"elipsoid shape %s\", str(shape))\n # import ipdb; ipdb.set_trace() # noqa BREAKPOINT\n x, y, z = np.indices(shape)\n center1 = ndradius\n mask = (\n ((x - ndradius[0]) ** 2) / ndradius[0] ** 2\n + ((y - ndradius[1]) ** 2) / ndradius[1] ** 2\n + ((z - ndradius[2]) ** 2) / ndradius[2] ** 2\n )\n # (y - ndradius[1])**2 < radius1**2\n # mask = mask radius1**1\n return mask < 1",
"def _generate_mask(self) -> ndarray:\n # calculate mean 3x3 (square nbhood) orography heights\n radius = number_of_grid_cells_to_distance(self.topography, 1)\n topo_nbhood = NeighbourhoodProcessing(\"square\", radius)(self.topography)\n topo_nbhood.convert_units(\"m\")\n\n # create mask\n mask = np.full(topo_nbhood.shape, False, dtype=bool)\n mask = np.where(topo_nbhood.data < self.orog_thresh_m, True, mask)\n mask = np.where(self.humidity.data < self.rh_thresh_ratio, True, mask)\n mask = np.where(abs(self.vgradz) < self.vgradz_thresh_ms, True, mask)\n return mask",
"def yank_circle_pixels(img, center, radius):\n x, y = _define_circle_points(center, radius) \n ## Filter out out-of-bounds points\n yx = zip(y, x) # yx b/c row,column\n y_max, x_max = img.shape\n inbounds = lambda yx: 0 <= yx[0] <= y_max and 0 <= yx[1] <= x_max\n yx_inbounds = filter(inbounds, yx)\n if len(yx) != len(yx_inbounds):\n warnings.warn(\"Circle is clipped by image limits.\")\n ## Find pix\n pix = [img[yx] for yx in yx_inbounds]\n return pix",
"def extract_circle(center, radius, coords):\n return np.where(((coords - center) ** 2).sum(axis=-1) < radius**2)[0]",
"def filter_density(mask, rad=3, size=5, fn = lambda m,i,j: m[i,j]):\n rows, cols = mask.shape\n X,Y = np.meshgrid(xrange(cols), xrange(rows))\n in_circle = lib.in_circle\n out = np.zeros((rows,cols), np.bool)\n for row,col in locations(mask.shape):\n\tif fn(mask,row,col):\n\t a = in_circle((col,row),rad)\n\t if np.sum(mask*a(X,Y))>size:\n\t\tout[row,col] = True\n return out"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Converts keypoints into a numpy array of form [[x, y]]
|
def keypoints_to_coords(keypoints):
return np.array([kp.pt for kp in keypoints])
|
[
"def get_gt_keypoints_array(eval_annotations):\n keypoints_list = []\n for eval_record in eval_annotations:\n keypoints_record = []\n\n keypoints = eval_record['joint_self']\n for keypoint in keypoints:\n #only pick (x,y) and drop is_visible\n keypoints_record.append(keypoint[:2])\n\n keypoints_list.append(keypoints_record)\n keypoints_array = np.array(keypoints_list, dtype='float64')\n # transpose array for computing PCKh\n keypoints_array = np.transpose(keypoints_array, [1, 2, 0])\n\n #print('keypoints_array shape: ', keypoints_array.shape)\n return keypoints_array",
"def to_keypoints(self):\n # TODO get rid of this deferred import\n from imgaug.augmentables.kps import Keypoint\n\n return [Keypoint(x=point[0], y=point[1]) for point in self.exterior]",
"def convert_to_2d_array(self,points):\n points = np.array(points)\n if len(points.shape) == 1:\n points = np.expand_dims(points, -1)\n return points",
"def pointvectors(self):\n return np.stack([self.x, self.y], axis=-1)",
"def points_dict_to_list(points):\n return [[p['x'], p['y']] for p in points.values()]",
"def drawKeypoints_Array(img0,pts):\n f,ax2 = plt.subplots(1, 1)\n cols = pts[:,0]\n rows = pts[:,1]\n ax2.imshow(cv2.cvtColor(img0, cv2.COLOR_BGR2RGB))\n ax2.scatter(cols, rows)\n plt.show()",
"def QPoint2numpy(_qpoint2d):\n\n pos2d = numpy.array([float(_qpoint2d.x()), float(_qpoint2d.y())])\n return pos2d",
"def point_cloud_to_array(xyz, dims):\n\n i, j, k = xyz.astype(np.int32).T\n return indices_to_array(i, j, k, dims)",
"def convert_to_points(b):\n return np.array(zip(list(b[0]), list(b[1])))",
"def get_keys_array(self):\n return JaggedArray( self.keys, self.bounds )",
"def collocation_points(self) -> np.ndarray:",
"def pts_of_grid2d(x):\n N = len(x)\n pts1 = []\n for xx in x:\n for yy in x:\n pts1.append([xx, yy])\n return np.reshape(pts1, (N*N, 2))",
"def pointsToPoseArray(self,points,distance) :\n pose_array = PoseArray()\n pose_array.header.frame_id = self.camera_model.tfFrame()\n for pnt in points :\n pose = Pose()\n ray = self.camera_model.projectPixelTo3dRay(pnt)\n # https://python.hotexamples.com/examples/image_geometry/PinholeCameraModel/projectPixelTo3dRay/python-pinholecameramodel-projectpixelto3dray-method-examples.html\n ray_z = [el / ray[2] for el in ray] # normalize the ray so its Z-component equals 1.0\n pt = [el * distance for el in ray_z] # multiply the ray by the depth; its Z-component should now equal the depth value\n pose.position.x = pt[0]\n pose.position.y = pt[1]\n pose.position.z = pt[2]\n pose_array.poses.append(pose)\n return pose_array",
"def _getPtychographyPositions(self) -> np.ndarray:\n\n p1 = self._scan_params.scan_area_buffer_npix\n p2 = self._probe_params.npix - p1 - self._obj_params.obj_w_border_npix\n positions_x = np.arange(p1, p2, self._scan_params.scan_step_npix)\n positions = []\n\n for r in positions_x:\n for c in positions_x:\n positions.append([r,c])\n return np.array(positions)",
"def transform_points(self):\n for key in self.keypoints:\n if self.keypoints[key].index is not 8:\n self.keypoints[key].x = self.keypoints[key].x - self.keypoints[8].x\n self.keypoints[key].y = self.keypoints[8].y - self.keypoints[key].y\n self.keypoints[8].x = 0\n self.keypoints[8].y = 0",
"def convert_mediapipe_to_numpy(landmarks) -> np.ndarray:\n return np.array([(e.x, e.y, e.z) for e in landmarks])",
"def x(self) -> Tensor:\n return self.keypoints[:, 0]",
"def convert_mediapipe_to_numpy(landmarks) -> np.ndarray:\n return np.array([(e.x, e.y, e.z) for e in landmarks.landmark])",
"def xy(self):\n xcol = self._xx.reshape(-1, 1)\n ycol = self._yy.reshape(-1, 1)\n return np.column_stack([xcol, ycol])",
"def key_pts_to_yolo(key_pts, w_img, h_img):\n x1 = max(0, min([pt[0] for pt in key_pts]))\n x2 = min(w_img, max([pt[0] for pt in key_pts]))\n y1 = max(0, min([pt[1] for pt in key_pts]))\n y2 = min(h_img, max([pt[1] for pt in key_pts]))\n x = (x2 + x1) / 2 / w_img\n y = (y2 + y1) / 2 / h_img\n width = (x2 - x1) / w_img\n height = (y2 - y1) / h_img\n return x, y, width, height"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Computes the affine transform of coords (form [[x, y]]) with transform_matrix.
|
def affine_transform(coords, transform_matrix):
# Add ones onto the end of every row, then transpose the matrix (columns are [x, y, 1])
num_pts, num_dims = coords.shape
with_ones = np.ones((num_pts, num_dims + 1))
with_ones[:, :-1] = coords
with_ones = with_ones.transpose()
# Array of form [[x...], [y...]]
transformed = np.matmul(transform_matrix, with_ones)
return transformed.transpose()
|
[
"def matrix_transform(coords, matrix):\n return ProjectiveTransform(matrix)(coords)",
"def affine_transform(pt, trans_mat):\n new_pt = np.array([pt[0], pt[1], 1.]).T\n new_pt = np.dot(trans_mat, new_pt)\n return new_pt[:2]",
"def affine(self):\n return Affine(*self.transform)",
"def transform(self, matrix):\n for index, point in enumerate(transform_points(self.points, matrix)):\n self.points[index].x = point[0]\n self.points[index].y = point[1]\n self.points[index].z = point[2]",
"def geometryTransformMatrix(*args, **kwargs):\n \n pass",
"def apply_affine(T, xyz):\n XYZ = np.dot(T[0:3,0:3], xyz)\n XYZ[0,:] += T[0,3]\n XYZ[1,:] += T[1,3]\n XYZ[2,:] += T[2,3]\n return XYZ",
"def getAffineTransform(self, coord1, coord2):\n A = []\n B = []\n for point in coord2:\n A.append([point[0], point[1], 1, 0, 0, 0])\n A.append([0, 0, 0, point[0], point[1], 1])\n for point in coord1:\n B.append(point[0])\n B.append(point[1])\n return np.reshape(np.dot(np.linalg.pinv(np.array(A)), np.array(B)),(2,3))\n #pts1 = coord1[0:3].astype(np.float32)\n #pts2 = coord2[0:3].astype(np.float32)\n #print(cv2.getAffineTransform(pts1, pts2))\n #return cv2.getAffineTransform(pts1, pts2)",
"def affine(self, transform, resample_algorithm=nearest, resize_canvas=True):\n pixels = resample_algorithm.affine(\n self,\n transform,\n resize_canvas=resize_canvas,\n )\n return self._copy(pixels)",
"def affine_transform_covariance( covarianceMatrix, transformMatrix ):\n raise NotImplementedError()",
"def affine_map(points1, points2):\n A = np.ones((4, 4))\n A[:, :3] = points1\n B = np.ones((4, 4))\n B[:, :3] = points2\n \n # solve 3 sets of linear equations to determine\n # transformation matrix elements\n matrix = np.eye(4)\n for i in range(3):\n # solve Ax = B; x is one row of the desired transformation matrix\n matrix[i] = np.linalg.solve(A, B[:, i]) \n \n return matrix",
"def th_affine2d(x, matrix, output_img_width, output_img_height):\n assert (matrix.ndim == 2)\n matrix = matrix[:2, :]\n transform_matrix = matrix\n src = x\n\n # cols, rows, channels = src.shape\n dst = cv2.warpAffine(src, transform_matrix, (output_img_width, output_img_height),\n cv2.INTER_AREA, cv2.BORDER_CONSTANT, borderValue=(0, 0, 0))\n # for gray image\n if dst.ndim == 2:\n dst = np.expand_dims(np.asarray(dst), axis=2)\n\n return dst",
"def affine_transformation(X_unprj, affine_x, affine_y, args, header):\n\tx_pred = np.dot(X_unprj, affine_x)\n\ty_pred = np.dot(X_unprj, affine_y)\n\treturn x_pred, y_pred",
"def th_affine2d(x, matrix, output_img_width, output_img_height):\n assert matrix.ndim == 2\n matrix = matrix[:2, :]\n transform_matrix = matrix\n src = x\n\n # cols, rows, channels = src.shape\n dst = cv2.warpAffine(\n src,\n transform_matrix,\n (output_img_width, output_img_height),\n cv2.INTER_AREA,\n cv2.BORDER_CONSTANT,\n borderValue=(0, 0, 0),\n )\n # for gray image\n if dst.ndim == 2:\n dst = np.expand_dims(np.asarray(dst), axis=2)\n\n return dst",
"def affine_transform(image, affine, offset=None, order=1):\n\n # sanity checks\n if not isinstance(image, np.ndarray):\n raise TypeError(\"Input image should be np.ndarray but is: \" + str(type(image)))\n # define affine if it doesn't exist\n if affine is None:\n affine = create_affine()\n if not isinstance(affine, np.ndarray):\n raise TypeError(\"Affine should be np.ndarray but is: \" + str(type(affine)))\n if not affine.shape == (3, 3):\n raise ValueError(\"Affine should have shape (3, 3)\")\n # define offset if it doesn't exist\n if offset is None:\n center = np.array(image.shape)\n offset = center - np.dot(affine, center)\n if not isinstance(offset, np.ndarray):\n raise TypeError(\"Offset should be np.ndarray but is: \" + str(type(offset)))\n if not offset.shape == (3,):\n raise ValueError(\"Offset should have shape (3,)\")\n\n # Apply affine\n # handle 4d\n if len(image.shape) > 3:\n # make 4d identity matrix and replace xyz component with 3d affine\n affine4d = np.eye(4)\n affine4d[:3, :3] = affine\n offset4d = np.append(offset, 0.)\n image = ndi.interpolation.affine_transform(image, affine4d, offset=offset4d, order=order, output=np.float32)\n # handle 3d\n else:\n image = ndi.interpolation.affine_transform(image, affine, offset=offset, order=order, output=np.float32)\n\n return image",
"def transform(self, matrix):\n point = transform_points([self.point], matrix)\n normal = transform_vectors([self.normal], matrix)\n self.point.x = point[0]\n self.point.y = point[1]\n self.point.z = point[2]\n self.normal.x = normal[0]\n self.normal.y = normal[1]\n self.normal.z = normal[2]",
"def getAffineTransform(self, coord1, coord2):\n # pts1 = coord1[0:3].astype(np.float32)\n # pts2 = coord2[0:3].astype(np.float32)\n # print(cv2.getAffineTransform(pts1, pts2))\n # return cv2.getAffineTransform(pts1, pts2)\n\n # Assume coord1 is an array of source/pixel and coord2 is known dst coordinates\n N, K = coord1.shape\n\n if K == 2:\n A = np.zeros([2 * N, 2 * (K + 1)])\n\n # Build matrix A from pixels\n for i in range(N):\n A[2 * i , 0 : K] = coord1[i, 0 : K].astype(np.float32)\n A[2 * i , K ] = 1\n A[2 * i + 1 , K + 1 : 2 * K + 1] = coord1[i, 0 : K].astype(np.float32)\n A[2 * i + 1 , 2 * K + 1 ] = 1\n # print(A)\n # Build b vector\n b = np.zeros([2 * N])\n for i in range(N):\n b[2 * i : 2 * i + 2] = coord2[i, 0 : K].astype(np.float32)\n # print(b)\n # Compute solution using peseudo inverse\n x = (np.linalg.inv(A.transpose().dot(A))).dot(A.transpose()).dot(b)\n # print(x)\n transformMatrixTop = np.reshape(x, [2, 3])\n transformMatrixBtm = np.array([0, 0, 1])\n result = np.vstack((transformMatrixTop, transformMatrixBtm))\n # print(result)\n return result\n else:\n A = np.zeros([3 * N, 3 * (K + 1)])\n\n # Build matrix A from pixels\n for i in range(N):\n A[3 * i , 0 : K] = coord1[i, 0 : K].astype(np.float32)\n A[3 * i , K ] = 1\n A[3 * i + 1 , K + 1 : 2 * K + 1] = coord1[i, 0 : K].astype(np.float32)\n A[3 * i + 1 , 2 * K + 1 ] = 1\n A[3 * i + 2 , 2 * K + 2 : 3 * K + 2] = coord1[i, 0 : K].astype(np.float32)\n A[3 * i + 2 , 3 * K + 2 ] = 1\n # Build b vector\n b = np.zeros([3 * N])\n for i in range(N):\n b[3 * i : 3 * i + 3] = coord2[i, 0 : K].astype(np.float32)\n # print(A)\n # print(b)\n # Compute solution using peseudo inverse\n # print(A.transpose().dot(A))\n x = (np.linalg.inv(A.transpose().dot(A))).dot(A.transpose()).dot(b)\n # print(x)\n transformMatrixTop = np.reshape(x, [3, 4])\n transformMatrixBtm = np.array([0, 0, 0, 1])\n result = np.vstack((transformMatrixTop, transformMatrixBtm))\n # print(result)\n return result",
"def setTransform(self, *args):\n return _coin.SbDPMatrix_setTransform(self, *args)",
"def test_affine_transform_order():\n\n # Translation matrix\n t = transform.affine_transform_matrix(translation=[2,1])\n # Rotation matrix\n r = transform.affine_transform_matrix(rotation=np.pi/3)\n # Composite\n a1 = transform.affine_transform_matrix(rotation=np.pi/3, translation=[2,1])\n # Order should be rotation then translation\n assert np.array_equal(t @ r, a1), 'Bad rotation+translation order'\n\n # Scale matrix\n s = transform.affine_transform_matrix(scale=(1.5, 2.))\n # Composite\n a2 = transform.affine_transform_matrix(scale=(1.5, 2.), rotation=np.pi/3, translation=[2,1])\n # Order should be scale, rotate, translate\n assert np.array_equal(t @ r @ s, a2), 'Bad scale+rotation+translation order'",
"def get_transposed_matrix_transformation(\n self, transposed_matrix: np.ndarray | list | tuple\n ):\n transposed_matrix = np.array(transposed_matrix)\n if transposed_matrix.shape == (2, 2):\n new_matrix = np.identity(3)\n new_matrix[:2, :2] = transposed_matrix\n transposed_matrix = new_matrix\n elif transposed_matrix.shape != (3, 3):\n raise ValueError(\"Matrix has bad dimensions\")\n return lambda point: np.dot(point, transposed_matrix)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Draws the polygon whose corner points are specified in clockwise order in polygon_clockwise (array of form [[x, y]]) onto a copy of img.
|
def draw_polygon(img, polygon_clockwise, color, thickness):
ret = np.copy(img)
num_corners = polygon_clockwise.shape[0]
for i in range(num_corners):
# Figure out which points to connect together
left_ind, right_ind = (i % num_corners), ((i + 1) % num_corners)
left, right = polygon_clockwise[left_ind], polygon_clockwise[right_ind]
# Draw a line between them (cv needs int tuples)
left_tup, right_tup = tuple(left.astype(int)), tuple(right.astype(int))
cv.line(ret, left_tup, right_tup, color, thickness)
return ret
|
[
"def visualize_affine_transform(polygon_clockwise, img, transform_matrix):\n \n # Transform the given polygon's corner points into new space\n new_poly = affine_transform(polygon_clockwise, transform_matrix)\n \n # Return the polygon drawn on the image\n return draw_polygon(img, new_poly, (0, 255, 0), 3)",
"def draw_polygon(canvas, polygon):\n\n # The polygon object has points, we need to make those points a list.\n points_list = gen_point_list(polygon)\n\n # Now that we have the points_list, we can draw the polygon\n canvas.polygon(points_list, fill=polygon.fill)",
"def polygon(self, points, color):\n i = 0\n matrix = np.zeros((len(x),2), dtype=np.int32)\n while i < len(points):\n matrix[i] = points[i]\n i+=1\n matrix.reshape((-1,1,2))\n polygon = cv2.polylines(self.img, [matrix], True, (255,0,0),\\\n thickness=3)\n cv2.imshow('polygon', self.img)",
"def fillConvexPoly(img, points, color, lineType=..., shift=...) -> img:\n ...",
"def draw_polygon(num_edges, to_filename, edge_length=30, rotate_degrees=0,\n image_width=100, image_height=100, show=False):\n assert num_edges > 2\n\n # first we make an unrotated polygon with the first point on the origin.\n x, y = 0, 0\n vertices = [] # list of tuples\n for angle in _angles_of_a_polygon(num_edges):\n x += math.cos(math.radians(angle)) * edge_length\n y += math.sin(math.radians(angle)) * edge_length\n vertex = (x, y)\n vertices.append(vertex)\n\n # rotate it\n vertices = _rotate_polygon(vertices, rotate_degrees)\n\n # offset it such that it's near the center. Having rotated around the origin (top left in PIL),\n # it may currently have a negative x or y, so \"off\" the visible image canvas. So we'll find\n # the left-most point and move it to a bit left of center, and the other points appropriately.\n center_x = image_width / 2\n center_y = image_height / 2\n lowest_x_seen, y_of_lowest_x = None, None\n for x, y in vertices:\n if lowest_x_seen is None or x < lowest_x_seen:\n lowest_x_seen = x\n y_of_lowest_x = y\n # calculate the offsets we need and apply to each vertex to approximately center the polygon.\n x_offset = center_x - lowest_x_seen - edge_length\n y_offset = center_y - y_of_lowest_x\n vertices = [(x + x_offset, y + y_offset) for x, y in vertices]\n\n # draw it\n image = Image.new(PIL_IMAGE_MODE, (image_width, image_height), 'white')\n drawer = ImageDraw.Draw(image)\n drawer.polygon(vertices, fill=128, outline=128)\n image.save(to_filename, \"PNG\")\n if show:\n image.show()\n\n return to_filename",
"def generate_wedge_mask(img, angle):\n\n # Obtain parameters for scaling\n height, width = img.shape[0], img.shape[1]\n\n # Creating a right triangle with the given angle and coordinates\n op_side = math.tan(math.radians(angle)) * img.shape[1]\n c = [0, width, width]\n r = [height, height, int(height - op_side)]\n\n # Generate map of three points that compose the right triangle\n rc = np.array((c, r)).T\n\n # Create a mask\n mask = np.zeros_like(img)\n\n # Draw wedge on the mask\n cv2.drawContours(mask, [rc], 0, 255, -1)\n\n # return mask\n return mask",
"def fill_poly(shape2d, poly, outline=True, fill=True):\n poly = list(map(tuple, poly)) # PIL...\n\n img = Image.new('L', shape2d, 0)\n ImageDraw.Draw(img).polygon(poly, outline=outline, fill=fill)\n mask = np.array(img).T # PIL works with x,y and not row,col\n\n return mask",
"def get_padded_polygon_image(enlargened_poly, img, mask, color=255):\n\n # mask to extract area of interest\n extracted_img = cv2.bitwise_and(img, img, mask=mask)\n # invert mask\n mask_inv = cv2.bitwise_not(mask)\n\n padded_mask = np.zeros(mask.shape, dtype=np.uint8)\n cv2.fillPoly(padded_mask, [np.int32(enlargened_poly)], (color))\n\n padding = cv2.bitwise_and(padded_mask, padded_mask, mask=mask_inv)\n padding = np.expand_dims(padding, 2)\n padding = np.repeat(padding, 3, 2)\n\n padded_img = cv2.add(padding, extracted_img)\n\n return padded_img, padded_mask",
"def draw_corners(self):\n for i in range(4):\n pyglet.graphics.draw(1, pyglet.gl.GL_POINTS,\\\n ('v2f', (self.corners[i][0],self.corners[i][1])),\\\n ('c3B', (0, 255, 255)))",
"def draw_contour_on_image(source, points_x, points_y):\n\n # Copy the image source to prevent modifying the original image\n src = np.copy(source)\n\n points = []\n for px, py in zip(points_x, points_y):\n points.append([px, py])\n\n points = np.array(points, np.int32)\n points = points.reshape((-1, 1, 2))\n\n image = cv2.polylines(src, [points], isClosed=True, color=(0, 255, 0), thickness=2)\n\n return image",
"def make_polygon(N,sides):\n # define the end-points\n theta = numpy.linspace(0, -2*numpy.pi, N+1) # equally spaced theta\n r = numpy.cos(numpy.pi/sides)/numpy.cos( # r(theta)\n theta % (2.*numpy.pi/sides)-numpy.pi/sides)\n x,y = r*numpy.cos(theta), r*numpy.sin(theta) # get the coordinates\n return panelize(x,y)",
"def polygonize(obj, np_img, np_mask, outshpFile=None):\n\n\tif outshpFile is None:\n\t\toutshpFile = obj.tmpshpFile1\n\t#--- open tmp file (GDAL) -----------------------------------------\n\togr_shp = ogr.GetDriverByName(\"ESRI Shapefile\").CreateDataSource( outshpFile )\n\n\t#--- get band (GDAL) -------------------------------------\n\tdatatype = 1 # uint8\n\tdrv = gdal.GetDriverByName('MEM')\n\tds_img = drv.Create( '', obj.cols, obj.rows, 1, datatype )\n\tds_img.SetProjection( obj.proj )\n\tds_img.SetGeoTransform( obj.geo )\n\tds_imgband = ds_img.GetRasterBand(1)\n\t#ds_imgband.WriteArray(np_img)\n\n\t#--- mask band (GDAL) -----------------------------------\n\tdatatype = 1 # uint8\n\tdrv = gdal.GetDriverByName('MEM')\n\tds_mask = drv.Create( '', obj.cols, obj.rows, 1, datatype )\n\tds_mask.SetProjection( obj.proj )\n\tds_mask.SetGeoTransform( obj.geo )\n\tds_maskband = ds_img.GetRasterBand(1)\n\tds_maskband.WriteArray(np_mask)\n\n\t#--- masking -------------------------------------------\n\tnp_img = np_img * np_mask\n\tds_imgband.WriteArray(np_img)\n\n\t#--- create layer (ogr) -------------------------------\n\togr_layer = ogr_shp.CreateLayer(\"polygonized\")\n\n\t#--- exec raster to polygon (GDAL) ----------------------------------\n\tgdal.Polygonize( ds_imgband, ds_maskband, ogr_layer, 0, [], callback=None )\n\n\n\t#--- number of features -----\n\tfeatureCount = ogr_layer.GetFeatureCount()\n\n\togr_shp = None\n\n\n\tprint(\"--, finished, polygonize()\")\n\n\treturn featureCount",
"def PolygonPatch(\n obj: Polygon,\n) -> PathPatch:\n from matplotlib.patches import PathPatch\n from matplotlib.path import Path\n\n def cw_coords(ring: LinearRing) -> npt.NDArray[Any]:\n \"\"\"\n Return Clockwise array coordinates\n\n Parameters\n ----------\n ring: shapely.geometry.polygon.LinearRing\n LinearRing\n\n Returns\n -------\n out: ndarray\n (n x 2) array of coordinate points.\n \"\"\"\n if ring.is_ccw:\n return np.asarray(ring.coords)[:, :2][::-1]\n return np.asarray(ring.coords)[:, :2]\n\n def ccw_coords(ring: LinearRing) -> npt.NDArray[Any]:\n \"\"\"\n Return Counter Clockwise array coordinates\n\n Parameters\n ----------\n ring: shapely.geometry.polygon.LinearRing\n LinearRing\n\n Returns\n -------\n out: ndarray\n (n x 2) array of coordinate points.\n \"\"\"\n if ring.is_ccw:\n return np.asarray(ring.coords)[:, :2]\n return np.asarray(ring.coords)[:, :2][::-1]\n\n # The interiors are holes in the Polygon\n # MPL draws a hole if the vertex points are specified\n # in an opposite direction. So we use Clockwise for\n # the exterior/shell and Counter-Clockwise for any\n # interiors/holes\n if obj.geom_type == \"Polygon\":\n _exterior = [Path(cw_coords(obj.exterior))]\n _interior = [Path(ccw_coords(ring)) for ring in obj.interiors]\n else:\n # A MultiPolygon has one or more Polygon geoms.\n # Concatenate the exterior of all the Polygons\n # and the interiors\n _exterior = []\n _interior = []\n for p in obj.geoms:\n _exterior.append(Path(cw_coords(p.exterior)))\n _interior.extend([Path(ccw_coords(ring)) for ring in p.interiors])\n\n path = Path.make_compound_path(*_exterior, *_interior)\n return PathPatch(path)",
"def crop_image(image, vertices):\n # Create a mask with the same dimensions as the input image.\n mask = np.zeros(image.shape, dtype=np.uint8)\n #get image shape\n h, w, c = image.shape\n # Fill the mask with white polygon.\n vertices = (vertices * np.array([[h, w]])).astype(np.int32)\n cv2.fillPoly(mask, vertices, (255, 255, 255))\n print(vertices)\n # Apply the mask to the input image.\n\n #NOTE: ignored bitwise mask due to scaling issues.\n #result = cv2.bitwise_and(image, mask)\n count = 1\n for vertex in vertices:\n Y = vertex[0][0][1]\n X = vertex[0][0][0]\n H = vertex[0][3][1]\n W = vertex[0][1][0]\n save_dir = os.getcwd() + \"/image_cache/image_\" + str(count) + \".jpg\"\n count += 1\n cv2.imwrite(save_dir,image[X:X+W, Y:Y+H])",
"def select_polygon(self, polygon, add):\n if self.data and self.lsx and self.lsy:\n polygon = [(p.x(), p.y()) for p in polygon]\n # a polygon should contain all pixel\n shiftx = _shift(self.lsx)\n shifty = _shift(self.lsy)\n points_edges = [self.data_points + [[shiftx, shifty]],\n self.data_points + [[-shiftx, shifty]],\n self.data_points + [[shiftx, -shifty]],\n self.data_points + [[-shiftx, -shifty]]]\n inp = in_polygon(points_edges[0], polygon)\n for p in points_edges[1:]:\n inp *= in_polygon(p, polygon)\n self.make_selection(inp, add)",
"def simple_polygon(points):\n \n # Firstly swap the bottommost (and if necessary leftmost) point to the\n # 0th position in the list. The first line finds the bottommost point,\n # and the next line finds its index, so it can be swapped to the front.\n bottommost = min(points, key=lambda p: (p.y, p.x))\n index = points.index(bottommost)\n points[0], points[index] = points[index], points[0]\n \n # Now just sort the rest by angle from points[0]\n rest = points[1:]\n # **** FIXME by inserting the missing line of code here ****\n # print('in func:')\n \n \n rest = sorted(rest, key=lambda x: points[0] - x)\n \n \n #print(rest)\n \n \n \n return [points[0]] + rest",
"def _draw_Path2D(path, shape):\n img = Image.new('1', shape)\n draw = lambda coords, val: ImageDraw.Draw(img).polygon(coords, val)\n # Return zeros for empty paths\n if path is None:\n return np.array(img)\n for poly in path.polygons_full:\n draw(poly.exterior.coords, True)\n for interior in poly.interiors:\n draw(interior.coords, False)\n return np.array(img)",
"def show_contours(image):\n global coords\n global corners\n io.imshow(image)\n for point in coords:\n plt.scatter([point[1]], [point[0]], s=2, c='r')\n for point in corners:\n plt.scatter([point[1]], [point[0]], s=2, c='w')\n plt.show()",
"def draw_points_copy(image, points, color=COLOR):\r\n drawn = np.zeros(shape=image.shape, dtype=image.dtype)\r\n drawn[:] = image\r\n\r\n for p in points:\r\n cv2.circle(drawn, (p[0], p[1]), 1, color, -1)\r\n\r\n return drawn"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Visualizes the affine transformation of transform_matrix by drawing a quadrilateral (corner points specified by quadr, an array of form [[x, y]], clockwise order) onto a copy of right_img.
|
def visualize_affine_transform(polygon_clockwise, img, transform_matrix):
# Transform the given polygon's corner points into new space
new_poly = affine_transform(polygon_clockwise, transform_matrix)
# Return the polygon drawn on the image
return draw_polygon(img, new_poly, (0, 255, 0), 3)
|
[
"def plot_proj_origin(chessPic, mtx, R, T, chess_dim, chess_case_len):\n pic = Image.open(chessPic)\n Rmat = np.matrix(np.zeros((3,3)))\n cv2.Rodrigues(R, Rmat)\n mat_pass = np.matrix(np.zeros((3, 4)))\n mat_pass[:, :3] = Rmat\n mat_pass[:, 3] = T\n\n plt.imshow(pic, cmap=\"gray\")\n\n x_grid = np.linspace(0., (chess_dim-1) * chess_case_len, chess_dim)\n y_grid = np.linspace(0., (chess_dim-1) * chess_case_len, chess_dim)\n for i in range(0, chess_dim):\n for j in range(0, chess_dim):\n vec_3D = np.matrix([x_grid[i], y_grid[j], 0, 1]).T\n proj = mtx * mat_pass * vec_3D\n plt.plot([float(proj[0] / proj[2])], [float(proj[1] / proj[2])], '.', color=\"blue\")\n ori, Xaxis = get_quiver([chess_case_len, 0., 0., 1.], mtx, mat_pass)\n ori, Yaxis = get_quiver([0., chess_case_len, 0., 1.], mtx, mat_pass)\n ori, Zaxis = get_quiver([0., 0., chess_case_len, 1.], mtx, mat_pass)\n\n plt.plot([float(proj[0] / proj[2])], [float(proj[1] / proj[2])], '.', color=\"blue\", label=\"Projected point\")\n vec_3D = np.matrix([0, 0, 0, 1]).T\n proj = mtx * mat_pass * vec_3D\n plt.plot([float(proj[0]/proj[2])], [float(proj[1]/proj[2])], '.', color=\"red\", label='Axis origin')\n plt.quiver(ori[0], ori[1], Xaxis[0], Xaxis[1], color=\"red\")\n plt.quiver(ori[0], ori[1], Yaxis[0], Yaxis[1], color=\"green\")\n plt.quiver(ori[0], ori[1], Zaxis[0], Zaxis[1], color=\"blue\")\n plt.xlim((0., pic.size[0]))\n plt.ylim((pic.size[1], 0.))\n plt.legend()",
"def _draw_unsampled_image(self, renderer, gc):\n trans = self.get_transform() # axes.transData\n\n # convert the coordinates to the intermediate coordinate (ic).\n # The transformation from the ic to the canvas is a pure\n # affine transform.\n\n # A straight-forward way is to use the non-affine part of the\n # original transform for conversion to the ic.\n\n # firs, convert the image extent to the ic\n x_llc, x_trc, y_llc, y_trc = self.get_extent()\n\n xy = trans.transform(np.array([(x_llc, y_llc),\n (x_trc, y_trc)]))\n\n _xx1, _yy1 = xy[0]\n _xx2, _yy2 = xy[1]\n\n extent_in_ic = _xx1, _xx2, _yy1, _yy2\n\n # define trans_ic_to_canvas : unless _image_skew_coordinate is\n # set, it is simply a affine part of the original transform.\n if self._image_skew_coordinate:\n # skew the image when required.\n x_lrc, y_lrc = self._image_skew_coordinate\n xy2 = trans.transform(np.array([(x_lrc, y_lrc)]))\n _xx3, _yy3 = xy2[0]\n\n tr_rotate_skew = self._get_rotate_and_skew_transform(_xx1, _yy1,\n _xx2, _yy2,\n _xx3, _yy3)\n trans_ic_to_canvas = tr_rotate_skew\n else:\n trans_ic_to_canvas = IdentityTransform()\n\n # Now, viewLim in the ic. It can be rotated and can be\n # skewed. Make it big enough.\n x1, y1, x2, y2 = self.axes.bbox.extents\n trans_canvas_to_ic = trans_ic_to_canvas.inverted()\n xy_ = trans_canvas_to_ic.transform(np.array([(x1, y1),\n (x2, y1),\n (x2, y2),\n (x1, y2)]))\n x1_, x2_ = min(xy_[:, 0]), max(xy_[:, 0])\n y1_, y2_ = min(xy_[:, 1]), max(xy_[:, 1])\n viewLim_in_ic = Bbox.from_extents(x1_, y1_, x2_, y2_)\n\n # get the image, sliced if necessary. This is done in the ic.\n im, xmin, ymin, dxintv, dyintv, sx, sy = \\\n self._get_unsampled_image(self._A, extent_in_ic, viewLim_in_ic)\n\n if im is None:\n return # I'm not if this check is required. -JJL\n\n fc = self.axes.patch.get_facecolor()\n bg = mcolors.colorConverter.to_rgba(fc, 0)\n im.set_bg(*bg)\n\n # image input dimensions\n im.reset_matrix()\n numrows, numcols = im.get_size()\n\n if numrows <= 0 or numcols <= 0:\n return\n im.resize(numcols, numrows) # just to create im.bufOut that\n # is required by backends. There\n # may be better solution -JJL\n\n im._url = self.get_url()\n im._gid = self.get_gid()\n\n renderer.draw_image(gc, xmin, ymin, im, dxintv, dyintv,\n trans_ic_to_canvas)",
"def draw(self, matrix, mario_pos):\r\n pass",
"def drawImagePair(self, modelPoints,ax):\r\n pixel_size = 0.0000024 # [m]\r\n\r\n # images coordinate systems\r\n pv.drawOrientation(self.RotationMatrix_Image1, self.PerspectiveCenter_Image1, 1,ax)\r\n pv.drawOrientation(self.RotationMatrix_Image2, self.PerspectiveCenter_Image2, 1,ax)\r\n\r\n # images frames\r\n pv.drawImageFrame((self.__image1.camera.principalPoint[0]*2), self.__image1.camera.principalPoint[1]*2,\r\n self.RotationMatrix_Image1, self.PerspectiveCenter_Image1,self.__image1.camera.focalLength,0.1,ax)\r\n pv.drawImageFrame(self.__image2.camera.principalPoint[0] * 2,\r\n self.__image2.camera.principalPoint[1] * 2,\r\n self.RotationMatrix_Image2, self.PerspectiveCenter_Image2,\r\n self.__image2.camera.focalLength, 0.1,ax)\r\n\r\n # draw rays from perspective centers to model points\r\n pv.drawRays(modelPoints,self.PerspectiveCenter_Image1,ax)\r\n pv.drawRays(modelPoints,self.PerspectiveCenter_Image2,ax)",
"def render_to_qimage_viewer(self):\n\n # What are the show parameters?\n cam_num = self.cpanel.selected_camera()\n sensor_ind = 0 if self.cpanel.cb_left_image.isChecked() else 1\n show_gray = False\n show_distorted = self.cpanel.rb_raw_video.isChecked()\n show_disparity = self.cpanel.rb_disparity_map.isChecked()\n show_undistorted = self.cpanel.rb_undistorted.isChecked()\n show_scharr = self.cpanel.rb_scharr.isChecked()\n show_scharr_thresh = self.cpanel.rb_scharr_thresh.isChecked()\n show_harris = self.cpanel.rb_harris.isChecked()\n show_slic = self.cpanel.rb_slic.isChecked() \n show_hist = self.cpanel.rb_hist.isChecked()\n show_planes = self.cpanel.rb_planes.isChecked()\n \n # We can only show cam-no '1' when we have a nondual camera\n if not self.pblock.results.cam_sensor_good(cam_num, sensor_ind):\n self.viewer.set_image(None) # Not a dual image!\n return\n\n # Load image from results\n res = self.pblock.results\n \n if False:\n pass\n elif show_hist:\n self.viewer.set_image(res.floor_histogram_image())\n elif show_distorted:\n self.viewer.set_image(res.equalized(cam_num, sensor_ind))\n elif show_gray:\n self.viewer.set_image(res.gray(cam_num, sensor_ind))\n elif show_undistorted:\n self.viewer.set_image(res.undistorted(cam_num, sensor_ind))\n elif show_disparity: \n ind = int(self.cpanel.disp_view_select_slider.value())\n if ind < TweakerResults.n_disparities():\n im = res.disparity_image(cam_num, ind)\n self.viewer.set_image(im)\n elif show_scharr:\n self.viewer.set_image(res.scharr_image(cam_num, sensor_ind))\n elif show_scharr_thresh:\n self.viewer.set_image(res.scharr_filter_image(cam_num, sensor_ind))\n elif show_harris:\n self.viewer.set_image(res.harris_image(cam_num, sensor_ind))\n elif show_slic:\n p = self.pblock.models[cam_num]\n self.viewer.set_image(res.slic_labeled_image(cam_num, sensor_ind,p))\n elif show_planes:\n cps = self.pblock.calib_plane_sets[cam_num]\n show_d = self.cpanel.plane_rb_show_d.isChecked()\n show_p3_res = self.cpanel.plane_rb_p3_result.isChecked()\n self.viewer.set_image(res.slic_label_with_calib(cam_num,\n sensor_ind,\n cps,\n show_d,\n show_p3_res))",
"def save_qr(self, fp=None, scale=10, show_result=True):\n i = Image.new('L', (self.qr_size, self.qr_size))\n i.putdata(self.qr.flatten())\n\n new_dim = self.qr_size * scale\n i = i.resize(size=(new_dim, new_dim))\n if fp:\n i.save(fp)\n print(\"QR saved at: {}\".format(abspath(fp)))\n if show_result:\n i.show()",
"def transform(self,transform):\n if (transform is None):\n return\n \n self.active = False\n\n # Calculate origin at center\n hx = self.size[0]/2.0\n hy = self.size[1]/2.0\n \n # Center as a vector\n origin = (self.pos[0]+hx,self.pos[1]+hy)\n \n # Make a 2x2 square\n bl = (-1,-1)\n br = ( 1,-1)\n tr = ( 1, 1)\n tl = (-1, 1)\n bl = transform.transform(bl)\n br = transform.transform(br)\n tr = transform.transform(tr)\n tl = transform.transform(tl)\n \n # Scale and shift by dimensions\n bl = (bl[0]*hx/2.0+origin[0],bl[1]*hy/2.0+origin[1])\n br = (br[0]*hx/2.0+origin[0],br[1]*hy/2.0+origin[1])\n tl = (tl[0]*hx/2.0+origin[0],tl[1]*hy/2.0+origin[1])\n tr = (tr[0]*hx/2.0+origin[0],tr[1]*hy/2.0+origin[1])\n\n self.corners = [bl[0],bl[1],br[0],br[1],tr[0],tr[1],tl[0],tl[1]]\n self.active = True",
"def plot_transform(img, arg1, arg2):\r\n t1 = transform_img(img, arg1[0], arg1[1], arg1[2], arg1[3])\r\n t2 = transform_img(img, arg2[0], arg2[1], arg2[2], arg2[3])\r\n c1 = (arg1[0], arg1[1])\r\n c2 = (arg2[0], arg2[1])\r\n p0 = (350, 350)\r\n p1 = transform_point(p0, (arg1[0], arg1[1]), arg1[2], arg1[3])\r\n p2 = transform_point(p0, (arg2[0], arg2[1]), arg2[2], arg2[3])\r\n\r\n fig, ax = plt.subplots(nrows=1, ncols=3, figsize=(30, 11))\r\n fig.suptitle(\"Scaled and rotated images\")\r\n ax[0].set_title(\"Original\")\r\n ax[0].imshow(img)\r\n\r\n ax[1].set_title(\"(x,y)=({},{}), Theta={}, Scale={}\".format(arg1[0], arg1[1], arg1[2], arg1[3]))\r\n ax[1].imshow(t1)\r\n ax[1].scatter(c1[0], c1[1], c='r', s=250)\r\n\r\n ax[2].set_title(\"(x,y)=({},{}), Theta={}, Scale={}\".format(arg2[0], arg2[1], arg2[2], arg2[3]))\r\n ax[2].imshow(t2)\r\n ax[2].scatter(c2[0], c2[1], c='r', s=250)\r\n\r\n plt.show()",
"def pw_affine(fromim,toim,fp,tp,tri):\n \n im = toim.copy()\n \n # check if image is grayscale or color\n is_color = len(fromim.shape) == 3\n \n # create image to warp to (needed if iterate colors)\n im_t = zeros(im.shape, 'uint8') \n \n for t in tri:\n # compute affine transformation\n H = homography.Haffine_from_points(tp[:,t],fp[:,t])\n \n if is_color:\n for col in range(fromim.shape[2]):\n im_t[:,:,col] = ndimage.affine_transform(\n fromim[:,:,col],H[:2,:2],(H[0,2],H[1,2]),im.shape[:2])\n else:\n im_t = ndimage.affine_transform(\n fromim,H[:2,:2],(H[0,2],H[1,2]),im.shape[:2])\n \n # alpha for triangle\n alpha = alpha_for_triangle(tp[:,t],im.shape[0],im.shape[1])\n \n # add triangle to image\n im[alpha>0] = im_t[alpha>0]\n \n return im",
"def draw_from_q_values(self, rgb, q_values, attempt=None):\n fig = plt.figure(figsize=(8,6))\n\n delta = int(self.camera.delta / 1.1)\n tmp = cv2.copyMakeBorder(q_values, delta, delta, delta, delta, cv2.BORDER_CONSTANT, None, np.NaN)\n # print(tmp)\n prob_plot = cv2.resize(tmp, (rgb.shape[0], rgb.shape[1] ))\n\n plt.imshow(rgb)\n\n\n if not attempt is None:\n # print('teste de desenho')\n # # h, w = q_values.shape[:2]\n tmp = np.zeros(q_values.shape, q_values.dtype)\n # # tmp = cv2.cvtColor(tmp, cv2.COLOR_GRAY2RGB)\n # # tmp = np.dstack((tmp, np.zeros((h, w), dtype=np.uint8) + 255))\n # # print(tmp[0,0,0])\n cv2.drawMarker(tmp, attempt, (225))\n # # cv2.imshow(\"Image\", cv2.cvtColor(tmp, cv2.COLOR_BGR2RGB))\n # plt.imshow(tmp, cmap='Reds')\n # # plt.show()\n # # cv2.waitKey()\n # # cv2.destroyAllWindows()\n # # tmp[tmp == 0] = np.NaN\n tmp = cv2.copyMakeBorder( tmp, delta, delta, delta, delta, cv2.BORDER_CONSTANT, None, np.NaN)\n tmp = cv2.resize(tmp, (rgb.shape[0], rgb.shape[1]))\n plt.imshow(tmp, alpha=0.2)\n\n plt.imshow(prob_plot, vmin=0.0, vmax=1.0, alpha=0.3)\n plt.axis('off')\n plt.colorbar()\n # plt.show()\n # redraw the canvas\n fig.canvas.draw()\n # convert canvas to image\n img = np.fromstring(fig.canvas.tostring_rgb(), dtype=np.uint8, sep='')\n img = img.reshape(fig.canvas.get_width_height()[::-1] + (3, ))\n\n plt.close(fig)\n\n # cv2.imshow(\"Test\", cv2.cvtColor(img, cv2.COLOR_BGR2RGB))\n # cv2.waitKey()\n # cv2.destroyAllWindows()\n\n return img",
"def draw(self, image, px, py, angle, color, map_resolution, alpha=1.0, draw_steering_details=True):",
"def draw(self, img) -> img:\n ...",
"def visualize_views(camera_matrix,\n rvecs,\n tvecs,\n board_width,\n board_height,\n square_size,\n cam_width=64 / 2,\n cam_height=48 / 2,\n scale_focal=40,\n patternCentric=False,\n figsize=(8, 8),\n save_dir=None\n ):\n i = 0\n extrinsics = np.zeros((len(rvecs), 6))\n for rot, trans in zip(rvecs, tvecs):\n extrinsics[i] = np.append(rot.flatten(), trans.flatten())\n i += 1\n # The extrinsics matrix is of shape (N,6) (No default)\n # Where N is the number of board patterns\n # the first 3 columns are rotational vectors\n # the last 3 columns are translational vectors\n\n fig = plt.figure(figsize=figsize)\n ax = fig.gca(projection='3d')\n ax.set_aspect(\"equal\")\n\n min_values, max_values = _draw_camera_boards(ax, camera_matrix, cam_width, cam_height,\n scale_focal, extrinsics, board_width,\n board_height, square_size, patternCentric)\n\n X_min = min_values[0]\n X_max = max_values[0]\n Y_min = min_values[1]\n Y_max = max_values[1]\n Z_min = min_values[2]\n Z_max = max_values[2]\n max_range = np.array([X_max - X_min, Y_max - Y_min, Z_max - Z_min]).max() / 2.0\n\n mid_x = (X_max + X_min) * 0.5\n mid_y = (Y_max + Y_min) * 0.5\n mid_z = (Z_max + Z_min) * 0.5\n ax.set_xlim(mid_x - max_range, mid_x + max_range)\n ax.set_ylim(mid_y - max_range, mid_y + max_range)\n ax.set_zlim(mid_z - max_range, mid_z + max_range)\n\n ax.set_xlabel('x')\n ax.set_ylabel('z')\n ax.set_zlabel('-y')\n if patternCentric:\n ax.set_title('Pattern Centric View')\n if save_dir:\n plt.savefig(os.path.join(save_dir, \"pattern_centric_view.png\"))\n else:\n ax.set_title('Camera Centric View')\n if save_dir:\n plt.savefig(os.path.join(save_dir, \"camera_centric_view.png\"))\n plt.show()",
"def render_image(self, rgbobj, dst_x, dst_y):\n pass",
"def draw_cairo_image(self, ctx, image_surface, top, left, width, height):\n\n width_ratio = float(width) / float(self.orig_width)\n height_ratio = float(height) / float(self.orig_height)\n scale_xy = min(height_ratio, width_ratio)\n\n #ctx.save()\n ctx.translate(left, top)\n ctx.scale(scale_xy, scale_xy)\n ctx.set_source_surface(image_surface)\n\n ctx.paint()\n #ctx.restore()\n\n self.da.set_size_request(-1, height)",
"def graph_transform2(self, vector=(1, 1), scale=1):\n Plane.init_cartesian2(plt, scale)\n ax = plt.gca()\n plt.title(\"Matrix Transformation\")\n # Determinant Area\n # Create parallelogram using: origin, basis vectors, and a point parallel to both basis vectors\n points = [(0, 0), (self.data[0][0], self.data[1][0]), (self.data[0][0] + self.data[0][1],\n self.data[1][0] + self.data[1][1]), (self.data[0][1], self.data[1][1]), (0, 0)]\n ax.add_patch(plt.Polygon(points))\n # Find center of parallelogram by getting average of x (and y) min and max\n sorted_x = sorted([0, self.data[0][0], self.data[0][1], self.data[0][0] + self.data[0][1]])\n sorted_y = sorted([0, self.data[1][0], self.data[1][1], self.data[1][0] + self.data[1][1]])\n ax.text((sorted_x[3] - sorted_x[0]) / 2, (sorted_y[3] - sorted_y[0]) / 2, f\"{self.determinant()}\")\n # Basis vectors\n plt.arrow(0, 0, self.data[0][0], self.data[1][0], head_width=(scale/50), color=\"g\", label=\"Basis i\")\n ax.text(self.data[0][0], self.data[1][0], f\"({self.data[0][0]}, {self.data[1][0]})\")\n plt.arrow(0, 0, self.data[0][1], self.data[1][1], head_width=(scale/50), color=\"b\", label=\"Basis j\")\n ax.text(self.data[0][1], self.data[1][1], f\"({self.data[0][1]}, {self.data[1][1]})\")\n # Pre-tranformation\n transformed = self * Matrix([vector[0], vector[1]])\n plt.arrow(0, 0, vector[0], vector[1], head_width=(scale/50), color=\"y\", label=\"Pre-transform\")\n ax.text(vector[0], vector[1], f\"({vector[0]}, {vector[1]})\")\n # Post-tranformation\n plt.arrow(0, 0, transformed.data[0][0], transformed.data[1][0], head_width=(scale/50),\n color=\"tab:orange\", label=\"Post-transform\")\n ax.text(transformed.data[0][0], transformed.data[1][0], f\"({transformed.data[0][0]}, {transformed.data[1][0]})\")\n \n # Display legend and graph\n ax.legend()\n plt.show()",
"def draw(self,pic):\n # By solving the boundary equation, we have x=a**2/sqrt(a**2+b**2)\n # print \"Drawing an ellipse\" \n self.points=[] \n if self.a>self.b:\n # first go from x axis\n points=self._standardDraw(pic,actuallyDraw=True)\n else:\n # change x and y axis to enable standard drawing process\n self.a, self.b=(self.b,self.a)\n points=self._standardDraw(pic,actuallyDraw=False)\n points=[(self.centerX+p[1]-self.centerY,self.centerY+p[0]-self.centerX) for p in points]\n for p in points:\n x=int(p[0])\n y=int(p[1])\n pic[x][y]=self.color\n self.a, self.b=(self.b,self.a)\n self.points=[p for p in points]\n self._duplicate(pic,points)",
"def camera_to_image(self, points):\n\n if self.distortion_coeffs is not None:\n result = project_points(points, self.distortion_coeffs, self.intrinsic_matrix)\n return result\n else:\n projected = points[:, :2] / points[:, 2:]\n return projected @ self.intrinsic_matrix[:2, :2].T + self.intrinsic_matrix[:2, 2]",
"def plot_church(self, idx=None):\n if idx is None: idx = np.random.choice(range(len(self)))\n\n img, tgt = self[idx]\n \n img = to_numpy(img)\n\n _ = plt.imshow(img)\n filepath = '/'.join(self.filepaths[idx].split('/')[-2:])\n height, width, channels = img.shape\n title = filepath + f' ({width} x {height})'\n plt.gcf().patch.set_facecolor('white')\n plt.title(title)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Algorithm (assume number of color channels identical) 1) Acquire SIFT keypoints and descriptors across each color channel 2) Match SIFT descriptors WITHIN color channels Produce an array of form [[i, j, dist, channel]], where i index of the keypoint/descriptor in left_img j index of the keypoint/descriptor in right_img dist euclidean distance between i,j descriptors channel color channel the match occurred in 3) Merge the matches (across all channels) together, sort by distance and take top k matches (lowest distance) 4) Use the tagged matches' keypoint coordinates in the affine transformation calculation
|
def visualize_sift_color_matches(left_img, right_img, threshold, k):
# Images should have same shape and number of color channels
assert [len(left_img.shape), len(right_img.shape)] == [3, 3]
assert left_img.shape[-1] == right_img.shape[-1]
# Grab number of colors (should be last element of shape)
num_colors = left_img.shape[-1]
# OpenCV's SIFT only works on color images for some reason, so
# replicate each color channel 3 times to make it pseudo-RGB
left_channels = (gray_to_color(left_img[..., i], num_colors) for i in range(num_colors))
right_channels = (gray_to_color(right_img[..., i], num_colors) for i in range(num_colors))
# Find keypoints and descriptors for left and right images
left_kps, left_descs = zip(*(extract_sift_data(channel) for channel in left_channels))
right_kps, right_descs = zip(*(extract_sift_data(channel) for channel in right_channels))
# Get matches within each channel, then tag with color channel number in last column
channel_matches = (
match_sift_descriptors(left_descs[i], right_descs[i], threshold)
for i in range(num_colors)
)
tagged_matches = (
np.hstack((matches, color * np.ones((matches.shape[0], 1)))).astype(int)
for (color, matches) in enumerate(channel_matches)
)
# Merge matches together, sort by distance (3rd element), then take top k
merged_matches = np.vstack([x for x in tagged_matches])
sorted_matches = merged_matches[np.argsort(merged_matches[:, 2])]
top_k_matches = sorted_matches[:k]
# Grab the points associated with each match
left_match_kp, right_match_kp = [], []
for (i, j, dist, channel) in top_k_matches:
left_match_kp += [left_kps[channel][i]]
right_match_kp += [right_kps[channel][j]]
# Convert keypoints into coordinates, then compute affine matrix
left_match_kp_coords = keypoints_to_coords(left_match_kp)
right_match_kp_coords = keypoints_to_coords(right_match_kp)
affine_matrix = solve_affine_transform(left_match_kp_coords, right_match_kp_coords, k)
# Determine four corners of the left (clockwise order)
left_h, left_w = left_img.shape[:2]
left_quadr = np.array([
[0, 0], [left_w, 0],
[left_w, left_h], [0, left_h]
])
# Visualize the affine transformation
return visualize_affine_transform(left_quadr, right_img, affine_matrix)
|
[
"def findMatchesBetweenImages(image_1, image_2, num_matches):\n # matches - type: list of cv2.DMath\n matches = None\n # image_1_kp - type: list of cv2.KeyPoint items.\n image_1_kp = None\n # image_1_desc - type: numpy.ndarray of numpy.uint8 values.\n image_1_desc = None\n # image_2_kp - type: list of cv2.KeyPoint items.\n image_2_kp = None\n # image_2_desc - type: numpy.ndarray of numpy.uint8 values.\n image_2_desc = None\n\n # COPY YOUR CODE FROM A7 HERE.\n\n # sift = SIFT()\n # image_1_kp, image_1_desc = sift.detectAndCompute(image_1, None)\n # image_2_kp, image_2_desc = sift.detectAndCompute(image_2, None)\n # bf = cv2.BFMatcher(cv2.NORM_HAMMING, crossCheck=True)\n # matches = bf.match(image_1_desc,image_2_desc)\n # matches = sorted(matches, key = lambda x:x.distance)\n # matches = matches[:num_matches]\n\n alg = cv2.ORB()\n # alg = cv2.SIFT()\n\n # 1. Compute SIFT keypoints and descriptors for both images\n image_1_kp, image_1_desc = alg.detectAndCompute(image_1,None)\n image_2_kp, image_2_desc = alg.detectAndCompute(image_2,None)\n\n # 2. Create a Brute Force Matcher, using the hamming distance (and set crossCheck to true).\n bf_matcher = cv2.BFMatcher(normType=cv2.NORM_HAMMING,crossCheck=True)\n\n # 3. Compute the matches between both images.\n matches = bf_matcher.match(image_1_desc,image_2_desc)\n\n # 4. Sort the matches based on distance so you get the best matches.\n # 5. ...the top 10 matches in a list.\n matches = sorted(matches, key = lambda x:x.distance)[:num_matches]\n\n\n return image_1_kp, image_2_kp, matches",
"def findSimilarities(self,a_imgPath1, a_imgPath2, a_outPathMatches,a_outPathOriginal,\n a_outPathNew, a_minHessian = 200, a_ratioThresh = 0.6):\n\n #-- Step 0: Read images; convert to grayscale\n img1 = cv.imread(a_imgPath1)\n # img1= cv.cvtColor(img1,cv.COLOR_BGR2GRAY)\n\n img2 = cv.imread(a_imgPath2)\n # img2= cv.cvtColor(img2,cv.COLOR_BGR2GRAY)\n\n\n #-- Step 1: Detect the keypoints using SURF Detector, compute the descriptors\n # minHessian is a threshold for the features detected; increasing this value\n # allows fewer features. 300-500 is a good default but feel free to play around with it\n minHessian = a_minHessian\n detector = cv.xfeatures2d_SURF.create(hessianThreshold=minHessian)\n keypoints1, descriptors1 = detector.detectAndCompute(img1, None)\n keypoints2, descriptors2 = detector.detectAndCompute(img2, None)\n\n\n #-- Match descriptor vectors with a FLANN based matcher\n # Since SURF is a floating-point descriptor NORM_L2 is used\n # Finds matches between key points in two images\n matcher = cv.DescriptorMatcher_create(cv.DescriptorMatcher_FLANNBASED)\n matches = matcher.knnMatch(descriptors1, descriptors2, 2)\n\n good_matches = self.filterMatches(a_ratioThresh,matches)\n\n\n # Keep only key points that were matched\n kp1Matched = [keypoints1[m.queryIdx] for m in good_matches]\n kp2Matched = [keypoints2[m.trainIdx] for m in good_matches]\n\n #-- Draw matches\n img_matches = np.empty((max(img1.shape[0], img2.shape[0]), img1.shape[1]+img2.shape[1], 3), dtype=np.uint8)\n cv.drawMatches(img1, keypoints1, img2, keypoints2, good_matches, img_matches, flags=cv.DrawMatchesFlags_NOT_DRAW_SINGLE_POINTS)\n # matchOriginal = cv.drawKeypoints(img1,kp1Matched,None,(255,0,0),4)\n # matchTrain = cv.drawKeypoints(img2,kp2Matched,None,(255,0,0),4)\n\n # Draw boxes around key matches\n bd = BoxDrawer(kp1Matched,30,img1,(51,255,255),2)\n img1 = bd.img\n bd = BoxDrawer(kp2Matched,30,img2,(51,255,255),2)\n img2 = bd.img\n\n # write out images\n cv.imwrite(a_outPathMatches, img_matches)\n cv.imwrite(a_outPathOriginal,img1)\n cv.imwrite(a_outPathNew, img2)",
"def findHomography(image_1_kp, image_2_kp, matches):\n #image_1_points = np.zeros((len(matches), 1, 2), dtype=np.float32)\n #image_2_points = np.zeros((len(matches), 1, 2), dtype=np.float32)\n\n # WRITE YOUR CODE HERE.\n\n # 1. Iterate through matches and:\n # 1a. Get the x, y location of the keypoint for each match. Look up\n # the documentation for cv2.DMatch. Image 1 is your query image,\n # and Image 2 is your train image. Therefore, to find the correct\n # x, y location, you index into image_1_kp using match.queryIdx,\n # and index into image_2_kp using match.trainIdx. The x, y point\n # is stored in each keypoint (look up documentation).\n # 1b. Set the keypoint 'pt' to image_1_points and image_2_points, it\n # should look similar to this inside your loop:\n # image_1_points[match_idx] = image_1_kp[match.queryIdx].pt\n image_1_points = np.float32([ image_1_kp[match.queryIdx].pt for match in matches ]).reshape(len(matches),1,2)\n image_2_points = np.float32([ image_2_kp[match.trainIdx].pt for match in matches ]).reshape(len(matches),1,2)\n\n # 2. Call cv2.findHomography and pass in image_1_points, image_2_points,\n # use method=cv2.RANSAC and ransacReprojThreshold=5.0. I recommend\n # you look up the documentation on cv2.findHomography to better\n # understand what these parameters mean.\n return cv2.findHomography(image_1_points, image_2_points, method=cv2.RANSAC, ransacReprojThreshold=5.0)[0]\n\n # 3. cv2.findHomography returns two values, the homography and a mask.\n # Ignore the mask, and simply return the homography.\n\n\n # Replace this return statement with the homography.\n #return homography\n # END OF FUNCTION",
"def drawMatches(img1, kp1, img2, kp2, matches):\n\n # Create a new output image that concatenates the two images together\n # (a.k.a) a montage\n rows1 = img1.shape[0]\n cols1 = img1.shape[1]\n rows2 = img2.shape[0]\n cols2 = img2.shape[1]\n\n out = np.zeros((max([rows1,rows2]),cols1+cols2,9), dtype='uint8')\n\n # Place the first image to the left\n out[:rows1,:cols1] = np.dstack([img1, img1, img1])\n\n # Place the next image to the right of it\n out[:rows2,cols1:] = np.dstack([img2, img2, img2])\n\n # For each pair of points we have between both images\n # draw circles, then connect a line between them\n for mat in matches:\n\n # Get the matching keypoints for each of the images\n img1_idx = mat.queryIdx\n img2_idx = mat.trainIdx\n\n # x - columns\n # y - rows\n (x1,y1) = kp1[img1_idx].pt\n (x2,y2) = kp2[img2_idx].pt\n\n # Draw a small circle at both co-ordinates\n # radius 4\n # colour blue\n # thickness = 1\n cv2.circle(out, (int(x1),int(y1)), 4, (255, 0, 0), 1) \n cv2.circle(out, (int(x2)+cols1,int(y2)), 4, (255, 0, 0), 1)\n\n # Draw a line in between the two points\n # thickness = 1\n # colour blue\n cv2.line(out, (int(x1),int(y1)), (int(x2)+cols1,int(y2)), (255, 0, 0), 1)\n\n\n # Show the image\n cv2.imshow('Matched Features', out)\n cv2.waitKey(0)\n cv2.destroyWindow('Matched Features')\n\n # Also return the image if you'd like a copy\n return out",
"def drawMatches(img1, kp1, img2, kp2, matches):\r\n\r\n # Create a new output image that concatenates the two images together\r\n # (a.k.a) a montage\r\n rows1 = img1.shape[0]\r\n cols1 = img1.shape[1]\r\n rows2 = img2.shape[0]\r\n cols2 = img2.shape[1]\r\n\r\n out = np.zeros((max([rows1,rows2]),cols1+cols2,3), dtype='uint8')\r\n\r\n # Place the first image to the left\r\n out[:rows1,:cols1] = np.dstack([img1, img1, img1])\r\n\r\n # Place the next image to the right of it\r\n out[:rows2,cols1:] = np.dstack([img2, img2, img2])\r\n\r\n # For each pair of points we have between both images\r\n # draw circles, then connect a line between them\r\n for mat in matches:\r\n\r\n # Get the matching keypoints for each of the images\r\n img1_idx = mat.queryIdx\r\n img2_idx = mat.trainIdx\r\n\r\n # x - columns\r\n # y - rows\r\n (x1,y1) = kp1[img1_idx].pt\r\n (x2,y2) = kp2[img2_idx].pt\r\n\r\n # Draw a small circle at both co-ordinates\r\n # radius 4\r\n # colour blue\r\n # thickness = 1\r\n cv2.circle(out, (int(x1),int(y1)), 4, (255, 0, 0), 1) \r\n cv2.circle(out, (int(x2)+cols1,int(y2)), 4, (255, 0, 0), 1)\r\n\r\n # Draw a line in between the two points\r\n # thickness = 1\r\n # colour blue\r\n cv2.line(out, (int(x1),int(y1)), (int(x2)+cols1,int(y2)), (255, 0, 0), 1)\r\n\r\n\r\n # Show the image\r\n cv2.imshow('Matched Features', out)\r\n cv2.waitKey(0)\r\n cv2.destroyWindow('Matched Features')\r\n\r\n # Also return the image if you'd like a copy\r\n return out",
"def drawMatches(img1, kp1, img2, kp2, matches):\n\n # Create a new output image that concatenates the two images together\n # (a.k.a) a montage\n rows1 = img1.shape[0]\n cols1 = img1.shape[1]\n rows2 = img2.shape[0]\n cols2 = img2.shape[1]\n\n out = np.zeros((max([rows1, rows2]), cols1+cols2, 3), dtype='uint8')\n\n # Place the first image to the left\n out[:rows1, :cols1] = np.dstack([img1, img1, img1])\n\n # Place the next image to the right of it\n out[:rows2, cols1:] = np.dstack([img2, img2, img2])\n\n # For each pair of points we have between both images\n # draw circles, then connect a line between them\n for mat in matches:\n\n # Get the matching keypoints for each of the images\n img1_idx = mat.queryIdx\n img2_idx = mat.trainIdx\n\n # x - columns\n # y - rows\n (x1, y1) = kp1[img1_idx].pt\n (x2, y2) = kp2[img2_idx].pt\n\n # Draw a small circle at both co-ordinates\n # radius 4\n # colour blue\n # thickness = 1\n cv2.circle(out, (int(x1), int(y1)), 4, (255, 0, 0), 1)\n cv2.circle(out, (int(x2)+cols1, int(y2)), 4, (255, 0, 0), 1)\n\n # Draw a line in between the two points\n # thickness = 1\n # colour blue\n cv2.line(out, (int(x1), int(y1)), (int(x2)+cols1, int(y2)), (255, 0, 0), 1)\n\n\n # Show the image\n cv2.imshow('Matched Features', out)\n cv2.waitKey(0)\n cv2.destroyWindow('Matched Features')\n\n # Also return the image if you'd like a copy\n return out",
"def drawMatches(img1, kp1, img2, kp2, matches, color=None):\n # We're drawing them side by side. Get dimensions accordingly.\n # Handle both color and grayscale images.\n if len(img1.shape) == 3:\n new_shape = (max(img1.shape[0], img2.shape[0]), img1.shape[1]+img2.shape[1], img1.shape[2])\n elif len(img1.shape) == 2:\n new_shape = (max(img1.shape[0], img2.shape[0]), img1.shape[1]+img2.shape[1])\n new_img = np.zeros(new_shape, type(img1.flat[0])) \n # Place images onto the new image.\n new_img[0:img1.shape[0],0:img1.shape[1]] = img1\n new_img[0:img2.shape[0],img1.shape[1]:img1.shape[1]+img2.shape[1]] = img2\n \n # Draw lines between matches. Make sure to offset kp coords in second image appropriately.\n r = 1\n thickness = 2\n if color:\n c = color\n for m in matches:\n # Generate random color for RGB/BGR and grayscale images as needed.\n if not color: \n c = np.random.randint(0,256,3) if len(img1.shape) == 3 else np.random.randint(0,256)\n c = (int(c[0]), int(c[1]), int(c[2]))\n # So the keypoint locs are stored as a tuple of floats. cv2.line(), like most other things,\n # wants locs as a tuple of ints.\n end1 = tuple(np.round(kp1[m.trainIdx].pt).astype(int))\n end2 = tuple(np.round(kp2[m.queryIdx].pt).astype(int) + np.array([img1.shape[1], 0]))\n cv2.line(new_img, end1, end2, c, thickness)\n cv2.circle(new_img, end1, r, c, thickness)\n cv2.circle(new_img, end2, r, c, thickness)\n return new_img",
"def features_matching_accross_all_pairs(self, kp, des):\n max_size = 2*self.nb_max_features\n FLANN_INDEX_LSH = 6\n index_params= dict(algorithm = FLANN_INDEX_LSH,\n table_number = 6, # 12\n key_size = 12, # 20\n multi_probe_level = 2) #2\n search_params = dict(checks=50)\n matcher = cv2.FlannBasedMatcher(index_params, search_params)\n # matcher = cv2.DescriptorMatcher_create(cv2.DescriptorMatcher_FLANNBASED)\n matched_pts = [[[] for j in range(max_size)] for i in range(len(kp))]\n max_idx = 0\n # Process all pairs of views\n for i in range(0, len(kp)):\n for j in range(i+1,len(kp)):\n matches = matcher.knnMatch(des[i],des[j],k=2)\n good_match_idx = 0\n for idx, pair in enumerate(matches):\n if len(pair) < 2:\n continue\n (m, n) = pair\n if m.distance < self.nn_match_ratio * n.distance:\n # Good matches\n pt1 = kp[i][m.queryIdx].pt\n pt1 = (u1, v1) = (int(round(pt1[0])), int(round(pt1[1])))\n pt2 = kp[j][m.trainIdx].pt\n pt2 = (int(round(pt2[0])), int(round(pt2[1])))\n try: # Check if the first feature point has already been selected\n pt1_idx = matched_pts[i].index(pt1)\n # If so, match the point in the 2nd view at the corresponding index\n matched_pts[j][pt1_idx] = pt2 # WARNING: Maybe check if there is already a point here and if it is the same?\n max_idx -= 1\n except ValueError:\n try: # Else check if the second feature point has already been selected\n pt2_idx = matched_pts[j].index(pt2)\n # If so, match the point in the 1st view at the corresponding index\n matched_pts[i][pt2_idx] = pt1 # WARNING: Maybe check if there is already a point here and if it is the same?\n max_idx -= 1\n except ValueError:\n try:\n matched_pts[i][max_idx + good_match_idx] = pt1\n matched_pts[j][max_idx + good_match_idx] = pt2\n except IndexError:\n print(\"Too many features found, try to increase the number of max features or decrease the nn_match_ratio.\")\n sys.exit()\n good_match_idx += 1\n max_idx = max_idx + good_match_idx\n\n return matched_pts",
"def alignImages(im1, im2):\n #adjust max_features and good_match_percents\n #print('Max features', MAX_FEATURES)\n #print('Using % good', GOOD_MATCH_PERCENT)\n #GOOD_MATCH_PERCENT = 0.15\n #print('Saved Homography:', H_SHORT)\n \n # Detect ORB features and compute descriptors.\n orb = cv2.ORB_create(MAX_FEATURES)\n keypoints1, descriptors1 = orb.detectAndCompute(im1, None)\n keypoints2, descriptors2 = orb.detectAndCompute(im2, None)\n\n # Match features.\n matcher = cv2.DescriptorMatcher_create(cv2.DESCRIPTOR_MATCHER_BRUTEFORCE_HAMMING)\n try:\n matches = matcher.match(descriptors1, descriptors2, None)\n except:\n matches = None\n #print('could not match features')\n \n if matches is not None:\n # Sort matches by likelihood of being a match.\n matches.sort(key=lambda x: x.distance, reverse=False)\n\n # Remove not so good matches.\n numGoodMatches = int(len(matches) * GOOD_MATCH_PERCENT)\n matches = matches[:numGoodMatches]\n\n # Draw top matches.\n imMatches = cv2.drawMatches(im1, keypoints1, im2, keypoints2, matches, None)\n #cv2.imshow('Matches', imMatches)\n #cv2.waitKey(2000)\n cv2.imwrite(\"/home/pi/PlantHealth/SavedImages/matches.jpg\", imMatches)\n \n # Extract location of good matches.\n points1 = np.zeros((len(matches), 2), dtype=np.float32)\n points2 = np.zeros((len(matches), 2), dtype=np.float32)\n\n for i, match in enumerate(matches):\n points1[i, :] = keypoints1[match.queryIdx].pt\n points2[i, :] = keypoints2[match.trainIdx].pt\n\n # Find homography or use a stored version in case of emergency\n # or if the homography seems inaccurate.\n try:\n h, mask = cv2.findHomography(points1, points2, cv2.RANSAC)\n except:\n h = H_SHORT #using stored homography\n #print('Using saved homography h:', h)\n finally:\n # Use homography.\n if h is None or not (np.allclose(h, H_SHORT, rtol=0, atol=0.5) \n or np.allclose(h, H, rtol=0, atol=0.5)):\n h = H_SHORT\n #print('Using saved homography h:', h)\n #print('Using homography h:', repr(h))\n height, width, channels = im2.shape\n im1Reg = cv2.warpPerspective(im1, h, (width, height))\n else:\n im1Reg = im1 #could not register the image\n return im1Reg",
"def compute_matching_score(feats0, kps0, feats1, kps1, H, h0, w0, h1, w1, thresh, keep=1000):\n \n # only keep keypoints that are present in the other image\n kps0, feats0 = keep_valid_keypoints(kps0, feats0, H, h1, w1)\n kps1, feats1 = keep_valid_keypoints(kps1, feats1, np.linalg.inv(H), h0, w0)\n \n # keep a certain number of keypoints\n # kps0, kps1, feats0, feats1 = [x[:keep] for x in (kps0, kps1, feats0, feats1)]\n \n # number of valid proposed matchings\n N0, N1 = kps0.shape[0], kps1.shape[0]\n\n # if none of the keypoints are present, return None\n if N0 == 0 or N1 == 0:\n return None\n \n # matches points from image 0 to image 1, using NN\n idxs = nn_match(feats0, feats1) # matched image 1 keypoint indices\n predicted = kps1[idxs] # matched image 1 keypoints\n \n # ground truth matched location\n gt = cv2.perspectiveTransform(kps0.reshape(N0, 1, 2).astype(np.float), H).reshape(N0, 2)\n correct0 = np.linalg.norm(predicted - gt, 2, axis=1) <= thresh\n \n # 1 to 0\n idxs = nn_match(feats1, feats0)\n predicted = kps0[idxs]\n gt = cv2.perspectiveTransform(kps1.reshape(N1, 1, 2).astype(np.float), np.linalg.inv(H)).reshape(N1, 2)\n correct1 = np.linalg.norm(predicted - gt, 2, axis=1) <= thresh\n \n return (np.sum(correct1) + np.sum(correct0)) / (N1 + N0)",
"def compareImageAgainstAnotherImageGetScore_Features(img1, img2, flag_debug):\n\n # parameters\n filterMatchRatio = 0.75\n\n\n # create a detector and matcher object\n detector, matcher = createDetectorMatcher()\n\n # error if no descriptors were created for either image\n features1, descriptors1 = (detector.detectAndCompute(img1, None))\n if descriptors1 is None or not len(descriptors1):\n print \"No features in img1: %d\" % len(features1)\n return 0.0\n features2, descriptors2 = (detector.detectAndCompute(img2, None))\n if descriptors2 is None or not len(descriptors2):\n print \"No features in img2: %d.\" % len(features2)\n return 0.0\n\n # calc matches between features\n raw_matches = matcher.knnMatch(descriptors1, trainDescriptors=descriptors2, k=2)\n p1, p2, matching_feature_pairs = filterMatches(features1, features2, raw_matches, filterMatchRatio)\n\n # now that we have features lined up, we want to see if there is actually a nice homography transform (rotation, scale) that is consistent with bringing features into alignment.\n\n # numpy arrays and constants used below\n origin = numpy.array([0,0,1])\n dx = numpy.array([1,0,1])\n dy = numpy.array([0,1,1])\n\n # default returns\n match_count = 0\n scale_amount = float('Inf')\n \n # We need at least 4 points to align.\n if len(p1)>=4:\n homography_mat, inlier_pt_mask = cv2.findHomography(p1, p2, cv2.RANSAC, 5.0)\n if homography_mat is not None:\n match_count = numpy.sum(inlier_pt_mask)\n # Sometimes matching faces are visible but the die is rotated. That is,\n # this die has 5 on top but 19 visible to the side, and the other die\n # has 19 on top but 5 visible. OpenCV may find a match, but the match\n # will not be pure translation/rotation, and will distort scale.\n h = homography_mat\n scale_amount = sum([abs(1.0 - numpy.linalg.norm(h.dot(dv) - h.dot(origin))) for dv in (dx, dy)])\n if scale_amount < 1.0:\n scale_amount = (1.0 / scale_amount if scale_amount > 0 else float('Inf'))\n\n # we may want to test scale_amount and disallow the matches if holography alignment scale is too far from 1.0\n\n return match_count",
"def homography(matches,kpList1,kpList2):\n\tsrcPts = np.float32([ kpList1[m.queryIdx].pt for m in matches ]).reshape(-1,1,2) \n\tdstPts = np.float32([ kpList2[m.trainIdx].pt for m in matches ]).reshape(-1,1,2)\n\n\tM, mask = cv2.findHomography(srcPts, dstPts, cv2.RANSAC,5.0)\n\t#mask specifies the inlier and outlier points, while M represents the perspective transformation necessary to transform one image into the other\n\n\tmatchesMask = mask.ravel().tolist() #ravel flattens the array into 1D, and then we put the mask in a list\n\treturn len(matchesMask)",
"def decompose_and_match(self, k=2, maxiteration=3, size=18, buf_dist=3,**kwargs):\n def mono_matches(a, b, aidx=None, bidx=None):\n \"\"\"\n Apply the FLANN match_features\n\n Parameters\n ----------\n a : object\n A node object\n\n b : object\n A node object\n\n aidx : iterable\n An index for the descriptors to subset\n\n bidx : iterable\n An index for the descriptors to subset\n \"\"\"\n # Subset if requested\n if aidx is not None:\n ad = a.descriptors[aidx]\n else:\n ad = a.descriptors\n\n if bidx is not None:\n bd = b.descriptors[bidx]\n else:\n bd = b.descriptors\n\n # Load, train, and match\n fl.add(ad, a.node_id, index=aidx)\n fl.train()\n matches = fl.query(bd, b.node_id, k, index=bidx)\n self._add_matches(matches)\n fl.clear()\n\n def func(group):\n ratio = 0.8\n res = [False] * len(group)\n if len(res) == 1:\n return [single]\n if group.iloc[0] < group.iloc[1] * ratio:\n res[0] = True\n return res\n\n # Grab the original image arrays\n sdata = self.source.get_array()\n ddata = self.destination.get_array()\n\n ssize = sdata.shape\n dsize = ddata.shape\n\n # Grab all the available candidate keypoints\n skp = self.source.get_keypoints()\n dkp = self.destination.get_keypoints()\n\n # Set up the membership arrays\n self.smembership = np.zeros(sdata.shape, dtype=np.int16)\n self.dmembership = np.zeros(ddata.shape, dtype=np.int16)\n self.smembership[:] = -1\n self.dmembership[:] = -1\n pcounter = 0\n\n # FLANN Matcher\n fl= FlannMatcher()\n\n for k in range(maxiteration):\n partitions = np.unique(self.smembership)\n for p in partitions:\n sy_part, sx_part = np.where(self.smembership == p)\n dy_part, dx_part = np.where(self.dmembership == p)\n\n # Get the source extent\n minsy = np.min(sy_part)\n maxsy = np.max(sy_part) + 1\n minsx = np.min(sx_part)\n maxsx = np.max(sx_part) + 1\n\n # Get the destination extent\n mindy = np.min(dy_part)\n maxdy = np.max(dy_part) + 1\n mindx = np.min(dx_part)\n maxdx = np.max(dx_part) + 1\n\n # Clip the sub image from the full images\n asub = sdata[minsy:maxsy, minsx:maxsx]\n bsub = ddata[mindy:maxdy, mindx:maxdx]\n\n # Utilize the FLANN matcher to find a match to approximate a center\n fl.add(self.destination.descriptors, self.destination.node_id)\n fl.train()\n\n scounter = 0\n decompose = False\n while True:\n sub_skp = skp.query('x >= {} and x <= {} and y >= {} and y <= {}'.format(minsx, maxsx, minsy, maxsy))\n # Check the size to ensure a valid return\n if len(sub_skp) == 0:\n break # No valid keypoints in this (sub)image\n if size > len(sub_skp):\n size = len(sub_skp)\n candidate_idx = np.random.choice(sub_skp.index, size=size, replace=False)\n candidates = self.source.descriptors[candidate_idx]\n matches = fl.query(candidates, self.source.node_id, k=3, index=candidate_idx)\n\n # Apply Lowe's ratio test to try to find a 'good' starting point\n mask = matches.groupby('source_idx')['distance'].transform(func).astype('bool')\n candidate_matches = matches[mask]\n match_idx = candidate_matches['source_idx']\n\n # Extract those matches that pass the ratio check\n sub_skp = skp.iloc[match_idx]\n\n # Check that valid points remain\n if len(sub_skp) == 0:\n break\n\n # Locate the candidate closest to the middle of all of the matches\n smx, smy = sub_skp[['x', 'y']].mean()\n mid = np.array([[smx, smy]])\n dists = cdist(mid, sub_skp[['x', 'y']])\n closest = sub_skp.iloc[np.argmin(dists)]\n closest_idx = closest.name\n soriginx, soriginy = closest[['x', 'y']]\n\n # Grab the corresponding point in the destination\n q = candidate_matches.query('source_idx == {}'.format(closest.name))\n dest_idx = q['destination_idx'].iat[0]\n doriginx = dkp.at[dest_idx, 'x']\n doriginy = dkp.at[dest_idx, 'y']\n\n if mindy + buf_dist <= doriginy <= maxdy - buf_dist\\\n and mindx + 3 <= doriginx <= maxdx - 3:\n # Point is good to split on\n decompose = True\n break\n else:\n scounter += 1\n if scounter >= maxiteration:\n break\n\n # Clear the Flann matcher for reuse\n fl.clear()\n\n # Check that the identified match falls within the (sub)image\n # This catches most bad matches that have passed the ratio check\n if not (buf_dist <= doriginx - mindx <= bsub.shape[1] - buf_dist) or not\\\n (buf_dist <= doriginy - mindy <= bsub.shape[0] - buf_dist):\n decompose = False\n\n if decompose:\n # Apply coupled decomposition, shifting the origin to the sub-image\n s_submembership, d_submembership = coupled_decomposition(asub, bsub,\n sorigin=(soriginx - minsx, soriginy - minsy),\n dorigin=(doriginx - mindx, doriginy - mindy),\n **kwargs)\n\n # Shift the returned membership counters to a set of unique numbers\n s_submembership += pcounter\n d_submembership += pcounter\n\n # And assign membership\n self.smembership[minsy:maxsy,\n minsx:maxsx] = s_submembership\n self.dmembership[mindy:maxdy,\n mindx:maxdx] = d_submembership\n pcounter += 4\n \n # Now match the decomposed segments to one another\n for p in np.unique(self.smembership):\n sy_part, sx_part = np.where(self.smembership == p)\n dy_part, dx_part = np.where(self.dmembership == p)\n\n # Get the source extent\n minsy = np.min(sy_part)\n maxsy = np.max(sy_part) + 1\n minsx = np.min(sx_part)\n maxsx = np.max(sx_part) + 1\n\n # Get the destination extent\n mindy = np.min(dy_part)\n maxdy = np.max(dy_part) + 1\n mindx = np.min(dx_part)\n maxdx = np.max(dx_part) + 1\n\n # Get the indices of the candidate keypoints within those regions / variables are pulled before decomp.\n sidx = skp.query('x >= {} and x <= {} and y >= {} and y <= {}'.format(minsx, maxsx, minsy, maxsy)).index\n didx = dkp.query('x >= {} and x <= {} and y >= {} and y <= {}'.format(mindx, maxdx, mindy, maxdy)).index\n # If the candidates < k, OpenCV throws an error\n if len(sidx) >= k and len(didx) >=k:\n mono_matches(self.source, self.destination, sidx, didx)\n mono_matches(self.destination, self.source, didx, sidx)",
"def findHomography(image_1_kp, image_2_kp, matches):\n # image_1_points = np.zeros((len(matches), 1, 2), dtype=np.float32)\n # image_2_points = np.zeros((len(matches), 1, 2), dtype=np.float32)\n image_1_points = np.array(map(lambda match: image_1_kp[match.queryIdx].pt, matches))\n image_2_points = np.array(map(lambda match: image_2_kp[match.trainIdx].pt, matches))\n h, _ = cv2.findHomography(image_1_points, image_2_points, cv2.RANSAC, 5.0)\n return h",
"def match_bf(img1path, img2path, num_keypoints=1000):\n orb = cv2.ORB(num_keypoints, 1.2)\n\n img_from = cv2.imread(img1path)\n img_to = cv2.imread(img2path)\n\n # comparision\n (kp1, des1) = orb.detectAndCompute(img_from, None)\n (kp2, des2) = orb.detectAndCompute(img_to, None)\n\n # matcher\n bf = cv2.BFMatcher(cv2.NORM_HAMMING, crossCheck=True)\n matches = bf.match(des1, des2)\n\n # sort matches\n matches = sorted(matches, key=lambda val: val.distance)\n\n return matches",
"def sift_correpondence(self, queueImages, tags, method):\n (keypoint1, descriptor1) = self.cornerpointdict[tags[0]]\n (keypoint2, descriptor2) = self.cornerpointdict[tags[1]]\n if method =='OpenCV':\n matchedpoints = cv.BFMatcher().knnMatch(descriptor1, descriptor2, k=2)\n filteredmatchedpoints = []\n for pointone, pointtwo in matchedpoints:\n if pointone.distance < (pointtwo.distance * 0.75):\n filteredmatchedpoints.append([pointone])\n self.correspondence[tags[2]]=filteredmatchedpoints\n result = cv.drawMatchesKnn(self.originalImages[queueImages[0]], keypoint1, self.originalImages[queueImages[1]],keypoint2, filteredmatchedpoints,None, flags=2)\n cv.imwrite(\"results/\"+ str(tags[2]) + \".jpg\", result)\n elif method =='Custom':\n tempdict = dict()\n for index,element in enumerate(descriptor1):\n list = []\n list2 = []\n for index2, element2 in enumerate(descriptor2):\n euclediandistance = np.sqrt(np.sum(np.square((element-element2))))\n list.append(euclediandistance)\n list2.append(keypoint2[index2])\n minimumvalue = min(list)\n id = list2[list.index(minimumvalue)]\n tempdict[(int(keypoint1[index].pt[1]),int(keypoint1[index].pt[0]))]=((int(id.pt[1]),int(id.pt[0])),minimumvalue)\n self.correspondence[tags[2]] = tempdict",
"def sift_match(img1, img2, ctr=None, theta=None, s=None, thresh=0.95, search_sz=100, debug=False):\r\n k1, v1 = sift_normal(img1)\r\n k2, v2 = sift_normal(img2)\r\n matches = find_matches(img1, img2, k1, k2, v1, v2, ctr=ctr, theta=theta, s=s, search_sz=search_sz, thresh=thresh,\r\n debug=debug)\r\n\r\n return matches",
"def ransac(keypoints1, keypoints2, matches, sampling_ratio=0.5, n_iters=500, threshold=20):\n N = matches.shape[0]\n n_samples = int(N * sampling_ratio)\n\n # Please note that coordinates are in the format (y, x)\n matched1 = pad(keypoints1[matches[:,0]])\n matched2 = pad(keypoints2[matches[:,1]])\n matched1_unpad = keypoints1[matches[:,0]]\n matched2_unpad = keypoints2[matches[:,1]]\n\n max_inliers = np.zeros(N)\n n_inliers = 0\n\n # RANSAC iteration start\n ### YOUR CODE HERE \n \n # Flip x and y coordinates\n matched1[:, [0,1]] = matched1[:, [1,0]]\n matched2[:, [0,1]] = matched2[:, [1,0]]\n matched1_unpad[:, [0,1]] = matched1_unpad[:, [1,0]]\n matched2_unpad[:, [0,1]] = matched2_unpad[:, [1,0]]\n \n # Ransac Loop\n for _ in range(n_iters):\n # Randomly pick n_samples\n rand_indices = np.random.choice(N, n_samples)\n rand_1 = matched1_unpad[rand_indices]\n rand_2 = matched2_unpad[rand_indices]\n \n # Compute H using these correspondences\n iter_H = compute_homography(rand_1, rand_2)\n \n # Count the number of inliers\n iter_n_inliers = 0\n iter_inliers = np.zeros(N)\n for i in range(N):\n p1 = matched1_unpad[i]\n p2 = matched2[i]\n p2_prime = np.dot(np.linalg.inv(iter_H), p2.transpose()).transpose()\n p2_prime = p2_prime[:2] / p2_prime[-1]\n dist = np.sum(np.square(p1 - p2_prime))\n \n if dist < threshold:\n iter_n_inliers += 1\n iter_inliers[i] = 1\n\n # Store the max number of inliers\n if iter_n_inliers > n_inliers:\n n_inliers = iter_n_inliers\n max_inliers = iter_inliers\n \n # Recomputing H with all of the max inliers\n max_inliers = max_inliers.astype(bool)\n max_src = matched1_unpad[max_inliers]\n max_dst = matched2_unpad[max_inliers]\n H = compute_homography(max_src, max_dst)\n ### END YOUR CODE\n \n return H, matches[max_inliers]",
"def feature_matching(input_frames, output_folder=None):\n print(\"[FEATURE MATCHING] : start matching. This will take some time...\")\n\n # distance threshold for keyframe criteria (described in the report)\n min_baseline_dist = max(input_frames[0].shape[:2]) / 17\n\n curr_keyframe = 0\n\n # Initiate SIFT detector\n sift = cv2.xfeatures2d.SIFT_create()\n\n # find the keypoints and descriptors with SIFT\n init_pts, init_des = sift.detectAndCompute(input_frames[curr_keyframe], None)\n\n keyframes = [curr_keyframe]\n\n # modified data structure store point traces\n # from https://jivp-eurasipjournals.springeropen.com/track/pdf/10.1186/s13640-017-0168-3\n point_tracks = np.asarray([{\n '2d_points': [(pt, des)],\n } for pt, des in zip(init_pts, init_des)])\n\n intermediate_frames_matches = {}\n\n while curr_keyframe < len(input_frames) - 1:\n curr_pts = [trace['2d_points'][-1] for trace in point_tracks]\n kp1, des1 = zip(*curr_pts)\n\n intermediate_matches = []\n\n # search for next keyframe\n next_frame = curr_keyframe + 1\n while next_frame < len(input_frames) - 1:\n kp2, des2 = sift.detectAndCompute(input_frames[next_frame], None)\n\n # match\n FLANN_INDEX_KDTREE = 0\n index_params = dict(algorithm=FLANN_INDEX_KDTREE, trees=5)\n search_params = dict(checks=50)\n\n flann = cv2.FlannBasedMatcher(index_params, search_params)\n all_matches = flann.knnMatch(np.asarray(des1), des2, k=2)\n\n # filter using Lowe's ratio test\n matches = [x[0] for x in list(filter(lambda x: x[0].distance < 0.7 * x[1].distance, all_matches))]\n\n # draw matches (optional)\n if output_folder is not None and len(matches) > 0:\n draw_matches(input_frames[curr_keyframe], kp1, input_frames[next_frame],\n kp2, matches, (curr_keyframe, next_frame), output_folder)\n\n # check keyframe criteria (distant enough and doesn't cut off too many matches)\n if len(point_tracks) > 1000:\n drop_rate = 0.8\n elif len(point_tracks) > 200:\n drop_rate = 0.6\n else:\n drop_rate = 0.5\n\n is_normal_frame = 1 - len(matches) / len(point_tracks) < drop_rate\n mean_dist = mean([x.distance for x in matches])\n is_keyframe = mean_dist > min_baseline_dist and is_normal_frame and len(matches) >= MIN_MATCHES\n\n # edge case when no frames matched the criteria, but there were really good candidates\n if not is_keyframe and next_frame == len(input_frames) - 1:\n normal_intermediate_frames = [i for i, x in enumerate(intermediate_matches) if x['is_normal']]\n mean_dists = [intermediate_matches[idx]['mean_dist'] for idx in normal_intermediate_frames]\n best_candidate = mean_dists.index(max(mean_dists))\n if mean_dists[best_candidate] >= min_baseline_dist * 0.9:\n is_keyframe = True\n kp2 = intermediate_matches[best_candidate]['kp']\n des2 = intermediate_matches[best_candidate]['des']\n matches = intermediate_matches[best_candidate]['matches']\n next_frame = intermediate_matches[best_candidate]['frame']\n intermediate_matches = intermediate_matches[:best_candidate]\n\n if not is_keyframe:\n intermediate_matches.append({\n 'frame': next_frame,\n 'matches': matches,\n 'mean_dist': mean_dist,\n 'kp': kp2,\n 'des': des2,\n 'is_normal': is_normal_frame\n })\n next_frame += 1\n continue\n\n # update existing point traces and save keyframe\n keyframes.append(next_frame)\n matched_kp1_idx = []\n for m in matches:\n point_tracks[m.queryIdx]['2d_points'].append((kp2[m.trainIdx], des2[m.trainIdx]))\n matched_kp1_idx.append(m.queryIdx)\n\n point_tracks = np.asarray([pt for pt in point_tracks if len(pt['2d_points']) == len(keyframes)])\n\n # match frames in-between the last two keyframes\n match_frames_between_keyframes(curr_keyframe, kp1, next_frame, kp2,\n intermediate_matches, matches, intermediate_frames_matches)\n\n curr_keyframe = next_frame\n break\n\n if next_frame == len(input_frames) - 1:\n break\n\n print(\"[FEATURE MATCHING] : finished matching. {} keyframes found\".format(len(keyframes)))\n return keyframes, point_tracks, intermediate_frames_matches"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
determine rank of a card.
|
def rank_card(card):
return RANKS[card[0]]
|
[
"def rank(card):\n\n if card % 100 == 1:\n return ' A'\n elif card % 100 == 11:\n return ' J'\n elif card % 100 == 12:\n return ' Q'\n elif card % 100 == 13:\n return ' K'\n else:\n return card % 100",
"def relative_rank(self, card):\n if card is None:\n return (-1, 0)\n if self.relative_suit(card) == self.trump:\n suit_score = 2\n elif self.relative_suit(card) == self.led_suit():\n suit_score = 1\n else:\n suit_score = 0\n\n if suit_score == 2 and card.rank == Rank.jack:\n if card.suit == self.trump:\n rank_score = 21\n else:\n rank_score = 20\n else:\n rank_score = int(card.rank)\n\n return (suit_score, rank_score)",
"def test_card_ranks(self):\n sf = \"6C 7C 8C 9C TC\".split()\n fk = \"9D 9H 9S 9C 7D\".split()\n fh = \"TD TC TH 7C 7D\".split()\n\n self.assertEqual(poker_game.card_ranks(sf), [10, 9, 8, 7, 6])\n self.assertEqual(poker_game.card_ranks(fk), [9, 9, 9, 9, 7])\n self.assertEqual(poker_game.card_ranks(fh), [10, 10, 10, 7, 7])",
"def get_card_index(self, rank='5', suit=1):\n return self.cards.index(Card(suit, rank))",
"def _get_card_score(card):\n suit_score = SUIT_SCORING[card[0]]\n try:\n value_score = int(card[1])\n except ValueError:\n value_score = NAN_VALUES_SCORING[card[1]]\n return suit_score * value_score",
"def rank(self):\n return self._get_data_value(\"Paper rank\")",
"def rank(self,letter):\n if letter in self._positive:\n return self._positive.index(letter)\n else:\n return self.cardinality()+self._negative.index(letter)",
"def test_hand_rank(self):\n\n sf = \"6C 7C 8C 9C TC\".split()\n fk = \"9D 9H 9S 9C 7D\".split()\n fh = \"TD TC TH 7C 7D\".split()\n\n self.assertEqual(poker_game.hand_rank(sf), (8, 10))\n self.assertEqual(poker_game.hand_rank(fk), (7, 9, 7))\n self.assertEqual(poker_game.hand_rank(fh), (6, 10, 7))",
"def hand_score(hand):\n rankhand=[]\n for card in hand:\n rankhand.append(card[0])\n rankhand.sort()\n totalpoint=0\n for rank in rankhand:\n if rank>=11 and rank<14:\n point=10\n elif rank <11:\n point=rank\n elif rank == 14:\n if totalpoint+11 > 21:\n point=1\n else:\n point=11\n totalpoint=totalpoint+point\n return totalpoint",
"def extract_ranks(hand):\n substitutions = {\n 'T': '10',\n 'J': '11',\n 'Q': '12',\n 'K': '13',\n 'A': '14',\n }\n ranks = [card[0] for card in hand]\n for idx, card_rank in enumerate(ranks):\n if card_rank in substitutions.keys():\n ranks[idx] = substitutions[card_rank]\n ranks = sorted(map(int, ranks), reverse=True)\n if ranks == [14, 5, 4, 3, 2]: #check for ace low straight\n return [5, 4, 3, 2, 1]\n return ranks",
"def play_card(self, rnd: PlayerRound) -> int:\r\n #Create Simulation stuff\r\n #simRound = get_round_from_player_round(rnd, rnd.hands)\r\n bestcard = self.montecarlotreesearch(rnd)\r\n\r\n return bestcard",
"def testRankNames(self):\n RN = ['Two', 'Three', 'Four', 'Five', 'Six',\n 'Seven', 'Eight', 'Nine', 'Ten', \n 'Jack', 'Queen', 'King', 'Ace']\n s = \"c\" #testing rank not suit\n for r in range(2,14):\n myCard = Card(r,s)\n self.assertEqual(myCard.rankName(),RN[r-2]) #index of rank - 2 ",
"def testRanks(self): #GIVEN\n \n for i in range(2,15):\n myCard = Card(i,'c')\n self.assertEqual(myCard.rank(),i) # verifies that the card's rank is 'i'",
"def _get_card_value(rank: str, suit: str) -> Tuple[int, str]:\n try:\n return int(rank), suit\n except ValueError:\n return CARD_MAPPED_VALUES.get(rank), suit",
"def calculate_vader_rank(sentence):\r\n score = analyser.polarity_scores(sentence)\r\n return score[\"compound\"]",
"def card(rank, suit):\n return card_game.Card(rank, suit)",
"def get_card_value(card_label):\r\n #numbers are converted to integers and and ace is assigned to 1 the rest (face cards) are assigned 10\r\n if card_label == '2' or card_label == '3' or card_label == '4' or card_label == '5' or card_label == '6' or card_label == '7' or card_label == '8' or card_label == '9' or card_label == '10':\r\n return int(card_label)\r\n elif card_label == 'A':\r\n return int(1)\r\n else:\r\n return int(10)",
"def hand_rank(self):\n # check for a straight flush using cards sums and properties\n if self.is_straight and self.is_flush and sum(self.numbers) == 60:\n return 10, 14, None\n # check for straight_flush\n elif self.is_straight and self.is_flush:\n return 9, max(self.numbers), None\n elif self.is_flush:\n return 6, max(self.numbers), None\n elif self.is_straight:\n return 5, max(self.numbers), None\n else:\n # we only enter the next cadence if there are pairings within the group\n if self.groups:\n # 4 of a kind if there is a group of 4\n if self.counts.get(4, False):\n card = self.counts.get(4)\n high_card = self.counts.get(1)\n return 8, card.pop(), high_card.pop()\n # full house if you have a group of 3 and of 2\n elif self.counts.get(3, False) and self.counts.get(2, False):\n three = self.counts.get(3).pop()\n two = self.counts.get(2).pop()\n return 7, three, two\n elif self.counts.get(3, False):\n three_of_a_kind_card = self.counts.get(3).pop()\n high_card = max(self.counts.get(1))\n return 4, three_of_a_kind_card, high_card\n elif len(self.counts.get(2, False)) == 2:\n pairs = self.counts.get(2)\n return 3, max(pairs), min(pairs)\n elif len(self.counts.get(2, False)) == 1:\n pair = self.counts.get(2).pop()\n return 2, pair, max(self.counts.get(1))\n else:\n junk_numbers = self.numbers\n high_card = max(self.numbers)\n junk_numbers.remove(high_card)\n next_high_card = max(junk_numbers)\n return 1, high_card, next_high_card",
"def get_target_rank(rank: int, partitioner: pace.util.CubedSpherePartitioner):\n if partitioner.layout == (1, 1):\n return 0\n if partitioner.layout == (2, 2):\n if partitioner.tile.on_tile_bottom(rank):\n if partitioner.tile.on_tile_left(rank):\n return 0 # \"00\"\n if partitioner.tile.on_tile_right(rank):\n return 1 # \"10\"\n if partitioner.tile.on_tile_top(rank):\n if partitioner.tile.on_tile_left(rank):\n return 2 # \"01\"\n if partitioner.tile.on_tile_right(rank):\n return 3 # \"11\"\n else:\n if partitioner.tile.on_tile_bottom(rank):\n if partitioner.tile.on_tile_left(rank):\n return 0 # \"00\"\n if partitioner.tile.on_tile_right(rank):\n return 2 # \"20\"\n else:\n return 1 # \"10\"\n if partitioner.tile.on_tile_top(rank):\n if partitioner.tile.on_tile_left(rank):\n return 6 # \"02\"\n if partitioner.tile.on_tile_right(rank):\n return 8 # \"22\"\n else:\n return 7 # \"12\"\n else:\n if partitioner.tile.on_tile_left(rank):\n return 3 # \"01\"\n if partitioner.tile.on_tile_right(rank):\n return 5 # \"21\"\n else:\n return 4 # \"11\""
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Return ``dict`` containing extended_properties names and values.
|
def get_extended_properties_dict(self):
properties = {}
for prop in self.extended_properties:
if prop.delete is False:
properties[prop.name] = prop.value
return properties
|
[
"def get_extended_properties_list(self):\n properties = []\n for prop in self.extended_properties:\n if prop.delete is False:\n new_prop = {\n 'name': prop.name,\n 'value': prop.value,\n 'type': prop.type,\n 'guid': prop.guid\n }\n properties.append(new_prop)\n return properties",
"def getExtendedProperties(self,):\n\n\t\turl = MozuUrl(\"/api/commerce/carts/current/extendedproperties\", \"GET\", UrlLocation.TenantPod, False);\n\t\tself.client.withResourceUrl(url).execute();\n\t\treturn self.client.result();",
"def getExtendedAttributes(self):\n ans=dict()\n attributes = self.getExtendedAttribute(\"attributenames\")\n if attributes is None:\n return None\n for attr in attributes:\n val=self.getExtendedAttribute(str(attr).rstrip())\n if val is not None:\n ans[str(attr).upper().rstrip()]=val\n if len(ans) > 0:\n return ans\n else:\n return None",
"def addExtendedProperties(self,extendedProperties):\n\n\t\turl = MozuUrl(\"/api/commerce/carts/current/extendedproperties\", \"POST\", UrlLocation.TenantPod, False);\n\t\tself.client.withResourceUrl(url).withBody(extendedProperties).execute();\n\t\treturn self.client.result();",
"def getPropertyMap(self, properties = None):\n if properties is None:\n properties = self.getProperties()\n\n rv = dict()\n for prefix in [\"omero\",\"Ice\"]:\n for k,v in properties.getPropertiesForPrefix(prefix).items():\n rv[k] = v\n return rv",
"def create_extended_property(self, name='', value='',\n property_type='Attribute'):\n prop = _ExtendedProperty(self)\n prop.name = name\n prop.value = value\n prop.type = property_type\n self.extended_properties.append(prop)",
"def props_to_dict(properties):\n ret_val = collections.defaultdict()\n for prop in properties:\n ret_val[prop.qualified_name] = prop.prop_val.value\n return ret_val",
"def get_registered_properties():\n return _metaschema_properties",
"def getProperties(self):\n # type: () -> Dict[str]\n pass",
"def key_properties(self):\n # adding a 'building' qualifier to title because these props are often combined\n # with sensor properties that also have a title.\n props = {'building_title': self.title,\n 'latitude': self.latitude,\n 'longitude': self.longitude}\n try:\n props.update( yaml.load(self.other_properties, Loader=yaml.FullLoader) )\n except:\n # ignore errors\n pass\n \n return props",
"def get_extended_facts(self):\n extended_facts = {\n \"connection\": {\n \"hostname\": self.hostname, # hostname used to connect to the device\n \"username\": self.username,\n \"transport\": self.transport,\n \"port\": self.netmiko_optional_args.get('port', None),\n \"profile\": self.profile,\n \"device_type\": self.device.device_type\n }\n }\n\n extended_facts['dns'] = self.get_dns()\n extended_facts['iphelpers'] = self.get_iphelpers()\n extended_facts['logging'] = self.get_logging()\n extended_facts['tacacs'] = self.get_tacacs()\n extended_facts['aaa'] = self.get_aaa()\n extended_facts['ssh'] = self.get_ssh()\n extended_facts['vty'] = self.get_vty()\n\n return extended_facts",
"def get_embedded_properties(self):\n\n comment = self.get_first_comment()\n\n # If there's no comment then there won't be any embedded properties. No\n # need to continue from here.\n if not comment: return\n\n # For `name` we only need to match whole words, as ROBLOX's\n # properties don't have any special characters. `value` on the other\n # hand can use any character.\n property_pattern = re.compile(r\"(?P<name>\\w+):\\s+(?P<value>.+)\")\n\n property_list = {}\n\n for match in property_pattern.finditer(comment):\n property_list[match.group(\"name\")] = match.group(\"value\")\n\n return property_list",
"def get_overrided_properties(self):\n items = {}\n for cl in self.admin_obj.__class__.mro():\n if cl is admin.ModelAdmin:\n break\n for k, v in cl.__dict__.items():\n if k not in items:\n items[k] = v\n return items",
"def exec_properties(self) -> Dict[str, Any]:\n exec_dict = {}\n for key, val in self._execution.properties.items():\n exec_dict[key] = getattr(val, val.WhichOneof('value'))\n\n for key, val in self._execution.custom_properties.items():\n exec_dict[key] = getattr(val, val.WhichOneof('value'))\n\n return exec_dict",
"def get_properties(self):\n key = (self.user_name, self.bucket_name, \"property_name\")\n data = yield get_relation(key)\n returnValue(dict([(x, ujson.loads(data[x])) for x in data]))",
"def _superdict(cls):\n d = OrderedDict()\n for base in reversed(cls.mro()):\n d.update(base.__dict__)\n return d",
"def get_properties(self):\n properties = []\n for property_value in self.properties.all():\n price = \"\"\n if property_value.property.is_select_field:\n try:\n option = PropertyOption.objects.get(pk=int(float(property_value.value)))\n except (PropertyOption.DoesNotExist, ValueError):\n value = property_value.value\n price = 0.0\n else:\n value = option.name\n price = option.price\n elif property_value.property.is_number_field:\n format_string = \"%%.%sf\" % property_value.property.decimal_places\n try:\n value = format_string % float(property_value.value)\n except ValueError:\n value = \"%.2f\" % float(property_value.value)\n else:\n value = property_value.value\n\n properties.append({\n \"name\": property_value.property.name,\n \"title\": property_value.property.title,\n \"unit\": property_value.property.unit,\n \"display_price\": property_value.property.display_price,\n \"value\": value,\n \"price\": price,\n \"obj\": property_value.property\n })\n\n return properties",
"def getValues(self):\r\n res = dict()\r\n for o in self.options:\r\n v = self.getValue(o.name)\r\n res[o.name] = v\r\n if o.longid: res[o.longid] = v\r\n if o.shortid: res[o.shortid] = v\r\n\r\n return res",
"def get_properties(self):\n return self._properties"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Return ``list`` containing ``dict``s of extended properties details.
|
def get_extended_properties_list(self):
properties = []
for prop in self.extended_properties:
if prop.delete is False:
new_prop = {
'name': prop.name,
'value': prop.value,
'type': prop.type,
'guid': prop.guid
}
properties.append(new_prop)
return properties
|
[
"def get_extended_properties_dict(self):\n properties = {}\n for prop in self.extended_properties:\n if prop.delete is False:\n properties[prop.name] = prop.value\n return properties",
"def getExtendedProperties(self,):\n\n\t\turl = MozuUrl(\"/api/commerce/carts/current/extendedproperties\", \"GET\", UrlLocation.TenantPod, False);\n\t\tself.client.withResourceUrl(url).execute();\n\t\treturn self.client.result();",
"def get_properties(self):\n properties = []\n for property_value in self.properties.all():\n price = \"\"\n if property_value.property.is_select_field:\n try:\n option = PropertyOption.objects.get(pk=int(float(property_value.value)))\n except (PropertyOption.DoesNotExist, ValueError):\n value = property_value.value\n price = 0.0\n else:\n value = option.name\n price = option.price\n elif property_value.property.is_number_field:\n format_string = \"%%.%sf\" % property_value.property.decimal_places\n try:\n value = format_string % float(property_value.value)\n except ValueError:\n value = \"%.2f\" % float(property_value.value)\n else:\n value = property_value.value\n\n properties.append({\n \"name\": property_value.property.name,\n \"title\": property_value.property.title,\n \"unit\": property_value.property.unit,\n \"display_price\": property_value.property.display_price,\n \"value\": value,\n \"price\": price,\n \"obj\": property_value.property\n })\n\n return properties",
"def get_registered_properties():\n return _metaschema_properties",
"def get_properties(self):\n return self._properties",
"def getProperties(self):\n # type: () -> Dict[str]\n pass",
"def getProperties(self):\n return self.properties",
"def getProperties(self):\n props = list(self._db.keys())\n return props",
"def properties(self):\n return ( Property(x) for x in self.property_codes )",
"def get_embedded_properties(self):\n\n comment = self.get_first_comment()\n\n # If there's no comment then there won't be any embedded properties. No\n # need to continue from here.\n if not comment: return\n\n # For `name` we only need to match whole words, as ROBLOX's\n # properties don't have any special characters. `value` on the other\n # hand can use any character.\n property_pattern = re.compile(r\"(?P<name>\\w+):\\s+(?P<value>.+)\")\n\n property_list = {}\n\n for match in property_pattern.finditer(comment):\n property_list[match.group(\"name\")] = match.group(\"value\")\n\n return property_list",
"def get_overrided_properties(self):\n items = {}\n for cl in self.admin_obj.__class__.mro():\n if cl is admin.ModelAdmin:\n break\n for k, v in cl.__dict__.items():\n if k not in items:\n items[k] = v\n return items",
"def getExtendedAttributes(self):\n ans=dict()\n attributes = self.getExtendedAttribute(\"attributenames\")\n if attributes is None:\n return None\n for attr in attributes:\n val=self.getExtendedAttribute(str(attr).rstrip())\n if val is not None:\n ans[str(attr).upper().rstrip()]=val\n if len(ans) > 0:\n return ans\n else:\n return None",
"def get_related_properties(self):\n return []",
"def _get_properties(self, force=False):\r\n return self._portal.get_properties(force)",
"def addExtendedProperties(self,extendedProperties):\n\n\t\turl = MozuUrl(\"/api/commerce/carts/current/extendedproperties\", \"POST\", UrlLocation.TenantPod, False);\n\t\tself.client.withResourceUrl(url).withBody(extendedProperties).execute();\n\t\treturn self.client.result();",
"def get_extended_facts(self):\n extended_facts = {\n \"connection\": {\n \"hostname\": self.hostname, # hostname used to connect to the device\n \"username\": self.username,\n \"transport\": self.transport,\n \"port\": self.netmiko_optional_args.get('port', None),\n \"profile\": self.profile,\n \"device_type\": self.device.device_type\n }\n }\n\n extended_facts['dns'] = self.get_dns()\n extended_facts['iphelpers'] = self.get_iphelpers()\n extended_facts['logging'] = self.get_logging()\n extended_facts['tacacs'] = self.get_tacacs()\n extended_facts['aaa'] = self.get_aaa()\n extended_facts['ssh'] = self.get_ssh()\n extended_facts['vty'] = self.get_vty()\n\n return extended_facts",
"def get_properties(self, the_filter=None):\n\t\t\n\t\tunfiltered_list = [card for group in self.properties for card in group]\n\t\tfiltered_list = []\n\t\t\n\t\tif the_filter is not None:\n\t\t\tfor value in the_filter.values():\n\t\t\t\tfiltered_list.append(unfiltered_list[value])\n\t\telse:\n\t\t \treturn unfiltered_list\n\n\t\treturn filtered_list",
"def getProperties(self, app):\n \n # Get the properties\n props = yield app.properties.get()\n \n # Marshal\n data = {}\n for i,p in enumerate(props):\n data[i] = marshal(p, self.pfields)\n \n returnValue(data)",
"def getPropertyItems(self, prefs):"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Add extended property to item.
|
def create_extended_property(self, name='', value='',
property_type='Attribute'):
prop = _ExtendedProperty(self)
prop.name = name
prop.value = value
prop.type = property_type
self.extended_properties.append(prop)
|
[
"def addExtendedProperties(self,extendedProperties):\n\n\t\turl = MozuUrl(\"/api/commerce/carts/current/extendedproperties\", \"POST\", UrlLocation.TenantPod, False);\n\t\tself.client.withResourceUrl(url).withBody(extendedProperties).execute();\n\t\treturn self.client.result();",
"def append_to_properties(self, item):\n if not isinstance(item, SpatialRegriddingProperty):\n raise TypeError(\"item is of incorrect type.\")\n self.__properties.append(item)",
"def addCustomProperty(self, key, value):\n\t\treturn self.dso.CustomProperties.Add(key, value)",
"def extend(self, item: Any) -> None:\n self.contents.extend(item)\n return self",
"def updateExtendedProperties(self,extendedProperties, upsert = False):\n\n\t\turl = MozuUrl(\"/api/commerce/carts/current/extendedproperties?upsert={upsert}\", \"PUT\", UrlLocation.TenantPod, False);\n\t\turl.formatUrl(\"upsert\", upsert);\n\t\tself.client.withResourceUrl(url).withBody(extendedProperties).execute();\n\t\treturn self.client.result();",
"def updateExtendedProperty(self,extendedProperty, key, upsert = False, responseFields = None):\n\n\t\turl = MozuUrl(\"/api/commerce/carts/current/extendedproperties/{key}?upsert={upsert}&responseFields={responseFields}\", \"PUT\", UrlLocation.TenantPod, False);\n\t\turl.formatUrl(\"key\", key);\n\t\turl.formatUrl(\"responseFields\", responseFields);\n\t\turl.formatUrl(\"upsert\", upsert);\n\t\tself.client.withResourceUrl(url).withBody(extendedProperty).execute();\n\t\treturn self.client.result();",
"def setExtended(self, extended): # real signature unknown; restored from __doc__\n pass",
"def add_property_for_channel(channel, property_name, value):",
"def AddCustomProperty(cybox_object, name, description, value):\n custom_property = cyboxObjectProperties.Property()\n custom_property.name = name\n custom_property.description = description\n custom_property._value = value\n\n if not cybox_object.custom_properties:\n cybox_object.custom_properties = (\n cyboxObjectProperties.CustomProperties())\n cybox_object.custom_properties.append(custom_property)",
"def add_node_property(self):\n raise NotImplementedError(\"add_node_property()\")",
"def properties_append(self, prop: ProductProperty):\n if not type(prop) == ProductProperty:\n raise TypeError(translate(\"ControlFileData\", \"Wrong type for property data\"))\n else:\n self._properties.append([prop.name, prop.type, prop.multivalue, prop.editable,\n prop.description, prop.values, prop.default])",
"def add_property(self, prop, objects=()):\n self._properties.add(prop)\n self._objects |= objects\n self._pairs.update((o, prop) for o in objects)",
"def register_property(prop):\n PROPERTIES.append(prop)\n return prop",
"def add_property_to_item(self, property, item):\n if property is not None and item is not None:\n LOGGER.debug(\"Adding property '%s' to item '%s'\" % (property.name,\n item.name))\n item.properties.append(property)\n self.__SESSION.commit()\n LOGGER.debug(\"Property has been added to item successfully!\")\n else:\n raise ValueError(\"Value of 'property' and 'item' parameter can't be None\")",
"def add_item(self, item):",
"def getExtendedProperties(self,):\n\n\t\turl = MozuUrl(\"/api/commerce/carts/current/extendedproperties\", \"GET\", UrlLocation.TenantPod, False);\n\t\tself.client.withResourceUrl(url).execute();\n\t\treturn self.client.result();",
"def addProperty(self,protein_name,category,this_dict):\n\n if self.isknownProtein(protein_name):\n if type(this_dict) is type({}):\n self.data[protein_name][category]=this_dict.copy()\n else:\n self.data[protein_name][category]=this_dict\n \n return 1\n return None",
"def is_extended(self, is_extended):\n\n self._is_extended = is_extended",
"def set_extras(blender_element, extras, exclude=[]):\n if not extras or not isinstance(extras, dict):\n return\n\n for custom_property, value in extras.items():\n if custom_property in BLACK_LIST:\n continue\n if custom_property in exclude:\n continue\n\n try:\n blender_element[custom_property] = value\n except Exception:\n # Try to convert to string\n try:\n blender_element[custom_property] = str(value)\n except Exception:\n print('Error setting property %s to value of type %s' % (custom_property, type(value)))"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Find previous power of two
|
def prevpow2(i):
# do not use numpy here, math is much faster for single values
buf = np.floor(np.log(i) / np.log(2))
return int(np.power(2, buf))
|
[
"def _nextpow2(self, val):\n\t\tval = val - 1\n\t\tval = (val >> 1) | val\n\t\tval = (val >> 2) | val\n\t\tval = (val >> 4) | val\n\t\tval = (val >> 8) | val\n\t\tval = (val >> 16) | val\n\t\tval = (val >> 32) | val\n\t\treturn np.log2(val + 1)",
"def closest_power_2(x):\n Max_power = int((log(x-0.1,2)))\n return 2**Max_power",
"def pow2(n): \n return 1<<n",
"def next_power_of_2(n):\n n -= 1 # greater than OR EQUAL TO n\n shift = 1\n while (n+1) & n: # n+1 is not a power of 2 yet\n n |= n >> shift\n shift *= 2\n return max(4, n+1)",
"def next_pow(x, power=2):\n return pow(power, np.ceil(np.log(x) / np.log(power)))",
"def power2(n):\n return 2 ** n",
"def find_next_multiple_of_power_two(number, initial=3):\n msb = number.bit_length()\n return 3 if number <= 1 else initial << msb - 2 << (1 & number >> msb - 2)",
"def two_pow(pow):\n\treturn 2**pow",
"def power_of_2_ge(number):\n exponent = math.log(number,2)\n if exponent != int(exponent):\n int_exp = int(exponent+1)\n return int(math.pow(2,int_exp))\n else:\n return number",
"def next_power(value, base=2):\n exponent = math.ceil(math.log(value, base))\n return base**exponent",
"def enclosing_power_of_two(value):\n return int(2**np.ceil(np.log2(value)))",
"def _factor_pow2(n):\n s = 0\n d = n\n while not d & 1:\n d >>= 1\n s += 1\n assert 2**s * d == n\n return s, d",
"def power(num1: int, num2: int) -> int:\n result = 1\n while num2 > 0:\n if num2 & 1:\n result = result * num1\n num1 = num1 ** 2\n num2 >>= 1\n return result",
"def power(a, b):\n\n if b == 0:\n return 1\n\n return a * power(a, (b - 1))",
"def log2(num):\n if is_power_of_2(num):\n ret = 0\n while True:\n if num >> ret == 1:\n return ret\n else:\n ret += 1\n else:\n return np.log2(num)",
"def power_remaining(self):",
"def MyPower2(self):",
"def factor_powers_of_2(n):\n s, d = 0, n\n while d % 2 == 0:\n d //= 2\n s += 1\n return s, d",
"def powers(n, exp):\n if exp < 0:\n exp = exp * -1\n return (1 / powers(n, exp))\n if exp == 0:\n return 1\n if exp == 1:\n return n\n else:\n return n * powers(n, exp-1)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Check if the user has enough balance
|
async def balance_check(self, user_id: int, guild_id: int, amount: int) -> bool:
balance = await self.currency_repository.get(user_id, guild_id)
if not bool(balance.amount >= amount):
raise NotEnoughBalance
return True
|
[
"async def above_balance(self, ctx, user):\r\n await ctx.send(f\"{user.mention} You exceeded your game balance. \" +\r\n \"Please wager a new amount.\")",
"def test_balance(self):\n response = self.auth('user')\n self.assertEquals(response.json()['results'][0]['user_balance'],\n self.user.user_balance.get().balance)",
"def has_enough_cash():\n r = requests.get('https://api.lendingclub.com/api/investor/v1/accounts/{}/availablecash'\n .format(investor_id), headers=headers)\n\n cash = r.json()['availableCash']\n logging.debug(cash)\n return True if cash > cash_reserves + amount else False",
"def test_check_balance():\n print('\\n', \"Checking wif balance\")\n call.nspv_login(wif_real)\n res = call.type_convert(call.nspv_listunspent())\n amount = res.get(\"balance\")\n if amount > 0.1:\n pass\n else:\n pytest.exit(\"Not enough balance, please use another wif\")",
"def funds_available(self):\n if self.is_exhausted:\n return False\n remaining = self.amount - self.amount_assigned\n if remaining == 0:\n self.is_exhausted = True\n self.save()\n return False\n\n ### TO DO ###\n # Catch exceptions where remaining is < 0\n return remaining",
"async def ask_balance(self, ctx):\r\n await ctx.send(\"What should be the starting game balance of all players?\")",
"def verify_balance(self):\n total_created = 0\n total_consumed = 0\n\n for consumed_coin in self.consumed_coins:\n total_consumed += consumed_coin.value\n for created_coin in self.created_coins:\n total_created += created_coin.value\n\n return total_consumed == total_created",
"def check_account():\n\n\tglobal account_balance\n\tprint(\"Your current account balance is :\", account_balance)",
"async def test_not_enough_money(\n self,\n conn,\n user_with_wallet,\n user2_with_wallet,\n ):\n await transfer_between_wallets(\n conn,\n from_wallet_id=user_with_wallet[1],\n to_wallet_id=user2_with_wallet[1],\n amount=Decimal('1000'),\n )\n\n transaction_info = await conn.fetchrow(transaction.select())\n assert transaction_info['from_wallet_id'] == 1\n assert transaction_info['to_wallet_id'] == 2\n assert transaction_info['state'] == 'FAILED'\n assert transaction_info['amount'] == Decimal('1000')\n assert transaction_info['exchange_from_rate'] is None\n assert transaction_info['exchange_to_rate'] is None\n assert transaction_info['failed_reason'] == 'NEM_FROM_WALLET'\n logs = list(await conn.fetch(transaction_log.select()))\n # First log is creation log\n assert len(logs) == 2\n log = logs[1]\n assert log['transaction_id'] == 1\n assert log['state'] == 'FAILED'\n assert log['comment'] == 'Not enough balance'",
"def is_balanced(self, threshold=1):\n return self.get_balance() <= threshold",
"def deposit(self,amount: float):\r\n try:\r\n if self.acct_type == \"savings\":\r\n if amount > self.Max.SAVINGS or amount > self.credit.limit:\r\n print(\"Maximum deposit exceeded. please try again\")\r\n else:\r\n self.balance = self.balance + amount\r\n else:\r\n if amount > self.Max.CURRENT:\r\n print(\"Maximum deposit exceeded. please try again\")\r\n else:\r\n self.balance = self.balance + amount\r\n except (TypeError,ValueError):\r\n print(\"An error occured\")",
"def onCheckBalance(self):\n account = self._bank.getAccount(self._acctNo)\n print(\"Current balance: \" + str(account.getBalance()))\n return",
"async def withdraw(self, ctx, amount: int):\n data = await BonfideCoin(self.bot).get(ctx.guild.id, ctx.author.id)\n if data is None:\n await self.add_to_db(ctx.guild.id, ctx.author.id)\n\n data = await BonfideCoin(self.bot).get(ctx.guild.id, ctx.author.id)\n if amount <= data.get(\"bank\"):\n query = \"\"\"UPDATE bonafidecoin SET bank = bank - $3, wallet = wallet + $3 WHERE guild_id = $1 AND user_id\n = $2 \"\"\"\n await self.bot.db.execute(query, ctx.guild.id, ctx.author.id, amount)\n return await ctx.send(\n f\"Successfully withdrawn <:coin:853891390537465858> **{amount}**.\"\n )\n\n return await ctx.send(\"You don't have sufficient balance to withdraw.\")",
"def check_funds(self, amount):\r\n result = False\r\n if self.__balance - amount >= 0:\r\n result = True\r\n return result",
"def get_balance(self):\n query = 'select sum(amount) from pizza_transactions where user_id=%s'\n self.cursor.execute(query, (self.user,))\n result = self.cursor.fetchall()\n balance = result[0][0]\n if balance is None:\n balance = 0.0\n return balance",
"def check_user():\n print 'Checking user'\n client = create_client()\n details = client.check_user()\n\n print \"Credit limit: %d / Credit remaining: %d\" % (details._creditLimit, details._creditRemaining)",
"def __cash_out_available_checker(self, cash: int) -> bool:\r\n self.__set_max_cash_available()\r\n try:\r\n assert cash <= self._max_cash\r\n except AssertionError:\r\n print(f\"There is no such amount of cash ({cash}) in ATM\")\r\n return False\r\n else:\r\n print(f\"\\n{cash} amount approved\")\r\n return True",
"def check_valid_bet(self, user):\n\n if user in self.users:\n return False\n \n return True",
"def bux_check(self, uid, amt):\n\n b = self.bot.buxman.get_bux(uid)\n if b > amt:\n return True\n else:\n return False",
"def negative(self):\n if self.value() <= (self.initialBalance * 0.995):\n return True\n return False"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Tests reading an R6 MAP file, specifically M01
|
def test_R6_MAP_Structure(self):
settings = load_settings(TEST_SETTINGS_FILE)
map_filepath = path.join(settings["gamePath_R6_EW"], "data", "map", "m01", "M01.map")
loadedFile = MAPLevelReader.MAPLevelFile()
readSucessfullyToEOF = loadedFile.read_file(map_filepath)
self.assertTrue(readSucessfullyToEOF, "Failed to read whole file")
self.check_section_strings(loadedFile)
self.assertEqual(loadedFile.materialListHeader.numMaterials, 263, "Unexpected number of materials")
self.assertEqual(loadedFile.geometryListHeader.count, 57, "Unexpected number of geometry objects")
self.assertEqual(loadedFile.portalList.portalCount, 65, "Unexpected number of portals")
self.assertEqual(loadedFile.lightList.lightCount, 162, "Unexpected number of lights")
self.assertEqual(loadedFile.objectList.objectCount, 38, "Unexpected number of objects")
self.assertEqual(loadedFile.roomList.roomCount, 47, "Unexpected number of rooms")
self.assertEqual(loadedFile.planningLevelList.planningLevelCount, 4, "Unexpected number of planning levels")
|
[
"def test_load_all_R6_maps(self):\n settings = load_settings(TEST_SETTINGS_FILE)\n\n discovered_files = gather_files_in_path(\".MAP\", settings[\"gamePath_R6_EW\"])\n\n for map_filepath in discovered_files:\n if map_filepath.endswith(\"obstacletest.map\") or map_filepath.endswith(\"mansion.map\") or map_filepath.endswith(\"m8.map\") or map_filepath.endswith(\"m14.map\"):\n #TODO: remove all of these maps, except obstacletest.map from this skip, once the last data structure is deciphered\n #I believe this is an early test map that was shipped by accident.\n # It's data structures are not consistent with the rest of the map files\n # and it is not used anywhere so it is safe to skip\n continue\n\n loadedFile = MAPLevelReader.MAPLevelFile()\n readSucessfullyToEOF = loadedFile.read_file(map_filepath)\n\n self.assertTrue(readSucessfullyToEOF, f'Failed to read whole file: {map_filepath}')\n\n self.check_section_strings(loadedFile)",
"def test_parse_map_file(self):\n\n correct_map = [0,1.,1.]\n parsed_map = fizzy.parse_map_file(self.map_file_handle, \"Class\", [u'ID0',u'ID1',u'ID2'])\n self.assertEqual(parsed_map, correct_map)",
"def test_R6_MAP_Materials(self):\n settings = load_settings(TEST_SETTINGS_FILE)\n\n map_filepath = path.join(settings[\"gamePath_R6_EW\"], \"data\", \"map\", \"m02\", \"mansion.map\")\n\n loadedFile = MAPLevelReader.MAPLevelFile()\n loadedFile.read_file(map_filepath)\n\n #TODO: This is currently disabled as this file has an unread part at the end, but the rest of this test is meaninful\n #self.assertTrue(readSucessfullyToEOF, \"Failed to read whole file\")\n #self.check_section_strings(loadedFile)\n\n self.assertEqual(loadedFile.materialListHeader.numMaterials, 137, \"Unexpected number of materials\")\n\n firstMaterial = loadedFile.materials[0]\n self.assertEqual(firstMaterial.get_material_game_version(), RSEGameVersions.RAINBOW_SIX, \"Wrong material format detected\")\n self.assertEqual(firstMaterial.versionNumber, 1, \"Wrong material version number\")\n self.assertEqual(firstMaterial.material_name.string, \"WI_plain5\", \"Wrong material name\")\n self.assertEqual(firstMaterial.texture_name.string, \"Wl_paper_congo_tan_leaves1.BMP\", \"Wrong texture name\")\n\n self.assertAlmostEqual(firstMaterial.opacity, 1.0, 3, \"Wrong opacity value\")\n self.assertAlmostEqual(firstMaterial.emissiveStrength, 0.0, 3, \"Wrong emissive strength value\")\n self.assertEqual(firstMaterial.textureAddressMode, 3, \"Wrong texture address mode value\")\n self.assertEqual(firstMaterial.ambientColorUInt, [25, 25, 25], \"Wrong ambient color\")\n self.assertEqual(firstMaterial.diffuseColorUInt, [255, 255, 255], \"Wrong diffuse color\")\n self.assertEqual(firstMaterial.specularColorUInt, [229, 229, 229], \"Wrong specular color\")\n self.assertEqual(firstMaterial.normalizedColors, False, \"Incorrectly determined whether colors are normalized in the file\")\n self.assertAlmostEqual(firstMaterial.specularLevel, 0.0, 3, \"Wrong specular value\")\n self.assertEqual(firstMaterial.twoSided, False, \"Wrong two sided material flag value\")",
"def test_mip_map_generation(self):\n settings = load_settings(TEST_SETTINGS_FILE)\n\n RSB_filepath = path.join(settings[\"gamePath_R6_EW\"], \"data\", \"texture\", \"08_engine.RSB\")\n\n loadedFile = RSBImageReader.RSBImageFile()\n readSucessfullyToEOF = loadedFile.read_file(RSB_filepath)\n\n self.assertTrue(readSucessfullyToEOF, \"Failed to read whole file\")\n\n fullColorImage = loadedFile.convert_full_color_image()\n\n mips = generate_mip_maps(fullColorImage)\n\n self.assertEqual(len(mips), 8, \"Failed to generate correct number of mipmaps\")",
"def test_load_map(self):\r\n test = Maps()\r\n test.load_map(path_to_map)\r\n self.assertIn(\"facile\", test.names)\r\n self.assertNotIn(\"empty\", test.names)\r\n self.assertEqual(len(test.drawings), 1)",
"def test_impossible_mip_map_generation(self):\n settings = load_settings(TEST_SETTINGS_FILE)\n\n RSB_filepath = path.join(settings[\"gamePath_R6_EW\"], \"data\", \"shell\", \"briefing\", \"Ac_a13.RSB\")\n\n loadedFile = RSBImageReader.RSBImageFile()\n readSucessfullyToEOF = loadedFile.read_file(RSB_filepath)\n\n self.assertTrue(readSucessfullyToEOF, \"Failed to read whole file\")\n\n fullColorImage = loadedFile.convert_full_color_image()\n\n mips = generate_mip_maps(fullColorImage)\n\n self.assertIsNone(mips, \"Did not return None, instead generated mip-maps\")",
"def test_load_random_map(self, map_name):\n m = maps.get(map_name)\n run_config = run_configs.get()\n\n with run_config.start() as controller:\n logging.info(\"Loading map: %s\", m.name)\n create = sc_pb.RequestCreateGame(local_map=sc_pb.LocalMap(\n map_path=m.path, map_data=m.data(run_config)))\n create.player_setup.add(type=sc_pb.Participant)\n create.player_setup.add(type=sc_pb.Computer, race=sc_common.Random,\n difficulty=sc_pb.VeryEasy)\n join = sc_pb.RequestJoinGame(race=sc_common.Random,\n options=sc_pb.InterfaceOptions(raw=True))\n\n controller.create_game(create)\n controller.join_game(join)\n\n # Verify it has the right mods and isn't running into licensing issues.\n info = controller.game_info()\n logging.info(\"Mods for %s: %s\", m.name, info.mod_names)\n self.assertIn(\"Mods/Void.SC2Mod\", info.mod_names)\n self.assertIn(\"Mods/VoidMulti.SC2Mod\", info.mod_names)\n\n # Verify it can be played without making actions.\n for _ in range(3):\n controller.step()\n controller.observe()",
"def ParseMap(map_file):\n ret = []\n f = open(map_file)\n if not f:\n return ret\n # look for the beginning of symbols\n for line in f:\n if line.startswith(\"Real\"):\n break\n else:\n return ret\n # Prepare RE for the line of the following form:\n # 7C1F 7C1F io_error\n r = re.compile('\\s*(\\w+)\\s*(\\w+)\\s*(\\w*)')\n\n for line in f:\n m = r.match(line.strip())\n if not m:\n continue\n ret.append((int(m.group(2), 16), m.group(3)))\n return ret",
"def test_reading_ucsc_mm9_chr10(self):\n path = \"MAF/ucsc_mm9_chr10.maf\"\n alignments = Align.parse(path, \"maf\")\n self.assertEqual(alignments.metadata[\"MAF Version\"], \"1\")\n self.assertEqual(alignments.metadata[\"Scoring\"], \"autoMZ.v1\")\n alignment = next(alignments)\n self.assertEqual(alignment.score, 6441)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3009319 : 3009319 + 162],\n \"TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACCCCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT\",\n )\n self.assertEqual(\n alignment[0],\n \"TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT\",\n )\n self.assertEqual(alignment.sequences[1].id, \"oryCun1.scaffold_133159\")\n self.assertEqual(len(alignment.sequences[1].seq), 13221)\n self.assertEqual(\n alignment.sequences[1].seq[11087 : 11087 + 164],\n \"TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT\",\n )\n self.assertEqual(\n alignment[1],\n \"TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99569899999998999999999999999999999999999999999999999999999999999999999757878999975999999999999999979999999999997899999999999997997999999869999996999988997997999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(len(alignment.sequences), 2)\n self.assertNotIn(\"empty\", alignment.annotations)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n # fmt: off\n np.array([[3009319, 3009392, 3009392, 3009481],\n [ 11087, 11160, 11162, 11251],\n ])\n # fmt: on\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3009319 TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAA\n 0 |||.||.||||||.|.||||||||||||||.|.|||||.||.....||..|.||||||..\noryCun1.s 11087 TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGG\n\nmm9.chr10 3009379 AATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCT\n 60 |||.|||||||||--|..||.||.|..|.||.||.|||.||....||..||....|.|||\noryCun1.s 11147 AATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCT\n\nmm9.chr10 3009437 CACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT 3009481\n 120 ....||||.|||.|||..|||..|.|..||.|||||.||||||| 164\noryCun1.s 11207 TGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT 11251\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=6441.000000\ns mm9.chr10 3009319 162 + 129993255 TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT\ns oryCun1.scaffold_133159 11087 164 + 13221 TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT\nq oryCun1.scaffold_133159 99569899999998999999999999999999999999999999999999999999999999999999999757878999975999999999999999979999999999997899999999999997997999999869999996999988997997999999\ni oryCun1.scaffold_133159 N 0 N 0\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'C', 'A', 'T', 'A', 'G', 'G', 'T', 'A', 'T', 'T', 'T', 'A',\n 'T', 'T', 'T', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'G', 'G',\n 'T', 'T', 'T', 'G', 'C', 'T', 'T', 'T', 'A', 'T', 'G', 'G', 'C',\n 'T', 'A', 'G', 'A', 'A', 'C', 'A', 'C', 'A', 'C', 'C', 'G', 'A',\n 'T', 'T', 'A', 'C', 'T', 'T', 'A', 'A', 'A', 'A', 'T', 'A', 'G',\n 'G', 'A', 'T', 'T', 'A', 'A', 'C', 'C', '-', '-', 'C', 'C', 'C',\n 'A', 'T', 'A', 'C', 'A', 'C', 'T', 'T', 'T', 'A', 'A', 'A', 'A',\n 'A', 'T', 'G', 'A', 'T', 'T', 'A', 'A', 'A', 'C', 'A', 'A', 'C',\n 'A', 'T', 'T', 'T', 'C', 'T', 'G', 'C', 'T', 'G', 'C', 'T', 'C',\n 'G', 'C', 'T', 'C', 'A', 'C', 'A', 'T', 'T', 'C', 'T', 'T', 'C',\n 'A', 'T', 'A', 'G', 'A', 'A', 'G', 'A', 'T', 'G', 'A', 'C', 'A',\n 'T', 'A', 'A', 'T', 'G', 'T', 'A', 'T', 'T', 'T', 'T', 'C', 'C',\n 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'T'],\n ['T', 'C', 'A', 'C', 'A', 'G', 'A', 'T', 'A', 'T', 'T', 'T', 'A',\n 'C', 'T', 'A', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'G', 'G',\n 'T', 'T', 'T', 'G', 'T', 'T', 'A', 'T', 'A', 'T', 'G', 'G', 'T',\n 'T', 'A', 'C', 'G', 'G', 'T', 'T', 'C', 'A', 'T', 'A', 'G', 'G',\n 'T', 'T', 'A', 'C', 'T', 'T', 'G', 'G', 'A', 'A', 'T', 'T', 'G',\n 'G', 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'T', 'T', 'C', 'T', 'T',\n 'A', 'T', 'T', 'C', 'A', 'T', 'T', 'G', 'C', 'A', 'G', 'A', 'A',\n 'T', 'T', 'G', 'G', 'T', 'T', 'A', 'C', 'A', 'C', 'T', 'G', 'T',\n 'G', 'T', 'T', 'C', 'T', 'T', 'G', 'A', 'C', 'C', 'T', 'T', 'T',\n 'G', 'C', 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'C', 'T', 'C', 'C',\n 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'C', 'T', 'G', 'A', 'T', 'G',\n 'T', 'C', 'A', 'A', 'A', 'T', 'A', 'C', 'T', 'T', 'T', 'C', 'C',\n 'C', 'T', 'T', 'T', 'G', 'G', 'T', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 103072)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3012076 : 3012076 + 365],\n \"AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGCACTCCCAACAGCAAGACACTAAGTTCACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCACCAAATTAAATAACCAGTGAGCAGAGTTGTGACGAGCATCAGGCTCTGGATTTAGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGATGAGTCAAGTGAAGGTCCTGAGACAACAAGTCCTCGGCTATGTGGGGGTGAGGGATGCAGCTGGAACCTCAGGGATCTCTGTAAGCAGTGGCATAAATGCTTGGCGGGAGAGAGCATGTTAGAGCTCACACGACATAGGAAGCCACTGAGACACTG\",\n )\n self.assertEqual(\n alignment[0],\n \"AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGC-----ACTCCCAACAGCAAGACACTAAGTT---------CACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCAC-----CAAATTAAATAACCAGTGAGCAGAGTTG--TGACGAGCATCAGGCTCTGGATTTAGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGAT--------------------------GAGTCAAGTGAAGGTCCTGAGACAA-------------------CAAGTCCTC----GGCTATGTGGGGGTGAGGG-------------ATGC----AG--------CTGGAACCTCAGGGA-TCTCTGT-AAGCAGTGGCATAAATGCTTGGCGG--GAGAGAGCATGTTAGAGCTCACACGACATAGGAAGCCACTGA--GACACTG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 174210431)\n self.assertEqual(\n alignment.sequences[1].seq[158049785 : 158049785 + 443],\n \"GAACACAAGTCCATGGCCTTTTCAACCACGTTAGGCGTTGGAGGCCACGTCAGCCCCCACAGATCCACTCTACAACTTTAGAAAGAATTTGTTAGGCACCAGTGGCTTGCTTCAGAGTTCTAGTTCCTACGCTGTCAGGGAGTCTACAGCAGCCCTATCCACAACTTACCTCCAGGATTTTGCTTAATTTCTGTGGAAAGCGATCTCAACTTCCCAGTTCACACACAGATGCAACCAGCATGAGACATTCCTAGAAATCAACAACCTTTGGTGACTGGTCTATCTCATGCTATTCTAAATACTGCTTGCTCACTTCATAAGTACGACATTCCAAGAGCACAAGGCTATCTGGTAAGGATGAGTATGGAGATAAATATTAACATCTTTTTACTGTGATGATTTGGCTGGAATAATTAAAACTTATATTTCCACTTATGAAGACT\",\n )\n self.assertEqual(\n alignment[1],\n \"AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCCAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTACTTATGAAGTGAGCAAGCAGTATTTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGCTGCTGTAGACTCCCTGACAGCGTAGGAACT--------AGAACTCTGAAGCAAGCCACTGGTGCCTAACAAATTCTTTCTAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACGTGGTTGAAAAGGCCATGGACTTGTGTTC\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157529165 : 157529165 + 443],\n \"GAACACAAGTCCATGGCCTTTTCAACCATGTTAGGCGTTGGAGGCCACGTCAGCCCCCACAGATCCACTCTACAACTTTATAAAGAATTTGTTAGGCACCAGTGGCTTGCTTCAGAGTTCTAGTTCCTATGCTGTCAGGGAGTCTACAGCATCCCTATCCACAACTTACCTCCAGGATTTTGCTTAATTTCTGTGGAAAGCGATCTCAACTTCCCAGTTCACACACAGATGCAACCAGCATGAGACATTCCTAGAAATCAACAACCTTTGGTGACTGGTCTATCTCATGCTATTCTACATACTGCTTGCTCACTTCACAAATACGACATTCCAAGAGCACAAGGCTATCTGGTAAGGATGAGTATGGAGATAAATATTAACATCTTTTTACTGTGATGATTTAGCTGGAATAATTAAAACTTATATTTCCACTTATGAAGACT\",\n )\n self.assertEqual(\n alignment[2],\n \"AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGATGCTGTAGACTCCCTGACAGCATAGGAACTAGAACTCTGAAGC----AAGCCA----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155039093 : 155039093 + 443],\n \"GAACACAAGTCCATGGCCTTTTCAACCATGTTAGGCGTTGGAGGCCACGTCAGCCCCCATGGATCCACTCTACAACTTTATAAAGAATTTGTTAGGCACCAGTGGCTTGCTTCAGAGTTCTAGTTCCTATGCTGTCAGGGAGTCTACAGCATCCCTATCCACAACTTACCTCCAGGATTTTGCTTAATTTCTGTGGAAAGCGATCTCAACTTCCCAGTTCACACACAGATGCAACCAGCATGAGACATTCCTAGAAATCAACAACCTTTGGTGACTGGTCTATCTCATGCTATTCTACATACTGCTTGCTCACTTCACAAATACGACATTCCAAGAGCACAAGGCTATCTGGTAAGGATGAGTATGGAGATAAATATTAACATCTTTTTACTGTGATGATTTAGCTGGAATAATTAAAACTTATATTTCCACTTATGAAGACT\",\n )\n self.assertEqual(\n alignment[3],\n \"AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGATAGGGATGCTGTAGACTCCCT---GACAGCATAGGAAC-TAGAACTCTGAAGC---AAGC----CA--------CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCCATGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(len(alignment.sequences), 4)\n self.assertNotIn(\"empty\", alignment.annotations)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3012076, 3012116, 3012116, 3012141, 3012141, 3012183,\n 3012183, 3012211, 3012211, 3012231, 3012235, 3012286,\n 3012286, 3012311, 3012311, 3012311, 3012320, 3012320,\n 3012320, 3012334, 3012335, 3012339, 3012339, 3012339,\n 3012339, 3012339, 3012343, 3012343, 3012345, 3012345,\n 3012345, 3012360, 3012360, 3012367, 3012367, 3012392,\n 3012392, 3012434, 3012434, 3012441],\n [158050228, 158050188, 158050183, 158050158, 158050149, 158050107,\n 158050102, 158050074, 158050072, 158050052, 158050052, 158050001,\n 158049975, 158049950, 158049942, 158049942, 158049933, 158049932,\n 158049929, 158049915, 158049914, 158049910, 158049906, 158049906,\n 158049906, 158049905, 158049901, 158049897, 158049895, 158049891,\n 158049887, 158049872, 158049871, 158049864, 158049863, 158049838,\n 158049836, 158049794, 158049792, 158049785],\n [157529608, 157529568, 157529563, 157529538, 157529529, 157529487,\n 157529482, 157529454, 157529452, 157529432, 157529432, 157529381,\n 157529355, 157529330, 157529322, 157529322, 157529313, 157529312,\n 157529309, 157529295, 157529294, 157529290, 157529286, 157529280,\n 157529278, 157529277, 157529273, 157529273, 157529271, 157529267,\n 157529267, 157529252, 157529251, 157529244, 157529243, 157529218,\n 157529216, 157529174, 157529172, 157529165],\n [155039536, 155039496, 155039491, 155039466, 155039457, 155039415,\n 155039410, 155039382, 155039380, 155039360, 155039360, 155039309,\n 155039283, 155039258, 155039250, 155039239, 155039230, 155039229,\n 155039229, 155039215, 155039215, 155039211, 155039207, 155039201,\n 155039201, 155039201, 155039197, 155039197, 155039195, 155039195,\n 155039195, 155039180, 155039179, 155039172, 155039171, 155039146,\n 155039144, 155039102, 155039100, 155039093],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3012076 AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGC-----ACTCCCAACAGCAAG\nponAbe2.c 158050228 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCCAAATCATCACAGTAAAAAG\npanTro2.c 157529608 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAG\nhg18.chr6 155039536 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAG\n\nmm9.chr10 3012131 ACACTAAGTT---------CACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCA\nponAbe2.c 158050168 ATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCG\npanTro2.c 157529548 ATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCG\nhg18.chr6 155039476 ATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCG\n\nmm9.chr10 3012182 C-----CAAATTAAATAACCAGTGAGCAGAGTTG--TGACGAGCATCAGGCTCTGGATTT\nponAbe2.c 158050108 TACTTATGAAGTGAGCAAGCAGTATTTAGAATAGCATGAGATAGACCAGTCACCAA----\npanTro2.c 157529488 TATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----\nhg18.chr6 155039416 TATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----\n\nmm9.chr10 3012235 AGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGAT---------\nponAbe2.c 158050052 AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTT\npanTro2.c 157529432 AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTT\nhg18.chr6 155039360 AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTT\n\nmm9.chr10 3012286 -----------------GAGTCAAGTGAAGGTCCTGAGACAA------------------\nponAbe2.c 158049992 GAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA----------\npanTro2.c 157529372 GAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA----------\nhg18.chr6 155039300 GAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGATAGGGATGCT\n\nmm9.chr10 3012311 -CAAGTCCTC----GGCTATGTGGGGGTGAGGG-------------ATGC----AG----\nponAbe2.c 158049942 -TAGGGCTGCTGTAGACTCCCTGACAGCGTAGGAACT--------AGAACTCTGAAGCAA\npanTro2.c 157529322 -TAGGGATGCTGTAGACTCCCTGACAGCATAGGAACTAGAACTCTGAAGC----AAGCCA\nhg18.chr6 155039240 GTAGACTCCCT---GACAGCATAGGAAC-TAGAACTCTGAAGC---AAGC----CA----\n\nmm9.chr10 3012345 ----CTGGAACCTCAGGGA-TCTCTGT-AAGCAGTGGCATAAATGCTTGGCGG--GAGAG\nponAbe2.c 158049891 GCCACTGGTGCCTAACAAATTCTTTCTAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGT\npanTro2.c 157529267 ----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGT\nhg18.chr6 155039195 ----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCCATGGGGGCTGACGT\n\nmm9.chr10 3012397 AGCATGTTAGAGCTCACACGACATAGGAAGCCACTGA--GACACTG 3012441\nponAbe2.c 158049831 GGCCTCCAACGCCTAACGTGGTTGAAAAGGCCATGGACTTGTGTTC 158049785\npanTro2.c 157529211 GGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC 157529165\nhg18.chr6 155039139 GGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC 155039093\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=103072.000000\ns mm9.chr10 3012076 365 + 129993255 AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGC-----ACTCCCAACAGCAAGACACTAAGTT---------CACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCAC-----CAAATTAAATAACCAGTGAGCAGAGTTG--TGACGAGCATCAGGCTCTGGATTTAGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGAT--------------------------GAGTCAAGTGAAGGTCCTGAGACAA-------------------CAAGTCCTC----GGCTATGTGGGGGTGAGGG-------------ATGC----AG--------CTGGAACCTCAGGGA-TCTCTGT-AAGCAGTGGCATAAATGCTTGGCGG--GAGAGAGCATGTTAGAGCTCACACGACATAGGAAGCCACTGA--GACACTG\ns ponAbe2.chr6 16160203 443 - 174210431 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCCAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTACTTATGAAGTGAGCAAGCAGTATTTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGCTGCTGTAGACTCCCTGACAGCGTAGGAACT--------AGAACTCTGAAGCAAGCCACTGGTGCCTAACAAATTCTTTCTAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACGTGGTTGAAAAGGCCATGGACTTGTGTTC\ni ponAbe2.chr6 N 0 C 0\ns panTro2.chr6 16379004 443 - 173908612 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGATGCTGTAGACTCCCTGACAGCATAGGAACTAGAACTCTGAAGC----AAGCCA----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC\nq panTro2.chr6 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----------9999999999999999999999999999999999999999999999999----999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni panTro2.chr6 N 0 C 0\ns hg18.chr6 15860456 443 - 170899992 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGATAGGGATGCTGTAGACTCCCT---GACAGCATAGGAAC-TAGAACTCTGAAGC---AAGC----CA--------CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCCATGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC\ni hg18.chr6 N 0 C 0\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 49128)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3012441 : 3012441 + 125],\n \"TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACCTGAATTGAATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGCTCGACAC\",\n )\n self.assertEqual(\n alignment[0],\n \"TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACCTGAATTG--AATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGCTCGACAC\",\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155038979 : 155038979 + 114],\n \"GCTTCCAGCATTTTCCATTGGCCCTCAGCAAGGTGCTCCCCAAGATCAGCGGTCAAGAGAGGTGGTCAATACACACCAGGTTACGTGAGGACTTGGTTATTCTAGAGGAACCCA\",\n )\n self.assertEqual(\n alignment[1],\n \"TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157529051 : 157529051 + 114],\n \"GCTTCCAGCATTTTCCATTGGCCCTCAGCAAGGTGCTCCCCAAGATCAGCGGTCAAGAGAGGTGGTCAATACACACCAGGTTACGTGAGGACTTGGTTATTCTAGAGGAACCCA\",\n )\n self.assertEqual(\n alignment[2],\n \"TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158049671 : 158049671 + 114],\n \"GCTTCCAGCATTTTCCATTGGCCCTCAGCAAGGTGCTCCCCAAGATCAACAGTCAAGACAGGTGGTCAATATAGACCAGGTTACGTGAGGACTTGGTTATTCTAGAGGAACCCA\",\n )\n self.assertEqual(\n alignment[3],\n \"TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTCTATATTGACCACCTGTCTTGACTGTTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[4].seq), 359464)\n self.assertEqual(\n alignment.sequences[4].seq[178838 : 178838 + 101],\n \"GCTTCCCGTGTTTGCTGTTGCCCCTCAGCAAAGGGCTCCCCAAGTTTGGTGGTCAGTGTAAACCCGGGTGAGTGAGGACTTGGCCAGGTCAGGGGGGCCCA\",\n )\n self.assertEqual(\n alignment[4],\n \"TGGGCCCCCCTGACCTGGCCAAG--TCCTCACTCACCCGGGTTTACACTGACCACC-------------AAACTTGGGGAG----------CCCTTTGCT-GAGGGGCAACAGCAAACACGGGAAGC\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999979999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(len(alignment.sequences), 5)\n self.assertNotIn(\"empty\", alignment.annotations)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3012441, 3012464, 3012466, 3012497, 3012508, 3012508,\n 3012520, 3012530, 3012539, 3012540, 3012566],\n [155039093, 155039070, 155039070, 155039039, 155039028, 155039026,\n 155039014, 155039014, 155039005, 155039005, 155038979],\n [157529165, 157529142, 157529142, 157529111, 157529100, 157529098,\n 157529086, 157529086, 157529077, 157529077, 157529051],\n [158049785, 158049762, 158049762, 158049731, 158049720, 158049718,\n 158049706, 158049706, 158049697, 158049697, 158049671],\n [ 178939, 178916, 178916, 178885, 178885, 178885,\n 178873, 178873, 178864, 178864, 178838],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3012441 TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACC\nhg18.chr6 155039093 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTC\npanTro2.c 157529165 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTC\nponAbe2.c 158049785 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTCTATATTGACCACCTGTC\notoGar1.s 178939 TGGGCCCCCCTGACCTGGCCAAG--TCCTCACTCACCCGGGTTTACACTGACCACC----\n\nmm9.chr10 3012501 TGAATTG--AATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGC\nhg18.chr6 155039035 TTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGC\npanTro2.c 157529107 TTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGC\nponAbe2.c 158049727 TTGACTGTTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGC\notoGar1.s 178885 ---------AAACTTGGGGAG----------CCCTTTGCT-GAGGGGCAACAGCAAACAC\n\nmm9.chr10 3012559 TCGACAC 3012566\nhg18.chr6 155038986 TGGAAGC 155038979\npanTro2.c 157529058 TGGAAGC 157529051\nponAbe2.c 158049678 TGGAAGC 158049671\notoGar1.s 178845 GGGAAGC 178838\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=49128.000000\ns mm9.chr10 3012441 125 + 129993255 TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACCTGAATTG--AATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGCTCGACAC\ns hg18.chr6 15860899 114 - 170899992 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16379447 114 - 173908612 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\nq panTro2.chr6 99999999999999999999999--99999999999999999999999999999999999999999999999999999999----------999999999-99999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16160646 114 - 174210431 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTCTATATTGACCACCTGTCTTGACTGTTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\ni ponAbe2.chr6 C 0 C 0\ns otoGar1.scaffold_334.1-359464 180525 101 - 359464 TGGGCCCCCCTGACCTGGCCAAG--TCCTCACTCACCCGGGTTTACACTGACCACC-------------AAACTTGGGGAG----------CCCTTTGCT-GAGGGGCAACAGCAAACACGGGAAGC\nq otoGar1.scaffold_334.1-359464 99999999999999999999999--9999999999999999999999999999999-------------999999999999----------999999999-99999979999999999999999999\ni otoGar1.scaffold_334.1-359464 N 0 C 0\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'G', 'G', 'G', 'T', 'C', 'C', 'C', 'C', 'T', 'T', 'G', 'G',\n 'C', 'A', 'C', 'A', 'T', 'C', 'C', 'A', 'G', 'A', 'T', 'C', 'T',\n 'C', 'C', 'C', 'C', 'A', 'G', 'T', 'T', 'A', 'A', 'C', 'C', 'T',\n 'G', 'T', 'C', 'C', 'T', 'G', 'C', 'T', 'T', 'A', 'G', 'A', 'C',\n 'C', 'A', 'C', 'T', 'T', 'A', 'C', 'C', 'T', 'G', 'A', 'A', 'T',\n 'T', 'G', '-', '-', 'A', 'A', 'T', 'T', 'G', 'G', 'G', 'A', 'G',\n 'G', 'A', 'G', 'A', 'G', 'A', 'A', 'A', 'G', 'A', 'A', 'G', 'C',\n 'C', 'A', 'G', 'T', 'T', 'T', 'C', 'C', 'C', 'A', 'G', 'A', 'G',\n 'A', 'G', 'G', 'G', 'A', 'A', 'A', 'A', 'G', 'G', 'A', 'A', 'A',\n 'A', 'G', 'C', 'T', 'C', 'G', 'A', 'C', 'A', 'C'],\n ['T', 'G', 'G', 'G', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'A', 'G',\n 'A', 'A', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T',\n 'C', 'C', 'T', 'C', 'A', 'C', 'G', 'T', 'A', 'A', 'C', 'C', 'T',\n 'G', 'G', 'T', 'G', 'T', 'G', 'T', 'A', 'T', 'T', 'G', 'A', 'C',\n 'C', 'A', 'C', 'C', 'T', 'C', 'T', 'C', 'T', 'T', 'G', 'A', 'C',\n 'C', 'G', 'C', 'T', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'G', 'G',\n 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'C', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G',\n 'G', 'G', 'C', 'C', 'A', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'A',\n 'T', 'G', 'C', 'T', 'G', 'G', 'A', 'A', 'G', 'C'],\n ['T', 'G', 'G', 'G', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'A', 'G',\n 'A', 'A', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T',\n 'C', 'C', 'T', 'C', 'A', 'C', 'G', 'T', 'A', 'A', 'C', 'C', 'T',\n 'G', 'G', 'T', 'G', 'T', 'G', 'T', 'A', 'T', 'T', 'G', 'A', 'C',\n 'C', 'A', 'C', 'C', 'T', 'C', 'T', 'C', 'T', 'T', 'G', 'A', 'C',\n 'C', 'G', 'C', 'T', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'G', 'G',\n 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'C', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G',\n 'G', 'G', 'C', 'C', 'A', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'A',\n 'T', 'G', 'C', 'T', 'G', 'G', 'A', 'A', 'G', 'C'],\n ['T', 'G', 'G', 'G', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'A', 'G',\n 'A', 'A', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T',\n 'C', 'C', 'T', 'C', 'A', 'C', 'G', 'T', 'A', 'A', 'C', 'C', 'T',\n 'G', 'G', 'T', 'C', 'T', 'A', 'T', 'A', 'T', 'T', 'G', 'A', 'C',\n 'C', 'A', 'C', 'C', 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'A', 'C',\n 'T', 'G', 'T', 'T', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'G', 'G',\n 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'C', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G',\n 'G', 'G', 'C', 'C', 'A', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'A',\n 'T', 'G', 'C', 'T', 'G', 'G', 'A', 'A', 'G', 'C'],\n ['T', 'G', 'G', 'G', 'C', 'C', 'C', 'C', 'C', 'C', 'T', 'G', 'A',\n 'C', 'C', 'T', 'G', 'G', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T',\n 'C', 'C', 'T', 'C', 'A', 'C', 'T', 'C', 'A', 'C', 'C', 'C', 'G',\n 'G', 'G', 'T', 'T', 'T', 'A', 'C', 'A', 'C', 'T', 'G', 'A', 'C',\n 'C', 'A', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'A', 'A', 'A', 'C', 'T', 'T', 'G', 'G', 'G',\n 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'C', 'C', 'C', 'T', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G',\n 'G', 'G', 'G', 'C', 'A', 'A', 'C', 'A', 'G', 'C', 'A', 'A', 'A',\n 'C', 'A', 'C', 'G', 'G', 'G', 'A', 'A', 'G', 'C']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 117109)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3012566 : 3012566 + 262],\n \"TGTGGGCTCCTCACTTTCCTGTCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTACAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCTGTCCTCTTTAGCTTATCTCAGGCAACCTATCTTATTTTGTTTGCTTTCAGAAGGCAAGCGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtgCGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG\",\n )\n self.assertEqual(\n alignment[0],\n \"--TGTGGGCTCCTCACTTTCCTG-TCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTACAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCTGTCCTCTTTAGC-------TTATCTCAGGCAACCTATCTTATTTTGTT-TGCTTTC--AGAAGGCAAG---CGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtgCGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155038780 : 155038780 + 199],\n \"CCAAAACTCATACACAACTCATCTTCTGGGAAAACAGAATAAGTAAGATGTGTTGCTAGAAATAAGGTAGTGAAGGAAAAAAATAAGAGGATTGATTGACAGGAATGAAAACTCAGACTGGATTTTGAGGCTGTTTCTGGATGGCTTCCACCAAAAACCATAGACCCATCTAAGATCAGGGATACAAGGAGGGCTCATG\",\n )\n self.assertEqual(\n alignment[1],\n \"CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTCTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157528852 : 157528852 + 199],\n \"CCAAAACTCATACACAACTCATCTTCTGGGAAAACAAAATAAGTAAGATGTGTTGCTAGAAATAAGGTAGTGAAGGAAAAAAATAAGAGGATTGATTGACAGGAATGAAAACTCAGACTGGATTTTGAGGCTGTTTCTGGATGGCTTCCACCAAAAACCATAGACCCATCTAAGATCAGGGATACAAGGAGGGCTCATG\",\n )\n self.assertEqual(\n alignment[2],\n \"CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158049472 : 158049472 + 199],\n \"CCAAAACTCATACACAACTCATCTTCTGGGAAAACAAAATAAGTAAGATATGTTGCTAGAAATAAGGTAATGAAGGAAAAAAACAAGAGGATTGATTGACAGGAATGACAACTCAGACTGGATTTTGAGGCTGTTTCTGGATGGCTTCCACCAAAAACCATAGACCCATCTAAGATCAGGGATACAAGGAGGGCTCATG\",\n )\n self.assertEqual(\n alignment[3],\n \"CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTGTCATTCCTGTCAATCAATCCTCTTGTTTTTTTCCTTCATTACC----TTATTTCTAGCAACATATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[4].seq), 359464)\n self.assertEqual(\n alignment.sequences[4].seq[178634 : 178634 + 204],\n \"TCAAAACTCATACACAAGTCACCACTTGTCTTCTGGGAAAACAAAACAAAGTAAGCTATGTCACCTGAAATAACAAGGCAACCTAAAAATAAGGGACTGATTGCCAGCAATGACCACAGAGACTGGGTTTTCAGGTGGTTTTCTGGACAGCTTTCCCCAGAAACCAGGGCTACGCCTAAGACAGAGACACGATGAGTGCATGTG\",\n )\n self.assertEqual(\n alignment[4],\n \"CACATGCACTCATCGTGTCTCTG-TCTTAGGCGTAGCCCTGGTTTCTGGGGAAAGCTGTCCAGAAAACCACCTGAAAACCCAGTCTCTGTGGTCATTGCTGGCAATCAGTCC-CTTATTTTTAGGTTGCCTTG------TTATTTCAGGTGACATAGCTTACTTTGTTTTGTTTTCCCAGAAGACAAGTGGTGACTTGTGTATGAGTTTTGA------------------------------------------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"cavPor2.scaffold_290371\")\n self.assertEqual(len(alignment.sequences[5].seq), 39932)\n self.assertEqual(\n alignment.sequences[5].seq[39417 : 39417 + 205],\n \"CTCAAACtcacacaaaattcatttatcttccaggaaaacagaacaaaataagatATGTTTTGCAATAACGAGGTCACTATGGGGTAAAAACAAGAGGATTGGCAGGAGGGAATAACAATTTAGACTAGGTTTTGAAGTTCTTTTCTGGATGGCTTTCACCAAAAACCACAGCCACACCTCGGATCAGGATCGCAAGGGATACGCA\",\n )\n self.assertEqual(\n alignment[5],\n \"--TGCGTATCCCTTGCGATCCTGATCCGAGGTGTGGCTGTGGTTTTTGGTGAAAGCCATCCAGAAAAGAACTTCAAAACCTAGTCTAAATTGTTATTCCCTCCTGCCAATCCTCTTGTTTTTACCCCATAGTGACCTCGTTATTGCAA--AACATatcttattttgttctgttttcctggaagataaa---tgaattttgtgtgaGTTTGAG------------------------------------------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(len(alignment.sequences), 6)\n self.assertNotIn(\"empty\", alignment.annotations)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3012566, 3012566, 3012587, 3012587, 3012626, 3012627,\n 3012675, 3012676, 3012695, 3012695, 3012695, 3012695,\n 3012704, 3012706, 3012718, 3012719, 3012724, 3012724,\n 3012731, 3012731, 3012737, 3012741, 3012741, 3012762,\n 3012828],\n [155038979, 155038977, 155038956, 155038955, 155038916, 155038916,\n 155038868, 155038867, 155038848, 155038847, 155038845, 155038845,\n 155038836, 155038834, 155038822, 155038822, 155038817, 155038816,\n 155038809, 155038807, 155038801, 155038801, 155038801, 155038780,\n 155038780],\n [157529051, 157529049, 157529028, 157529027, 157528988, 157528988,\n 157528940, 157528939, 157528920, 157528919, 157528917, 157528917,\n 157528908, 157528906, 157528894, 157528894, 157528889, 157528888,\n 157528881, 157528879, 157528873, 157528873, 157528873, 157528852,\n 157528852],\n [158049671, 158049669, 158049648, 158049647, 158049608, 158049608,\n 158049560, 158049559, 158049540, 158049539, 158049537, 158049537,\n 158049528, 158049526, 158049514, 158049514, 158049509, 158049508,\n 158049501, 158049499, 158049493, 158049493, 158049493, 158049472,\n 158049472],\n [ 178838, 178836, 178815, 178815, 178776, 178775,\n 178727, 178727, 178708, 178707, 178707, 178707,\n 178698, 178696, 178684, 178683, 178678, 178677,\n 178670, 178668, 178662, 178658, 178655, 178634,\n 178634],\n [ 39622, 39622, 39601, 39600, 39561, 39560,\n 39512, 39511, 39492, 39491, 39489, 39485,\n 39476, 39476, 39464, 39463, 39458, 39457,\n 39450, 39448, 39442, 39438, 39438, 39417,\n 39417],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3012566 --TGTGGGCTCCTCACTTTCCTG-TCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTA\nhg18.chr6 155038979 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATC\npanTro2.c 157529051 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATC\nponAbe2.c 158049671 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATC\notoGar1.s 178838 CACATGCACTCATCGTGTCTCTG-TCTTAGGCGTAGCCCTGGTTTCTGGGGAAAGCTGTC\ncavPor2.s 39622 --TGCGTATCCCTTGCGATCCTGATCCGAGGTGTGGCTGTGGTTTTTGGTGAAAGCCATC\n\nmm9.chr10 3012623 CAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCT\nhg18.chr6 155038919 CAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTT\npanTro2.c 157528991 CAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTT\nponAbe2.c 158049611 CAG-AAACAGCCTCAAAATCCAGTCTGAGTTGTCATTCCTGTCAATCAATCCTCTTGTTT\notoGar1.s 178779 CAGAAAACCACCTGAAAACCCAGTCTCTGTGGTCATTGCTGGCAATCAGTCC-CTTATTT\ncavPor2.s 39564 CAGAAAAGAACTTCAAAACCTAGTCTAAATTGTTATTCCCTCCTGCCAATCCTCTTGTTT\n\nmm9.chr10 3012683 GTCCTCTTTAGC-------TTATCTCAGGCAACCTATCTTATTTTGTT-TGCTTTC--AG\nhg18.chr6 155038860 TTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTCTGTTTTCCCAG\npanTro2.c 157528932 TTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTTTGTTTTCCCAG\nponAbe2.c 158049552 TTTTCCTTCATTACC----TTATTTCTAGCAACATATCTTAC-TTATTTTGTTTTCCCAG\notoGar1.s 178720 TTAGGTTGCCTTG------TTATTTCAGGTGACATAGCTTACTTTGTTTTGTTTTCCCAG\ncavPor2.s 39504 TTACCCCATAGTGACCTCGTTATTGCAA--AACATatcttattttgttctgttttcctgg\n\nmm9.chr10 3012733 AAGGCAAG---CGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtg\nhg18.chr6 155038805 AAGA-------TGAGTTGTGTATGAGTTTTGG----------------------------\npanTro2.c 157528877 AAGA-------TGAGTTGTGTATGAGTTTTGG----------------------------\nponAbe2.c 158049497 AAGA-------TGAGTTGTGTATGAGTTTTGG----------------------------\notoGar1.s 178666 AAGACAAGTGGTGACTTGTGTATGAGTTTTGA----------------------------\ncavPor2.s 39446 aagataaa---tgaattttgtgtgaGTTTGAG----------------------------\n\nmm9.chr10 3012790 CGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG 3012828\nhg18.chr6 155038780 -------------------------------------- 155038780\npanTro2.c 157528852 -------------------------------------- 157528852\nponAbe2.c 158049472 -------------------------------------- 158049472\notoGar1.s 178634 -------------------------------------- 178634\ncavPor2.s 39417 -------------------------------------- 39417\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=117109.000000\ns mm9.chr10 3012566 262 + 129993255 --TGTGGGCTCCTCACTTTCCTG-TCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTACAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCTGTCCTCTTTAGC-------TTATCTCAGGCAACCTATCTTATTTTGTT-TGCTTTC--AGAAGGCAAG---CGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtgCGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG\ns hg18.chr6 15861013 199 - 170899992 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTCTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16379561 199 - 173908612 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\nq panTro2.chr6 999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999-999999999999999999999-------999999999999999999999------------------------------------------------------------------\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16160760 199 - 174210431 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTGTCATTCCTGTCAATCAATCCTCTTGTTTTTTTCCTTCATTACC----TTATTTCTAGCAACATATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\ni ponAbe2.chr6 C 0 C 0\ns otoGar1.scaffold_334.1-359464 180626 204 - 359464 CACATGCACTCATCGTGTCTCTG-TCTTAGGCGTAGCCCTGGTTTCTGGGGAAAGCTGTCCAGAAAACCACCTGAAAACCCAGTCTCTGTGGTCATTGCTGGCAATCAGTCC-CTTATTTTTAGGTTGCCTTG------TTATTTCAGGTGACATAGCTTACTTTGTTTTGTTTTCCCAGAAGACAAGTGGTGACTTGTGTATGAGTTTTGA------------------------------------------------------------------\nq otoGar1.scaffold_334.1-359464 99999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999------9999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------------------------------------\ni otoGar1.scaffold_334.1-359464 C 0 C 0\ns cavPor2.scaffold_290371 310 205 - 39932 --TGCGTATCCCTTGCGATCCTGATCCGAGGTGTGGCTGTGGTTTTTGGTGAAAGCCATCCAGAAAAGAACTTCAAAACCTAGTCTAAATTGTTATTCCCTCCTGCCAATCCTCTTGTTTTTACCCCATAGTGACCTCGTTATTGCAA--AACATatcttattttgttctgttttcctggaagataaa---tgaattttgtgtgaGTTTGAG------------------------------------------------------------------\nq cavPor2.scaffold_290371 --99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999997999999999999999999999999999999999999999--99999999999999999999999999999999999999---999999999999999999999------------------------------------------------------------------\ni cavPor2.scaffold_290371 N 0 C 0\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 128047)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3012828 : 3012828 + 168],\n \"TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATGCACTTAGCACAGCCTGCCCTGAGGGATGAACACTATTGTTAAAGAACTATTCCGCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT\",\n )\n self.assertEqual(\n alignment[0],\n \"TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATGCACTTAGCACAGCCTGCCCTGAGGGAT----GAACACT--ATTGTTAA-AGAACTATTCCGCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_290371\")\n self.assertEqual(len(alignment.sequences[1].seq), 39932)\n self.assertEqual(\n alignment.sequences[1].seq[39251 : 39251 + 166],\n \"ATATGACCAGCAGATGGCACTAGAATCCCACGGAACCTGAAGTTGCCTCCTGCTAAACAGCTTTGCTGACAATAAAGGTCTCAGAGCTACTAGAGCGAACCATGATAACCTCATTATTTTCataaatgcttaaatataagACTATTTAGCTGTCAAGACATCCCAC\",\n )\n self.assertEqual(\n alignment[1],\n \"-----GTGGGATGTCTTGACAGCTAAATAGTcttatatttaagcatttatGAAAATAATGAGGTTATCATGGTTCGCTCTAGTAGCTCTGAGACCTTT--ATTGTCAGCAAAGCTGTTTAGC--AGGAGGCAACTTCAGGTTCCGTGGGATTCTAGTGCCATCTGCTGGTCATAT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[2].seq), 359464)\n self.assertEqual(\n alignment.sequences[2].seq[178473 : 178473 + 161],\n \"CTGTGACCAGCAGATGGCGCTAAAATCCCACAGATCCTGAGGCTGCTGCTCCGCAAAACCGCTTCCCTGACAGTAGCCTCTCACTTCTAAGGGGCTGAGCTAAGTTTATCATTTCAACAAATGTTTAAATAGAACACTATTTGCCTGTCACGAATGTCCAC\",\n )\n self.assertEqual(\n alignment[2],\n \"-----GTGGACATTCGTGACAGGCAAATAGTGTTCTATTTAAACATTTGTTGAAATGATAAACTTAGCTCAGCC--CCTT---AGAAGTG-AGAGGCT--ACTGTCAGGGAAGCGGTTTTGCG-GAGCAGCAGCCTCAGGATCTGTGGGATTTTAGCGCCATCTGCTGGTCACAG\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999989996999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158049311 : 158049311 + 161],\n \"ATGTGACCAGCAGATGGCATTAGAGTCCCACAGATCCTGAGATTGAGCCTTAGCTAAACAACTTCACTAGGCATACCACATCTGTCAAGGCAGGTTATGCTAAGCTTATTATTTTCATAAATGTTTAAATATAACGCTATTTGGTTGTCAGGATAGTCCAC\",\n )\n self.assertEqual(\n alignment[3],\n \"-----GTGGACTATCCTGACAACCAAATAGCGTTATATTTAAACATTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGTTTAGCT-AAGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAT\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 173908612)\n self.assertEqual(\n alignment.sequences[4].seq[157528691 : 157528691 + 161],\n \"GTGTGACCAGCAGATGGCATTAGAGTCCCACAGATCCTGAGATTGAGCCATAGCTAAGCAACTTCACTAGGCATACCACATCTGTCAAGGCAGGTTATGCTAAGCTTATTATTTTCATAAACGTTTAAATATAACGCTATTTGGTTGTCAAGATAGTCCGC\",\n )\n self.assertEqual(\n alignment[4],\n \"-----GCGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155038619 : 155038619 + 161],\n \"GTGTGACCAGCAGATGGCATTAGAGTCCCACAGATCCTGAGATTGAGCCATAGCTAAGCAACTTCACTAGGCATACCACATCTGTCAAGGCAGGTTATGCTAAGCTTATTATTTTCACAAACGTTTAAATATAACGCTATTTGGTTGTCAAGATAGTCCAC\",\n )\n self.assertEqual(\n alignment[5],\n \"-----GTGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTGTGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[6].seq), 100002)\n self.assertEqual(\n alignment.sequences[6].seq[87492 : 87492 + 169],\n \"TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATGAGTTTGTCATAACTGCCTCCTCCCAAGTGGGAAGCTGAAGCACCAAGTACTGACTCAGCAGTCCCTGACCTCACATCCATGGAAATCTAGTGACATCTGCTGGACACAT\",\n )\n self.assertEqual(\n alignment[6],\n \"TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATGAGTTTGTCATAACT-GCCTCCTCCCAAGTG-GGAAGCTGAAGCACCAA-GTACTGACTCAGC--AGTCCCTGACCTCA-CATCCATGGAAATCTAGTGACATCTGCTGGACACAT\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"9998999999897966589999999999967689989799789997987889999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 7564)\n self.assertEqual(len(alignment.sequences), 7)\n self.assertNotIn(\"empty\", alignment.annotations)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3012828, 3012833, 3012902, 3012903, 3012904, 3012908,\n 3012911, 3012915, 3012915, 3012915, 3012921, 3012922,\n 3012922, 3012926, 3012930, 3012930, 3012943, 3012944,\n 3012945, 3012959, 3012960, 3012996],\n [ 39417, 39417, 39348, 39347, 39346, 39342,\n 39339, 39335, 39332, 39331, 39325, 39324,\n 39324, 39320, 39316, 39315, 39302, 39302,\n 39302, 39288, 39287, 39251],\n [ 178634, 178634, 178565, 178565, 178565, 178561,\n 178561, 178557, 178554, 178554, 178548, 178547,\n 178547, 178543, 178539, 178538, 178525, 178524,\n 178524, 178510, 178509, 178473],\n [158049472, 158049472, 158049403, 158049402, 158049401, 158049397,\n 158049394, 158049390, 158049387, 158049387, 158049381, 158049381,\n 158049381, 158049381, 158049377, 158049376, 158049363, 158049362,\n 158049362, 158049348, 158049347, 158049311],\n [157528852, 157528852, 157528783, 157528782, 157528781, 157528777,\n 157528774, 157528770, 157528767, 157528767, 157528761, 157528761,\n 157528761, 157528761, 157528757, 157528756, 157528743, 157528742,\n 157528742, 157528728, 157528727, 157528691],\n [155038780, 155038780, 155038711, 155038710, 155038709, 155038705,\n 155038702, 155038698, 155038695, 155038695, 155038689, 155038689,\n 155038689, 155038689, 155038685, 155038684, 155038671, 155038670,\n 155038670, 155038656, 155038655, 155038619],\n [ 87492, 87497, 87566, 87566, 87567, 87571,\n 87574, 87578, 87581, 87581, 87587, 87588,\n 87590, 87594, 87598, 87598, 87611, 87611,\n 87611, 87625, 87625, 87661],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3012828 TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATG\ncavPor2.s 39417 -----GTGGGATGTCTTGACAGCTAAATAGTcttatatttaagcatttatGAAAATAATG\notoGar1.s 178634 -----GTGGACATTCGTGACAGGCAAATAGTGTTCTATTTAAACATTTGTTGAAATGATA\nponAbe2.c 158049472 -----GTGGACTATCCTGACAACCAAATAGCGTTATATTTAAACATTTATGAAAATAATA\npanTro2.c 157528852 -----GCGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTATGAAAATAATA\nhg18.chr6 155038780 -----GTGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTGTGAAAATAATA\nechTel1.s 87492 TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATG\n\nmm9.chr10 3012888 CACTTAGCACAGCCTGCCCTGAGGGAT----GAACACT--ATTGTTAA-AGAACTATTCC\ncavPor2.s 39362 AGGTTATCATGGTTCGCTCTAGTAGCTCTGAGACCTTT--ATTGTCAGCAAAGCTGTTTA\notoGar1.s 178579 AACTTAGCTCAGCC--CCTT---AGAAGTG-AGAGGCT--ACTGTCAGGGAAGCGGTTTT\nponAbe2.c 158049417 AGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGTTTA\npanTro2.c 157528797 AGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTA\nhg18.chr6 155038725 AGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTA\nechTel1.s 87552 AGTTTGTCATAACT-GCCTCCTCCCAAGTG-GGAAGCTGAAGCACCAA-GTACTGACTCA\n\nmm9.chr10 3012941 GCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT\ncavPor2.s 39304 GC--AGGAGGCAACTTCAGGTTCCGTGGGATTCTAGTGCCATCTGCTGGTCATAT\notoGar1.s 178527 GCG-GAGCAGCAGCCTCAGGATCTGTGGGATTTTAGCGCCATCTGCTGGTCACAG\nponAbe2.c 158049365 GCT-AAGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAT\npanTro2.c 157528745 GCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\nhg18.chr6 155038673 GCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\nechTel1.s 87609 GC--AGTCCCTGACCTCA-CATCCATGGAAATCTAGTGACATCTGCTGGACACAT\n\nmm9.chr10 3012996\ncavPor2.s 39251\notoGar1.s 178473\nponAbe2.c 158049311\npanTro2.c 157528691\nhg18.chr6 155038619\nechTel1.s 87661\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=128047.000000\ns mm9.chr10 3012828 168 + 129993255 TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATGCACTTAGCACAGCCTGCCCTGAGGGAT----GAACACT--ATTGTTAA-AGAACTATTCCGCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT\ns cavPor2.scaffold_290371 515 166 - 39932 -----GTGGGATGTCTTGACAGCTAAATAGTcttatatttaagcatttatGAAAATAATGAGGTTATCATGGTTCGCTCTAGTAGCTCTGAGACCTTT--ATTGTCAGCAAAGCTGTTTAGC--AGGAGGCAACTTCAGGTTCCGTGGGATTCTAGTGCCATCTGCTGGTCATAT\nq cavPor2.scaffold_290371 -----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--9999999999999999999999--999999999999999999999999999999999999999999999999999\ni cavPor2.scaffold_290371 C 0 C 0\ns otoGar1.scaffold_334.1-359464 180830 161 - 359464 -----GTGGACATTCGTGACAGGCAAATAGTGTTCTATTTAAACATTTGTTGAAATGATAAACTTAGCTCAGCC--CCTT---AGAAGTG-AGAGGCT--ACTGTCAGGGAAGCGGTTTTGCG-GAGCAGCAGCCTCAGGATCTGTGGGATTTTAGCGCCATCTGCTGGTCACAG\nq otoGar1.scaffold_334.1-359464 -----999999999999999999999999999999999999999999999999999999999999999999999--9999---9999999-9999999--99999999999999999999989-996999999999999999999999999999999999999999999999999\ni otoGar1.scaffold_334.1-359464 C 0 C 0\ns ponAbe2.chr6 16160959 161 - 174210431 -----GTGGACTATCCTGACAACCAAATAGCGTTATATTTAAACATTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGTTTAGCT-AAGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAT\ni ponAbe2.chr6 C 0 C 0\ns panTro2.chr6 16379760 161 - 173908612 -----GCGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\nq panTro2.chr6 -----9999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999-------9999999999999999999-999999999999999999999999999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns hg18.chr6 15861212 161 - 170899992 -----GTGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTGTGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\ni hg18.chr6 C 0 C 0\ns echTel1.scaffold_288249 87492 169 + 100002 TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATGAGTTTGTCATAACT-GCCTCCTCCCAAGTG-GGAAGCTGAAGCACCAA-GTACTGACTCAGC--AGTCCCTGACCTCA-CATCCATGGAAATCTAGTGACATCTGCTGGACACAT\nq echTel1.scaffold_288249 99989999998979665899999999999676899897997899979878899999999999999999999999-999999999999999-99999999999999999-9999999999999--99999999999999-999999999999999999999999999999999999\ni echTel1.scaffold_288249 N 0 I 7564\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 98097)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3012996 : 3012996 + 222],\n \"AGATGTCTGCTGTGGAGACCTGGCCAACTTTGCTTTCTTCAAAAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCATTAGGAAGGCGACCTCTAGTGCACAAACCTTGACATTTTCCCTTTTAATGGAATTTAACAGAAGTTCAGGATGTTCTTTGGGTAATTTACAATTAGGGGGCAAAAATCAAAAGTATTTCGAGCATATCAAAACTGTTAGCTATG\",\n )\n self.assertEqual(\n alignment[0],\n \"AGATGTCTGCTGTGGAGA-------CCTGGCCAACTTTG----CTT--TCTTC-----AAAAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCA-----TTAGGAAGGCGACCTCTAGTGCACAAACCTTGAC-ATTTTCCCTTTTAATGGAA-TTTAACAGAAGTTCAGGATGTTCTTTGGGTAATTTACAATT---A----GGGGGCAAAAATCAAAAGTATTTCGAGCATATCAAAACTGTTAGCTATG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_290371\")\n self.assertEqual(len(alignment.sequences[1].seq), 39932)\n self.assertEqual(\n alignment.sequences[1].seq[39074 : 39074 + 177],\n \"AAATGcctctgcttttccttttctagctgtAAATTGTTTAAATGGAATTCTGAACCTGACAGAGTcgaagaaaaaaattgcaaagctTTTCCGCTAGAGGTCACTCTCCCCACTATGTGGTGTGGTCGGCTTTAGCGCGGAAGACTGGAGTTAGCCAGCCCGTGGCTGCAGACGTCA\",\n )\n self.assertEqual(\n alignment[1],\n \"TGACGTCTGCAGCCACGG-------GCTGGCTAACTCCA--GTCTT--CCGCG-----CTAAAGCCGAC--------------------CACACCACATAGTGGGGAGAGTGACCTCTAGCGGAAAagctttgca-atttttttcttc----gAC-TCTGTCAG--GTTCAGAATTCCATTTAAACAATTTacagct---a----gaaaaggaaaagcagaggCATTT--------------------------\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999997999999999995699999999999336991774687\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 170899992)\n self.assertEqual(\n alignment.sequences[2].seq[155038435 : 155038435 + 184],\n \"ATACTCTTACCTCCCCCCACCATTACAAATTGTCTAAATGGCATTCTAAGCCTTTATGAATTCAATTAAAAAGAAAAATGCCAAGGCCTGCTCGCTAGAGGTCGCTCTCCTAACTATGGGGTCCTGTTAGTCTTATAGAGTAAGACAGCAGAGTAGGCCAAGAAAGTGATGGCAGCAGCCATCA\",\n )\n self.assertEqual(\n alignment[2],\n \"TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGC-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 14)\n self.assertEqual(alignment.sequences[3].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 173908612)\n self.assertEqual(\n alignment.sequences[3].seq[157528507 : 157528507 + 184],\n \"ATACTCTTACCTCCCCCCACCATTACAAATTGTCTAAATGGCATTCTAAGCCTTTATGAATTTAATTAAAAAGAAAAATTCCAAGGCCTGCTCGCTAGAGGTCGCTCTCCTAACCATGGGGTCCTGTTAGTCTTATAGAATAAGACAGCAGAGTAGGCCAAGAAAGTGATGGCAGCAGCCATCA\",\n )\n self.assertEqual(\n alignment[3],\n \"TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ATTCT-----ATAAGACTAAC--------------------AGGACCCCATGGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTAAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 14)\n self.assertEqual(alignment.sequences[4].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 174210431)\n self.assertEqual(\n alignment.sequences[4].seq[158049094 : 158049094 + 217],\n \"CATCATTGACAGGTTTGAATACATTCAATATTTATACTCTTACCTCCCCCCACCATTACAAATTGTCTAAATGGCATTCTAAGCCTTTATGAATTCAATTAAAAAGAAAAATTCCAAGGCCTGCTCGCTAGAGGTCGCTCTCCTAACTATGGGGTCCTGTTAGTCTTATAGAGTAAGACGGCCTAGTAGGCCAAGAAAGTGATGGCAGCAGCCATCA\",\n )\n self.assertEqual(\n alignment[4],\n \"TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTAGGCCGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTATAAATATTGAATGTAT-TCAAACCTGTCAATGATG\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 2)\n self.assertEqual(alignment.sequences[5].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[5].seq), 359464)\n self.assertEqual(\n alignment.sequences[5].seq[178247 : 178247 + 226],\n \"TAACAAGGCTGAATGCCAGCAATATTTGCACTCTCAGGTCCCCACACATACACTATGAATTGTCTAACTTGCATTTTGAGCCGTTGTAAAATTCAATTAAAAAGAAAAAAATCCAAGGCTTGTTCACCAGAGGTCGCTCTAGTAACTGCAGGGTCCGATTTTTCTTTTGTTGCAGAATTTAAGACGGTGGAGTTGGCAGGGAAAGCGGTGGTGGCGGCGGCCGTCC\",\n )\n self.assertEqual(\n alignment[5],\n \"GGACGGCCGCCGCCACCACCGCTTTCCCTGCCAACTCCACCGTCTTAAATTCTGCAACAAAAGAAAAAT--------------------CGGACCCTGCAGTTACTAGAGCGACCTCTGGTGAACAAGCCTTGGATTTTTTTCTTTTTAATTGAATTTTACAAC-GGCTCAAAATGCAAGTTAGACAATTCATAGTGTATGTGTGGGGACCTGAGAGTGCAAATATTGCTGGCAT-TCAGCCTTGTTA------\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999989999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999699999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 2931)\n self.assertEqual(alignment.sequences[6].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[6].seq), 498454)\n self.assertEqual(\n alignment.sequences[6].seq[331078 : 331078 + 159],\n \"TAATTATAAGTTGTCTAAATGGCATTTGAACCTTTATAAATTCTGTTTTAAAGAAAAATTCCAAGGTTTGCTCACTAGAGGTCTCCTCTCCCGGAGGATCCAGTTTGTCTTTCGTTGAGAGAGCTGAGTGGTCCAAGAAAGTGACAGCTGTAGCCATCA\",\n )\n self.assertEqual(\n alignment[6],\n \"TGATGGCTACAGCTGTCA---CTTTCTTGGACCACTCAGCTCTCTC--AAC-------GAAAGACAAAC--------------------TGGATCCTCCGG---GAGAGGAGACCTCTAGTGAGCAAACCTTGGA-ATTTTTCTTTAAAACAGAA-TTTATAAA-GGTTCA-AATGCCATTTAGACAACTTATAATT---A-----------------------------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"234233433332122232158211222021213444332433213323732111754365002326236241111233524253535324593652222413766453735782535545832457354545484445655854554657999679999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 4145)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 7)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3012996, 3013014, 3013014, 3013014, 3013028, 3013028,\n 3013028, 3013031, 3013031, 3013034, 3013036, 3013036,\n 3013047, 3013067, 3013074, 3013074, 3013077, 3013108,\n 3013108, 3013120, 3013124, 3013127, 3013127, 3013135,\n 3013136, 3013137, 3013142, 3013143, 3013168, 3013168,\n 3013169, 3013169, 3013184, 3013192, 3013199, 3013200,\n 3013212, 3013218],\n [ 39251, 39233, 39233, 39233, 39219, 39219,\n 39217, 39214, 39214, 39211, 39209, 39209,\n 39198, 39198, 39191, 39186, 39183, 39152,\n 39152, 39140, 39140, 39137, 39137, 39129,\n 39129, 39129, 39124, 39123, 39098, 39098,\n 39097, 39097, 39082, 39074, 39074, 39074,\n 39074, 39074],\n [155038619, 155038601, 155038601, 155038597, 155038583, 155038581,\n 155038579, 155038576, 155038576, 155038573, 155038571, 155038571,\n 155038560, 155038560, 155038553, 155038548, 155038545, 155038514,\n 155038514, 155038502, 155038498, 155038495, 155038495, 155038487,\n 155038487, 155038486, 155038481, 155038480, 155038455, 155038455,\n 155038454, 155038450, 155038435, 155038435, 155038435, 155038435,\n 155038435, 155038435],\n [157528691, 157528673, 157528673, 157528669, 157528655, 157528653,\n 157528651, 157528648, 157528648, 157528645, 157528643, 157528643,\n 157528632, 157528632, 157528625, 157528620, 157528617, 157528586,\n 157528586, 157528574, 157528570, 157528567, 157528567, 157528559,\n 157528559, 157528558, 157528553, 157528552, 157528527, 157528527,\n 157528526, 157528522, 157528507, 157528507, 157528507, 157528507,\n 157528507, 157528507],\n [158049311, 158049293, 158049293, 158049289, 158049275, 158049273,\n 158049271, 158049268, 158049268, 158049265, 158049263, 158049263,\n 158049252, 158049252, 158049245, 158049240, 158049237, 158049206,\n 158049206, 158049194, 158049190, 158049187, 158049187, 158049179,\n 158049179, 158049178, 158049173, 158049172, 158049147, 158049147,\n 158049146, 158049142, 158049127, 158049119, 158049112, 158049112,\n 158049100, 158049094],\n [ 178473, 178455, 178452, 178448, 178434, 178432,\n 178430, 178427, 178425, 178422, 178420, 178415,\n 178404, 178404, 178397, 178392, 178389, 178358,\n 178357, 178345, 178341, 178338, 178337, 178329,\n 178329, 178328, 178323, 178322, 178297, 178294,\n 178293, 178289, 178274, 178266, 178259, 178259,\n 178247, 178247],\n [ 331237, 331219, 331219, 331215, 331201, 331199,\n 331197, 331194, 331194, 331191, 331191, 331191,\n 331180, 331180, 331173, 331168, 331168, 331137,\n 331137, 331125, 331121, 331118, 331118, 331110,\n 331110, 331109, 331104, 331104, 331079, 331079,\n 331078, 331078, 331078, 331078, 331078, 331078,\n 331078, 331078],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3012996 AGATGTCTGCTGTGGAGA-------CCTGGCCAACTTTG----CTT--TCTTC-----AA\ncavPor2.s 39251 TGACGTCTGCAGCCACGG-------GCTGGCTAACTCCA--GTCTT--CCGCG-----CT\nhg18.chr6 155038619 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ACTCT-----AT\npanTro2.c 157528691 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ATTCT-----AT\nponAbe2.c 158049311 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTAGGCCGTCTT--ACTCT-----AT\notoGar1.s 178473 GGACGGCCGCCGCCACCACCGCTTTCCCTGCCAACTCCACCGTCTTAAATTCTGCAACAA\ntupBel1.s 331237 TGATGGCTACAGCTGTCA---CTTTCTTGGACCACTCAGCTCTCTC--AAC-------GA\n\nmm9.chr10 3013038 AAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCA-----TTAGGAAGGCGACCTCTAG\ncavPor2.s 39207 AAAGCCGAC--------------------CACACCACATAGTGGGGAGAGTGACCTCTAG\nhg18.chr6 155038569 AAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAG\npanTro2.c 157528641 AAGACTAAC--------------------AGGACCCCATGGTTAGGAGAGCGACCTCTAG\nponAbe2.c 158049261 AAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAG\notoGar1.s 178413 AAGAAAAAT--------------------CGGACCCTGCAGTTACTAGAGCGACCTCTGG\ntupBel1.s 331189 AAGACAAAC--------------------TGGATCCTCCGG---GAGAGGAGACCTCTAG\n\nmm9.chr10 3013093 TGCACAAACCTTGAC-ATTTTCCCTTTTAATGGAA-TTTAACAGAAGTTCAGGATGTTCT\ncavPor2.s 39167 CGGAAAagctttgca-atttttttcttc----gAC-TCTGTCAG--GTTCAGAATTCCAT\nhg18.chr6 155038529 CGAGCAGGCCTTGGC-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCAT\npanTro2.c 157528601 CGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTAAA-TTCATAAA-GGCTTAGAATGCCAT\nponAbe2.c 158049221 CGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCAT\notoGar1.s 178373 TGAACAAGCCTTGGATTTTTTTCTTTTTAATTGAATTTTACAAC-GGCTCAAAATGCAAG\ntupBel1.s 331152 TGAGCAAACCTTGGA-ATTTTTCTTTAAAACAGAA-TTTATAAA-GGTTCA-AATGCCAT\n\nmm9.chr10 3013151 TTGGGTAATTTACAATT---A----GGGGGCAAAAATCAAAAGTATTTCGAGCATATCAA\ncavPor2.s 39115 TTAAACAATTTacagct---a----gaaaaggaaaagcagaggCATTT------------\nhg18.chr6 155038472 TTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT--------------------\npanTro2.c 157528544 TTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT--------------------\nponAbe2.c 158049164 TTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTATAAATATTGAATGTAT-TCAA\notoGar1.s 178314 TTAGACAATTCATAGTGTATGTGTGGGGACCTGAGAGTGCAAATATTGCTGGCAT-TCAG\ntupBel1.s 331096 TTAGACAACTTATAATT---A---------------------------------------\n\nmm9.chr10 3013204 AACTGTTAGCTATG 3013218\ncavPor2.s 39074 -------------- 39074\nhg18.chr6 155038435 -------------- 155038435\npanTro2.c 157528507 -------------- 157528507\nponAbe2.c 158049108 ACCTGTCAATGATG 158049094\notoGar1.s 178255 CCTTGTTA------ 178247\ntupBel1.s 331078 -------------- 331078\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=98097.000000\ns mm9.chr10 3012996 222 + 129993255 AGATGTCTGCTGTGGAGA-------CCTGGCCAACTTTG----CTT--TCTTC-----AAAAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCA-----TTAGGAAGGCGACCTCTAGTGCACAAACCTTGAC-ATTTTCCCTTTTAATGGAA-TTTAACAGAAGTTCAGGATGTTCTTTGGGTAATTTACAATT---A----GGGGGCAAAAATCAAAAGTATTTCGAGCATATCAAAACTGTTAGCTATG\ns cavPor2.scaffold_290371 681 177 - 39932 TGACGTCTGCAGCCACGG-------GCTGGCTAACTCCA--GTCTT--CCGCG-----CTAAAGCCGAC--------------------CACACCACATAGTGGGGAGAGTGACCTCTAGCGGAAAagctttgca-atttttttcttc----gAC-TCTGTCAG--GTTCAGAATTCCATTTAAACAATTTacagct---a----gaaaaggaaaagcagaggCATTT--------------------------\nq cavPor2.scaffold_290371 999999999999999999-------99999999999999--99999--99999-----99999999999--------------------9999999999999999999999999999999999999999999999-999999999999----999-99999999--9999999999999999997999999999995---6----99999999999336991774687--------------------------\ni cavPor2.scaffold_290371 C 0 N 0\ns hg18.chr6 15861373 184 - 170899992 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGC-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------\ni hg18.chr6 C 0 I 14\ns panTro2.chr6 16379921 184 - 173908612 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ATTCT-----ATAAGACTAAC--------------------AGGACCCCATGGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTAAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------\nq panTro2.chr6 999999999999999999---9999999999999999999999999--99999-----99999999999--------------------9999999999999999999999999999999999999999999999-9999999999999999999-99999999-99999999999999999999999999999999---99999999999999999999----------------------------------\ni panTro2.chr6 C 0 I 14\ns ponAbe2.chr6 16161120 217 - 174210431 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTAGGCCGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTATAAATATTGAATGTAT-TCAAACCTGTCAATGATG\ni ponAbe2.chr6 C 0 I 2\ns otoGar1.scaffold_334.1-359464 180991 226 - 359464 GGACGGCCGCCGCCACCACCGCTTTCCCTGCCAACTCCACCGTCTTAAATTCTGCAACAAAAGAAAAAT--------------------CGGACCCTGCAGTTACTAGAGCGACCTCTGGTGAACAAGCCTTGGATTTTTTTCTTTTTAATTGAATTTTACAAC-GGCTCAAAATGCAAGTTAGACAATTCATAGTGTATGTGTGGGGACCTGAGAGTGCAAATATTGCTGGCAT-TCAGCCTTGTTA------\nq otoGar1.scaffold_334.1-359464 999998999999999999999999999999999999999999999999999999999999999999999--------------------999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999699999999999999999999999999-999999999999------\ni otoGar1.scaffold_334.1-359464 C 0 I 2931\ns tupBel1.scaffold_114895.1-498454 167217 159 - 498454 TGATGGCTACAGCTGTCA---CTTTCTTGGACCACTCAGCTCTCTC--AAC-------GAAAGACAAAC--------------------TGGATCCTCCGG---GAGAGGAGACCTCTAGTGAGCAAACCTTGGA-ATTTTTCTTTAAAACAGAA-TTTATAAA-GGTTCA-AATGCCATTTAGACAACTTATAATT---A-----------------------------------------------------\nq tupBel1.scaffold_114895.1-498454 234233433332122232---1582112220212134443324332--133-------23732111754--------------------365002326236---2411112335242535353245936522224-1376645373578253554-58324573-545454-8444565585455465799967999---9-----------------------------------------------------\ni tupBel1.scaffold_114895.1-498454 N 0 I 4145\ne echTel1.scaffold_288249 87661 7564 + 100002 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3013218 : 3013218 + 219],\n \"agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggatctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacacagaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAAAAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT\",\n )\n self.assertEqual(\n alignment[0],\n \"agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggatctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacacagaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAAAAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (178247, 175316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155038435, 155038421))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157528507, 157528493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158049094, 158049092))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3013218, 3013437]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3013218 agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggat\n\nmm9.chr10 3013278 ctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacaca\n\nmm9.chr10 3013338 gaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAA\n\nmm9.chr10 3013398 AAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT 3013437\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3013218 219 + 129993255 agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggatctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacacagaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAAAAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I\ne hg18.chr6 15861557 14 - 170899992 I\ne panTro2.chr6 16380105 14 - 173908612 I\ne ponAbe2.chr6 16161337 2 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['a', 'g', 'c', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't',\n 'g', 'g', 'c', 'a', 'c', 'a', 'c', 'a', 'c', 'c', 't', 't', 't',\n 'a', 'c', 't', 'c', 'c', 'c', 'a', 'g', 'c', 'a', 't', 't', 't',\n 'g', 'g', 'g', 'g', 'g', 'g', 'c', 'a', 'g', 'a', 'g', 'g', 'c',\n 'a', 'g', 'g', 't', 'g', 'g', 'a', 't', 'c', 't', 'g', 't', 'g',\n 'a', 'g', 't', 't', 't', 'g', 'a', 'g', 'g', 'c', 'c', 'a', 'g',\n 'c', 'c', 't', 'g', 'g', 't', 'c', 't', 'a', 'c', 'a', 'g', 'a',\n 'g', 'g', 'g', 'a', 'g', 't', 'c', 't', 'c', 'a', 'g', 'g', 'a',\n 'c', 'a', 'g', 'c', 'c', 'a', 'g', 'a', 'g', 'c', 't', 'a', 'c',\n 'a', 'c', 'a', 'g', 'a', 'a', 'a', 't', 'a', 'a', 'c', 'c', 't',\n 'g', 'c', 'c', 't', 'a', 'g', 'a', 'a', 'a', 'a', 'a', 'c', 'a',\n 'a', 'a', 'a', 'c', 'a', 'a', 'a', 'a', 'c', 'a', 'a', 'a', 'a',\n 'c', 'a', 't', 'c', 'a', 'a', 'a', 'a', 'c', 't', 'c', 'a', 'a',\n 'a', 'a', 'c', 'a', 'a', 'a', 'T', 'A', 'A', 'A', 'A', 'A', 'A',\n 'A', 'A', 'T', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'C', 'A',\n 'A', 'C', 'C', 'T', 'A', 'A', 'A', 'C', 'C', 'A', 'A', 'A', 'T',\n 'A', 'A', 'C', 'A', 'A', 'A', 'A', 'C', 'A', 'C', 'T']],\n dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 40604)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3013437 : 3013437 + 166],\n \"TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAAGAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCAGACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA\",\n )\n self.assertEqual(\n alignment[0],\n \"TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAAGAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCAGACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 173908612)\n self.assertEqual(\n alignment.sequences[1].seq[157528363 : 157528363 + 130],\n \"TATCAAACAGCCCATGAATGCAAAACGATACACCCATAAAATAGGATGTAATCGCCAAAATCTAATTCTATTGCATCTAGAAGATCTTTATCCACAGTGAAAAGAGTTGAACATCATTGACAGGTTTGAA\",\n )\n self.assertEqual(\n alignment[1],\n \"TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999099999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 14)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 9106)\n self.assertEqual(alignment.sequences[2].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 170899992)\n self.assertEqual(\n alignment.sequences[2].seq[155038291 : 155038291 + 130],\n \"TATCAAACAGCCCATGAATGCAAAACGATACACCCATAAAATAGGATGTAATCGCCAAAATCTAATTCTATTGCATCTAGAAGATCTTTATCCACAGTGAAAAGAGTTGAACATCATTGACAGGTTTGAA\",\n )\n self.assertEqual(\n alignment[2],\n \"TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 14)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 9085)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158048983 : 158048983 + 109],\n \"TATCAAACAGCCCATGAATGCAAAACGATACACCCATAAAATAGGATGTAATCGCCAAAATCTAATTCTATTGCATCTAGAAGATCTTTATCCACAGTGAAAAGAGTTG\",\n )\n self.assertEqual(\n alignment[3],\n \"---------------------CAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 2)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 8044)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (178247, 175316))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 4)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 3)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3013437, 3013458, 3013509, 3013545, 3013603],\n [157528493, 157528472, 157528421, 157528421, 157528363],\n [155038421, 155038400, 155038349, 155038349, 155038291],\n [158049092, 158049092, 158049041, 158049041, 158048983],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3013437 TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAA\npanTro2.c 157528493 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAA\nhg18.chr6 155038421 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAA\nponAbe2.c 158049092 ---------------------CAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAA\n\nmm9.chr10 3013497 GAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCA\npanTro2.c 157528433 TAGAATTAGATT------------------------------------TTGGCGATTACA\nhg18.chr6 155038361 TAGAATTAGATT------------------------------------TTGGCGATTACA\nponAbe2.c 158049053 TAGAATTAGATT------------------------------------TTGGCGATTACA\n\nmm9.chr10 3013557 GACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA 3013603\npanTro2.c 157528409 TCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA 157528363\nhg18.chr6 155038337 TCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA 155038291\nponAbe2.c 158049029 TCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA 158048983\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=40604.000000\ns mm9.chr10 3013437 166 + 129993255 TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAAGAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCAGACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA\ns panTro2.chr6 16380119 130 - 173908612 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\nq panTro2.chr6 999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------9999999999999999999999999999999999999099999999999999999999\ni panTro2.chr6 I 14 I 9106\ns hg18.chr6 15861571 130 - 170899992 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\ni hg18.chr6 I 14 I 9085\ns ponAbe2.chr6 16161339 109 - 174210431 ---------------------CAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\ni ponAbe2.chr6 I 2 I 8044\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'C', 'C', 'A', 'A', 'A', 'A', 'T', 'G', 'G', 'T', 'T', 'A',\n 'G', 'C', 'T', 'A', 'T', 'G', 'C', 'C', 'C', 'A', 'A', 'C', 'T',\n 'C', 'C', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'C', 'C', 'A', 'A',\n 'G', 'A', 'A', 'A', 'A', 'T', 'A', 'T', 'C', 'C', 'T', 'A', 'A',\n 'C', 'C', 'A', 'T', 'G', 'T', 'A', 'A', 'G', 'A', 'G', 'A', 'G',\n 'C', 'T', 'A', 'G', 'C', 'C', 'T', 'G', 'T', 'T', 'G', 'G', 'T',\n 'G', 'G', 'C', 'A', 'G', 'C', 'C', 'A', 'A', 'G', 'C', 'C', 'T',\n 'G', 'A', 'T', 'G', 'G', 'T', 'G', 'G', 'C', 'A', 'G', 'A', 'C',\n 'T', 'A', 'G', 'A', 'T', 'T', 'G', 'A', 'T', 'G', 'G', 'T', 'G',\n 'C', 'C', 'A', 'G', 'A', 'C', 'T', 'A', 'C', 'T', 'T', 'T', 'A',\n 'T', 'G', 'G', 'C', 'T', 'G', 'T', 'A', 'T', 'C', 'A', 'T', 'T',\n 'T', 'T', 'C', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'T', 'G',\n 'T', 'T', 'G', 'T', 'G', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'C', 'A', 'A', 'A', 'C', 'C', 'T', 'G', 'T', 'C', 'A',\n 'A', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'C', 'A', 'A', 'C', 'T',\n 'C', 'T', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'G', 'T', 'G', 'G',\n 'A', 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'C', 'T', 'T', 'C', 'T',\n 'A', 'G', 'A', 'T', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'A', 'A',\n 'T', 'T', 'A', 'G', 'A', 'T', 'T', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'T', 'T', 'G', 'G', 'C', 'G', 'A', 'T', 'T',\n 'A', 'C', 'A', 'T', 'C', 'C', 'T', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'C', 'G', 'T', 'T',\n 'T', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'G', 'G',\n 'C', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'T', 'A'],\n ['T', 'T', 'C', 'A', 'A', 'A', 'C', 'C', 'T', 'G', 'T', 'C', 'A',\n 'A', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'C', 'A', 'A', 'C', 'T',\n 'C', 'T', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'G', 'T', 'G', 'G',\n 'A', 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'C', 'T', 'T', 'C', 'T',\n 'A', 'G', 'A', 'T', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'A', 'A',\n 'T', 'T', 'A', 'G', 'A', 'T', 'T', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'T', 'T', 'G', 'G', 'C', 'G', 'A', 'T', 'T',\n 'A', 'C', 'A', 'T', 'C', 'C', 'T', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'C', 'G', 'T', 'T',\n 'T', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'G', 'G',\n 'C', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'A', 'C', 'T',\n 'C', 'T', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'G', 'T', 'G', 'G',\n 'A', 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'C', 'T', 'T', 'C', 'T',\n 'A', 'G', 'A', 'T', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'A', 'A',\n 'T', 'T', 'A', 'G', 'A', 'T', 'T', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'T', 'T', 'G', 'G', 'C', 'G', 'A', 'T', 'T',\n 'A', 'C', 'A', 'T', 'C', 'C', 'T', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'C', 'G', 'T', 'T',\n 'T', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'G', 'G',\n 'C', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'T', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3013603 : 3013603 + 1041],\n \"CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgctgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacccgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagttcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcatacctttaatatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcgttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggattccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactagagtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagtcattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaaccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgaggttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggtcctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGTGTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCTTGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAGTATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaaaaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGATTTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCTTGTTTGTTTTGGTCAATGCAG\",\n )\n self.assertEqual(\n alignment[0],\n \"CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgctgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacccgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagttcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcatacctttaatatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcgttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggattccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactagagtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagtcattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaaccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgaggttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggtcctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGTGTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCTTGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAGTATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaaaaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGATTTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCTTGTTTGTTTTGGTCAATGCAG\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (178247, 175316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155038291, 155029206))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157528363, 157519257))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158048983, 158040939))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3013603, 3014644]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3013603 CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgc\n\nmm9.chr10 3013663 tgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacc\n\nmm9.chr10 3013723 cgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagt\n\nmm9.chr10 3013783 tcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcataccttta\n\nmm9.chr10 3013843 atatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcg\n\nmm9.chr10 3013903 ttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggatt\n\nmm9.chr10 3013963 ccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactaga\n\nmm9.chr10 3014023 gtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagt\n\nmm9.chr10 3014083 cattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaa\n\nmm9.chr10 3014143 ccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgagg\n\nmm9.chr10 3014203 ttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggt\n\nmm9.chr10 3014263 cctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGT\n\nmm9.chr10 3014323 GTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCT\n\nmm9.chr10 3014383 TGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAG\n\nmm9.chr10 3014443 TATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaa\n\nmm9.chr10 3014503 aaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGAT\n\nmm9.chr10 3014563 TTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCT\n\nmm9.chr10 3014623 TGTTTGTTTTGGTCAATGCAG 3014644\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3013603 1041 + 129993255 CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgctgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacccgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagttcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcatacctttaatatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcgttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggattccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactagagtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagtcattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaaccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgaggttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggtcctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGTGTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCTTGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAGTATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaaaaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGATTTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCTTGTTTGTTTTGGTCAATGCAG\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I\ne hg18.chr6 15861701 9085 - 170899992 I\ne panTro2.chr6 16380249 9106 - 173908612 I\ne ponAbe2.chr6 16161448 8044 - 174210431 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 19159)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014644 : 3014644 + 45],\n \"CCTGTACCCTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG\",\n )\n self.assertEqual(\n alignment[0], \"CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG\"\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155029160 : 155029160 + 46],\n \"AAAAGTTTAGGATTAAAACAAAATTCTCATAAAAGAAAGGTATAGG\",\n )\n self.assertEqual(\n alignment[1], \"CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT\"\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 9085)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157519211 : 157519211 + 46],\n \"AAAAGTTTAGGATTAAAACAAAATTCTCATAAAAGAAAGGTATAGG\",\n )\n self.assertEqual(\n alignment[2], \"CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT\"\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 9106)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[3].seq), 133105)\n self.assertEqual(\n alignment.sequences[3].seq[6182 : 6182 + 46],\n \"CCTATACCTTTCTTTCATGAGAATTTTGTTTGAATCCTAAACTTTT\",\n )\n self.assertEqual(\n alignment[3], \"CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[4].seq), 10574)\n self.assertEqual(\n alignment.sequences[4].seq[9373 : 9373 + 34],\n \"GGAAGTTTTGAATTAAAGCATAATTCTAACCAAA\",\n )\n self.assertEqual(\n alignment[4], \"------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC\"\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"9999969989999999999999998699989997\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (178247, 175316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158048983, 158040939))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 5)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 4)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3014644, 3014652, 3014652, 3014653, 3014664, 3014665,\n 3014684, 3014685, 3014689],\n [155029206, 155029198, 155029195, 155029194, 155029183, 155029183,\n 155029164, 155029164, 155029160],\n [157519257, 157519249, 157519246, 157519245, 157519234, 157519234,\n 157519215, 157519215, 157519211],\n [ 6182, 6190, 6193, 6194, 6205, 6205,\n 6224, 6224, 6228],\n [ 9407, 9407, 9407, 9407, 9396, 9396,\n 9377, 9377, 9373],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014644 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG 3014689\nhg18.chr6 155029206 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT 155029160\npanTro2.c 157519257 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT 157519211\ncalJac1.C 6182 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT 6228\nloxAfr1.s 9407 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC 9373\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=19159.000000\ns mm9.chr10 3014644 45 + 129993255 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG\ns hg18.chr6 15870786 46 - 170899992 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT\ni hg18.chr6 I 9085 C 0\ns panTro2.chr6 16389355 46 - 173908612 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT\nq panTro2.chr6 99999999999999999999999-9999999999999999999-9999\ni panTro2.chr6 I 9106 C 0\ns calJac1.Contig6394 6182 46 + 133105 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT\ni calJac1.Contig6394 N 0 C 0\ns loxAfr1.scaffold_75566 1167 34 - 10574 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC\nq loxAfr1.scaffold_75566 ------------99999699899-9999999999999869998-9997\ni loxAfr1.scaffold_75566 N 0 C 0\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I\ne ponAbe2.chr6 16161448 8044 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'C', 'T', 'G', 'T', 'A', 'C', 'C', '-', '-', '-', 'C', 'T',\n 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'G', 'A', 'A', 'T', 'T', 'T',\n 'T', 'T', 'G', 'T', 'T', 'T', 'C', 'A', 'G', 'T', 'G', 'T', 'T',\n 'A', 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G'],\n ['C', 'C', 'T', 'A', 'T', 'A', 'C', 'C', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', 'T', 'A', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'T', 'T',\n 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'C', 'T',\n 'A', 'A', 'A', 'C', '-', 'T', 'T', 'T', 'T'],\n ['C', 'C', 'T', 'A', 'T', 'A', 'C', 'C', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', 'T', 'A', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'T', 'T',\n 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'C', 'T',\n 'A', 'A', 'A', 'C', '-', 'T', 'T', 'T', 'T'],\n ['C', 'C', 'T', 'A', 'T', 'A', 'C', 'C', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', 'C', 'A', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'T', 'T',\n 'T', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'A', 'T', 'C', 'C', 'T',\n 'A', 'A', 'A', 'C', '-', 'T', 'T', 'T', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T',\n 'T', 'T', 'G', 'G', 'T', 'T', 'A', 'G', 'A', 'A', '-', 'T', 'T',\n 'A', 'T', 'G', 'C', 'T', 'T', 'T', 'A', 'A', 'T', 'T', 'C', 'A',\n 'A', 'A', 'A', 'C', '-', 'T', 'T', 'C', 'C']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 40840)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014689 : 3014689 + 53],\n \"GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCTTTGGAAAGAGTTG\",\n )\n self.assertEqual(\n alignment[0], \"GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG\"\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155029107 : 155029107 + 53],\n \"CCACTATTTCCCAAAAGATTAGATATTTCACAGATTAAATGGTTTATGATCCC\",\n )\n self.assertEqual(\n alignment[1], \"GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\"\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 401)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157519158 : 157519158 + 53],\n \"CCACTATTTCCCAAAAGATTAGATATTTCACAGATTAAATGGTTTATGATCCC\",\n )\n self.assertEqual(\n alignment[2], \"GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\"\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 400)\n self.assertEqual(alignment.sequences[3].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[3].seq), 133105)\n self.assertEqual(\n alignment.sequences[3].seq[6228 : 6228 + 53],\n \"GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTTTGGGAAACAGTGG\",\n )\n self.assertEqual(\n alignment[3], \"GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 2)\n self.assertEqual(alignment.sequences[4].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[4].seq), 359464)\n self.assertEqual(\n alignment.sequences[4].seq[175264 : 175264 + 52],\n \"CAGCTATTGCCCAAGTGATTTGATATTTCATAGATTAAAAGTTTATGCTTCC\",\n )\n self.assertEqual(\n alignment[4], \"GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG\"\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"7455455669566996656997698955556899975999984787795599\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 2931)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 2)\n self.assertEqual(alignment.sequences[5].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[5].seq), 10574)\n self.assertEqual(\n alignment.sequences[5].seq[9319 : 9319 + 54],\n \"CAGCTTTTTCCCCTGAAGATTTGGCATTTCGCAGACTAAATGGTTTATACTCCC\",\n )\n self.assertEqual(\n alignment[5], \"GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG\"\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"899989799999979999999999999999797999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 2)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158048983, 158040939))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 6)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 3)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3014689, 3014702, 3014703, 3014729, 3014729, 3014742],\n [155029160, 155029147, 155029146, 155029120, 155029120, 155029107],\n [157519211, 157519198, 157519197, 157519171, 157519171, 157519158],\n [ 6228, 6241, 6242, 6268, 6268, 6281],\n [ 175316, 175303, 175303, 175277, 175277, 175264],\n [ 9373, 9360, 9359, 9333, 9332, 9319],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014689 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG\nhg18.chr6 155029160 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\npanTro2.c 157519211 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\ncalJac1.C 6228 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG\notoGar1.s 175316 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG\nloxAfr1.s 9373 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG\n\nmm9.chr10 3014742\nhg18.chr6 155029107\npanTro2.c 157519158\ncalJac1.C 6281\notoGar1.s 175264\nloxAfr1.s 9319\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=40840.000000\ns mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG\ns hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\ni hg18.chr6 C 0 I 401\ns panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\nq panTro2.chr6 9999999999999999999999999999999999999999-9999999999999\ni panTro2.chr6 C 0 I 400\ns calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG\ni calJac1.Contig6394 C 0 I 2\ns otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG\nq otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599\ni otoGar1.scaffold_334.1-359464 I 2931 I 2\ns loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG\nq loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999\ni loxAfr1.scaffold_75566 C 0 I 2\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne ponAbe2.chr6 16161448 8044 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['G', 'G', 'G', 'A', 'G', 'C', 'A', 'T', 'A', 'A', 'A', 'A', 'C',\n 'T', 'C', 'T', 'A', 'A', 'A', 'T', 'C', 'T', 'G', 'C', 'T', 'A',\n 'A', 'A', 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'T', 'C', 'C', 'C',\n 'T', '-', 'T', 'T', 'G', 'G', 'A', 'A', 'A', 'G', 'A', 'G', 'T',\n 'T', 'G'],\n ['G', 'G', 'G', 'A', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'C', 'C',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'G', 'T', 'G', 'A',\n 'A', 'A', 'T', 'A', 'T', 'C', 'T', 'A', 'A', 'T', 'C', 'T', 'T',\n 'T', '-', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'T', 'A', 'G', 'T',\n 'G', 'G'],\n ['G', 'G', 'G', 'A', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'C', 'C',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'G', 'T', 'G', 'A',\n 'A', 'A', 'T', 'A', 'T', 'C', 'T', 'A', 'A', 'T', 'C', 'T', 'T',\n 'T', '-', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'T', 'A', 'G', 'T',\n 'G', 'G'],\n ['G', 'G', 'G', 'A', 'T', 'C', 'A', 'T', 'A', 'A', 'G', 'C', 'C',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'G', 'T', 'G', 'A',\n 'A', 'A', 'T', 'G', 'T', 'G', 'A', 'A', 'A', 'T', 'C', 'T', 'T',\n 'T', '-', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'C', 'A', 'G', 'T',\n 'G', 'G'],\n ['G', 'G', 'A', 'A', 'G', 'C', 'A', 'T', 'A', 'A', 'A', 'C', 'T',\n '-', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'A', 'T', 'G', 'A',\n 'A', 'A', 'T', 'A', 'T', 'C', 'A', 'A', 'A', 'T', 'C', 'A', 'C',\n 'T', '-', 'T', 'G', 'G', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'C',\n 'T', 'G'],\n ['G', 'G', 'G', 'A', 'G', 'T', 'A', 'T', 'A', 'A', 'A', 'C', 'C',\n 'A', 'T', 'T', 'T', 'A', 'G', 'T', 'C', 'T', 'G', 'C', 'G', 'A',\n 'A', 'A', 'T', 'G', 'C', 'C', 'A', 'A', 'A', 'T', 'C', 'T', 'T',\n 'C', 'A', 'G', 'G', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'G', 'C',\n 'T', 'G']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 411)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014742 : 3014742 + 36],\n \"AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA\",\n )\n self.assertEqual(alignment[0], \"AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA\")\n self.assertEqual(alignment.sequences[1].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[1].seq), 133105)\n self.assertEqual(\n alignment.sequences[1].seq[6283 : 6283 + 28], \"AAATGTATGATCTCCCCATCCTGCCCTG\"\n )\n self.assertEqual(alignment[1], \"AAATGTA-----TGATCTCCCCATCCTGCCCTG---\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 2)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 54)\n self.assertEqual(alignment.sequences[2].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[2].seq), 359464)\n self.assertEqual(\n alignment.sequences[2].seq[175231 : 175231 + 31],\n \"TGCACGGAGGGGGTGAGGGCATCAGAAATCT\",\n )\n self.assertEqual(alignment[2], \"AGATTTC-----TGATGCCCTCACCCCCTCCGTGCA\")\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9996999965974999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 2)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 24)\n self.assertEqual(alignment.sequences[3].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[3].seq), 10574)\n self.assertEqual(\n alignment.sequences[3].seq[9290 : 9290 + 27], \"TGTGGGGGTGGGGGGTGGCATAAGCCT\"\n )\n self.assertEqual(alignment[3], \"AGGCTTA-----TG----CCACCCCCCACCCCCACA\")\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"], \"999999999997999999999999999\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 2)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 25)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155029107, 155028706))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157519158, 157518758))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158048983, 158040939))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 4)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 5)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[3014742, 3014749, 3014754, 3014756, 3014760, 3014775, 3014778],\n [ 6283, 6290, 6290, 6292, 6296, 6311, 6311],\n [ 175262, 175255, 175255, 175253, 175249, 175234, 175231],\n [ 9317, 9310, 9310, 9308, 9308, 9293, 9290],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014742 AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA 3014778\ncalJac1.C 6283 AAATGTA-----TGATCTCCCCATCCTGCCCTG--- 6311\notoGar1.s 175262 AGATTTC-----TGATGCCCTCACCCCCTCCGTGCA 175231\nloxAfr1.s 9317 AGGCTTA-----TG----CCACCCCCCACCCCCACA 9290\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=411.000000\ns mm9.chr10 3014742 36 + 129993255 AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA\ns calJac1.Contig6394 6283 28 + 133105 AAATGTA-----TGATCTCCCCATCCTGCCCTG---\ni calJac1.Contig6394 I 2 I 54\ns otoGar1.scaffold_334.1-359464 184202 31 - 359464 AGATTTC-----TGATGCCCTCACCCCCTCCGTGCA\nq otoGar1.scaffold_334.1-359464 9996999-----965974999999999999999999\ni otoGar1.scaffold_334.1-359464 I 2 I 24\ns loxAfr1.scaffold_75566 1257 27 - 10574 AGGCTTA-----TG----CCACCCCCCACCCCCACA\nq loxAfr1.scaffold_75566 9999999-----99----997999999999999999\ni loxAfr1.scaffold_75566 I 2 I 25\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne hg18.chr6 15870885 401 - 170899992 I\ne panTro2.chr6 16389454 400 - 173908612 I\ne ponAbe2.chr6 16161448 8044 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'A', 'G', 'T', 'T', 'C', 'C', 'C', 'T', 'C', 'C', 'A', 'T',\n 'A', 'A', 'T', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'T', 'C', 'C',\n 'C', 'A', 'C', 'C', 'C', 'C', 'C', 'A', 'C', 'A'],\n ['A', 'A', 'A', 'T', 'G', 'T', 'A', '-', '-', '-', '-', '-', 'T',\n 'G', 'A', 'T', 'C', 'T', 'C', 'C', 'C', 'C', 'A', 'T', 'C', 'C',\n 'T', 'G', 'C', 'C', 'C', 'T', 'G', '-', '-', '-'],\n ['A', 'G', 'A', 'T', 'T', 'T', 'C', '-', '-', '-', '-', '-', 'T',\n 'G', 'A', 'T', 'G', 'C', 'C', 'C', 'T', 'C', 'A', 'C', 'C', 'C',\n 'C', 'C', 'T', 'C', 'C', 'G', 'T', 'G', 'C', 'A'],\n ['A', 'G', 'G', 'C', 'T', 'T', 'A', '-', '-', '-', '-', '-', 'T',\n 'G', '-', '-', '-', '-', 'C', 'C', 'A', 'C', 'C', 'C', 'C', 'C',\n 'C', 'A', 'C', 'C', 'C', 'C', 'C', 'A', 'C', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014778 : 3014778 + 17], \"TCCCATGTCCACCCTGA\"\n )\n self.assertEqual(alignment[0], \"TCCCATGTCCACCCTGA\")\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(record.seq), 10574)\n self.assertEqual(segment, (9290, 9265))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6311, 6365))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (175231, 175207))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155029107, 155028706))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157519158, 157518758))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158048983, 158040939))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 8)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3014778, 3014795]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014778 TCCCATGTCCACCCTGA 3014795\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3014778 17 + 129993255 TCCCATGTCCACCCTGA\ne loxAfr1.scaffold_75566 1284 25 - 10574 I\ne calJac1.Contig6394 6311 54 + 133105 I\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 184233 24 - 359464 I\ne hg18.chr6 15870885 401 - 170899992 I\ne panTro2.chr6 16389454 400 - 173908612 I\ne ponAbe2.chr6 16161448 8044 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'C', 'C', 'C', 'A', 'T', 'G', 'T', 'C', 'C', 'A', 'C', 'C',\n 'C', 'T', 'G', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, -12243)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014795 : 3014795 + 47],\n \"GTTTCAGGGGCAGCTCGCTGTTAGCAGCTAAGGCATGGTGTCTCTCA\",\n )\n self.assertEqual(\n alignment[0],\n \"GTTTCAGGGGCAGCTCGCTG----------------TTAGCAG-CTAAGGCATGGTGTCTCTCA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[1].seq), 359464)\n self.assertEqual(\n alignment.sequences[1].seq[175147 : 175147 + 60],\n \"AGAAATACACCCCACCTAAACCATCTAAACCAAATATCCATGACTGCAACTTGTTCCCGA\",\n )\n self.assertEqual(\n alignment[1],\n \"---TCGGGAACAAGTTGCAGTCATGGATAT-TTGGTTTAGATGGTTTAGGTGGGGTGTATTTCT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"899999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 24)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[2].seq), 133105)\n self.assertEqual(\n alignment.sequences[2].seq[6365 : 6365 + 39],\n \"GCCATGAATATTTTAGACATGCAGGTGTGGCGTGTTTCT\",\n )\n self.assertEqual(\n alignment[2],\n \"-------------------GCCATGAATAT-----TTTAGAC-ATGCAGGTGTGGCGTGTTTCT\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 54)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155028686 : 155028686 + 20],\n \"AGAAACATGCCACACCTGCt\",\n )\n self.assertEqual(\n alignment[3],\n \"--------------------------------------------aGCAGGTGTGGCATGTTTCT\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 401)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 173908612)\n self.assertEqual(\n alignment.sequences[4].seq[157518738 : 157518738 + 20],\n \"AGAAACATGCCACACCTGCt\",\n )\n self.assertEqual(\n alignment[4],\n \"--------------------------------------------aGCAGGTGTGGCATGTTTCT\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"], \"99999999999999999999\"\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 400)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 174210431)\n self.assertEqual(\n alignment.sequences[5].seq[158040919 : 158040919 + 20],\n \"AGAAACATGCCACACCTGCt\",\n )\n self.assertEqual(\n alignment[5],\n \"--------------------------------------------aGCAGGTGTGGCATGTTTCT\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 8044)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[6].seq), 498454)\n self.assertEqual(\n alignment.sequences[6].seq[326906 : 326906 + 27],\n \"AGCGATGCGCCACACCCACATTTCTAA\",\n )\n self.assertEqual(\n alignment[6],\n \"------------------------------------TTAGAAA-TGTGGGTGTGGCGCATCGCT\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"], \"999999999999989998899999699\"\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 4145)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[7].seq), 10026)\n self.assertEqual(\n alignment.sequences[7].seq[2184 : 2184 + 26], \"GAACCATGCCACACCTAAATTTCTAA\"\n )\n self.assertEqual(\n alignment[7],\n \"------------------------------------TTAGAAA-TTTAGGTGTGGCATGGTTC-\",\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"], \"42558311324566557465575854\"\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[8].seq), 10574)\n self.assertEqual(\n alignment.sequences[8].seq[9203 : 9203 + 62],\n \"aGAGATACAGCAAACCTCAATTTCTGAAACAACGTATTGATGTCCTAAACTTGCTCTCAAAC\",\n )\n self.assertEqual(\n alignment[8],\n \"GTT-TGAGAGCAAGTTTAGGACATCAATACGTTGTTTCAGAAA-TTGAGGTTTGCTGTATCTCt\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 25)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 9)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3014795, 3014798, 3014799, 3014814, 3014815, 3014815,\n 3014815, 3014815, 3014815, 3014821, 3014822, 3014822,\n 3014841, 3014842],\n [ 175207, 175207, 175206, 175191, 175190, 175180,\n 175180, 175176, 175175, 175169, 175168, 175167,\n 175148, 175147],\n [ 6365, 6365, 6365, 6365, 6366, 6376,\n 6376, 6376, 6377, 6383, 6383, 6384,\n 6403, 6404],\n [155028706, 155028706, 155028706, 155028706, 155028706, 155028706,\n 155028706, 155028706, 155028706, 155028706, 155028706, 155028706,\n 155028687, 155028686],\n [157518758, 157518758, 157518758, 157518758, 157518758, 157518758,\n 157518758, 157518758, 157518758, 157518758, 157518758, 157518758,\n 157518739, 157518738],\n [158040939, 158040939, 158040939, 158040939, 158040939, 158040939,\n 158040939, 158040939, 158040939, 158040939, 158040939, 158040939,\n 158040920, 158040919],\n [ 326933, 326933, 326933, 326933, 326933, 326933,\n 326933, 326933, 326933, 326927, 326926, 326926,\n 326907, 326906],\n [ 2210, 2210, 2210, 2210, 2210, 2210,\n 2210, 2210, 2210, 2204, 2203, 2203,\n 2184, 2184],\n [ 9265, 9262, 9262, 9247, 9246, 9236,\n 9235, 9231, 9230, 9224, 9223, 9223,\n 9204, 9203],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014795 GTTTCAGGGGCAGCTCGCTG----------------TTAGCAG-CTAAGGCATGGTGTCT\notoGar1.s 175207 ---TCGGGAACAAGTTGCAGTCATGGATAT-TTGGTTTAGATGGTTTAGGTGGGGTGTAT\ncalJac1.C 6365 -------------------GCCATGAATAT-----TTTAGAC-ATGCAGGTGTGGCGTGT\nhg18.chr6 155028706 --------------------------------------------aGCAGGTGTGGCATGT\npanTro2.c 157518758 --------------------------------------------aGCAGGTGTGGCATGT\nponAbe2.c 158040939 --------------------------------------------aGCAGGTGTGGCATGT\ntupBel1.s 326933 ------------------------------------TTAGAAA-TGTGGGTGTGGCGCAT\ncavPor2.s 2210 ------------------------------------TTAGAAA-TTTAGGTGTGGCATGG\nloxAfr1.s 9265 GTT-TGAGAGCAAGTTTAGGACATCAATACGTTGTTTCAGAAA-TTGAGGTTTGCTGTAT\n\nmm9.chr10 3014838 CTCA 3014842\notoGar1.s 175151 TTCT 175147\ncalJac1.C 6400 TTCT 6404\nhg18.chr6 155028690 TTCT 155028686\npanTro2.c 157518742 TTCT 157518738\nponAbe2.c 158040923 TTCT 158040919\ntupBel1.s 326910 CGCT 326906\ncavPor2.s 2187 TTC- 2184\nloxAfr1.s 9207 CTCt 9203\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=-12243.000000\ns mm9.chr10 3014795 47 + 129993255 GTTTCAGGGGCAGCTCGCTG----------------TTAGCAG-CTAAGGCATGGTGTCTCTCA\ns otoGar1.scaffold_334.1-359464 184257 60 - 359464 ---TCGGGAACAAGTTGCAGTCATGGATAT-TTGGTTTAGATGGTTTAGGTGGGGTGTATTTCT\nq otoGar1.scaffold_334.1-359464 ---899999999999999999999999999-999999999999999999999999999999999\ni otoGar1.scaffold_334.1-359464 I 24 C 0\ns calJac1.Contig6394 6365 39 + 133105 -------------------GCCATGAATAT-----TTTAGAC-ATGCAGGTGTGGCGTGTTTCT\ni calJac1.Contig6394 I 54 C 0\ns hg18.chr6 15871286 20 - 170899992 --------------------------------------------aGCAGGTGTGGCATGTTTCT\ni hg18.chr6 I 401 C 0\ns panTro2.chr6 16389854 20 - 173908612 --------------------------------------------aGCAGGTGTGGCATGTTTCT\nq panTro2.chr6 --------------------------------------------99999999999999999999\ni panTro2.chr6 I 400 C 0\ns ponAbe2.chr6 16169492 20 - 174210431 --------------------------------------------aGCAGGTGTGGCATGTTTCT\ni ponAbe2.chr6 I 8044 C 0\ns tupBel1.scaffold_114895.1-498454 171521 27 - 498454 ------------------------------------TTAGAAA-TGTGGGTGTGGCGCATCGCT\nq tupBel1.scaffold_114895.1-498454 ------------------------------------9999999-99999989998899999699\ni tupBel1.scaffold_114895.1-498454 I 4145 C 0\ns cavPor2.scaffold_216473 7816 26 - 10026 ------------------------------------TTAGAAA-TTTAGGTGTGGCATGGTTC-\nq cavPor2.scaffold_216473 ------------------------------------4255831-1324566557465575854-\ni cavPor2.scaffold_216473 N 0 C 0\ns loxAfr1.scaffold_75566 1309 62 - 10574 GTT-TGAGAGCAAGTTTAGGACATCAATACGTTGTTTCAGAAA-TTGAGGTTTGCTGTATCTCt\nq loxAfr1.scaffold_75566 999-999999999999999999999999999999999999999-99999999999999999999\ni loxAfr1.scaffold_75566 I 25 C 0\ne echTel1.scaffold_288249 87661 7564 + 100002 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['G', 'T', 'T', 'T', 'C', 'A', 'G', 'G', 'G', 'G', 'C', 'A', 'G',\n 'C', 'T', 'C', 'G', 'C', 'T', 'G', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'A',\n 'G', 'C', 'A', 'G', '-', 'C', 'T', 'A', 'A', 'G', 'G', 'C', 'A',\n 'T', 'G', 'G', 'T', 'G', 'T', 'C', 'T', 'C', 'T', 'C', 'A'],\n ['-', '-', '-', 'T', 'C', 'G', 'G', 'G', 'A', 'A', 'C', 'A', 'A',\n 'G', 'T', 'T', 'G', 'C', 'A', 'G', 'T', 'C', 'A', 'T', 'G', 'G',\n 'A', 'T', 'A', 'T', '-', 'T', 'T', 'G', 'G', 'T', 'T', 'T', 'A',\n 'G', 'A', 'T', 'G', 'G', 'T', 'T', 'T', 'A', 'G', 'G', 'T', 'G',\n 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'T', 'T', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', 'G', 'C', 'C', 'A', 'T', 'G', 'A',\n 'A', 'T', 'A', 'T', '-', '-', '-', '-', '-', 'T', 'T', 'T', 'A',\n 'G', 'A', 'C', '-', 'A', 'T', 'G', 'C', 'A', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'G', 'T', 'G', 'T', 'T', 'T', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'a', 'G', 'C', 'A', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'T', 'T', 'T', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'a', 'G', 'C', 'A', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'T', 'T', 'T', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'a', 'G', 'C', 'A', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'T', 'T', 'T', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'A',\n 'G', 'A', 'A', 'A', '-', 'T', 'G', 'T', 'G', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'G', 'C', 'A', 'T', 'C', 'G', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'A',\n 'G', 'A', 'A', 'A', '-', 'T', 'T', 'T', 'A', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'G', 'T', 'T', 'C', '-'],\n ['G', 'T', 'T', '-', 'T', 'G', 'A', 'G', 'A', 'G', 'C', 'A', 'A',\n 'G', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C', 'A', 'T', 'C', 'A',\n 'A', 'T', 'A', 'C', 'G', 'T', 'T', 'G', 'T', 'T', 'T', 'C', 'A',\n 'G', 'A', 'A', 'A', '-', 'T', 'T', 'G', 'A', 'G', 'G', 'T', 'T',\n 'T', 'G', 'C', 'T', 'G', 'T', 'A', 'T', 'C', 'T', 'C', 't']],\n dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 320596)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014842 : 3014842 + 186],\n \"CTTGGGATGCTTTATAGTGGAAATGGAAAGCAATTTATTTAGATCTTAAATCATTTTGAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCTTCATTTTTAAAATATTGCATCCTATAATACACATAAATCTTGTTCTCGtttttatttttttatttatttatttttttttcttt\",\n )\n self.assertEqual(\n alignment[0],\n \"C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGATCTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCTTCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtttttatttttt----tatt-tat-----------------------ttattttttttt------------cttt\",\n )\n self.assertEqual(alignment.sequences[1].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[1].seq), 10574)\n self.assertEqual(\n alignment.sequences[1].seq[8958 : 8958 + 245],\n \"AGATTTGGCCAAAGTCAATGAAAAAAGAGAGAGAGAGTGAACTTGCTAAGACACCTGCTTAAAAAGGGAATGAGATTTTGAAAAGATGCTGTGTGTGGTATAAAACCCAATTTTTTTTTTTAAATGAGGGTATTGTTCACAGGAATATTAAAGTGAAAATTTCATTATACTTCAAAGGGATTTATGGCCAAAAGAAACAGTGTGACTTTCACTTCAGCtttaaaaaaaaaaaaaaatcaaaaata\",\n )\n self.assertEqual(\n alignment[1],\n \"tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGCCATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCCTCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATTCCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGACTTTGGCCAAATCT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[2].seq), 10026)\n self.assertEqual(\n alignment.sequences[2].seq[1986 : 1986 + 198],\n \"agagaaagagagactaaTAAACCTGCCAGAAGAAGGAAATGAGATGTTGGAAATATGCTGTATGTGGTACAAAATCCAAACTTTTTTAAATGAGGGCATTGTTAGTAGGAATATTAATGTGATCATTTTATTATACTTCAAAAGGATTTAAGTCCTAAAGAAACAGGGTGCCTTTCATTCCAACTGTGAATATCCAAA\",\n )\n self.assertEqual(\n alignment[2],\n \"---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCCTCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATTTCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt------------ctct\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"610137772001955312362668764253688587789879568878689568989568988778987788768588885664786777656586678636299978766899797899369899566878676899958889788869976598977898999989967788999979899987999997779899\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[3].seq), 498454)\n self.assertEqual(\n alignment.sequences[3].seq[326691 : 326691 + 215],\n \"AAGTCAATAGACAAAAAGGGAACTTGCTAATAAACCTGCCAAAAAAGGAAATGAGATTTTGGAAATATGCTGTACGTGGTATAAAATCCCAGATTTTGTAAAATGAGGGCATTGTTCACAGGAATAGTAAAGTGATCATTTTATTATACTTCAAAAGGATTTAAGACCTACAGACACAGTGTGCTTTTTATTTCAGCTGTAAAAAATCCAAAAGG\",\n )\n self.assertEqual(\n alignment[3],\n \"CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGTCTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCCTCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATTTCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG------------ACTT\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"98999999989999999899999999999999999999999999999999999999999999999999989999999999999999999999999998999999999999999999988999999999739999999989999999999999999799999999999999999999769984999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 174210431)\n self.assertEqual(\n alignment.sequences[4].seq[158040700 : 158040700 + 219],\n \"AAGTAAATAAGAGAGAGAGATAACTTGCTATAAATAAACCTGCCAAGAAAGGAAATGAGATTTCAGAAATATGCTGCATGTGGTATAAAATCCAGGATTTTTTTAAAAGAGGACATTGCTCACAGGAGTATTAAAGTGATCGTTTTATTATACTTCAAAAGTATTTAAGACCTAAAGAAACAGTGTGCCTTCCATTTCAGCTATAAAAAGTCCAAAAGG\",\n )\n self.assertEqual(\n alignment[4],\n \"CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCCTCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTTCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT------------ACTT\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 173908612)\n self.assertEqual(\n alignment.sequences[5].seq[157518570 : 157518570 + 168],\n \"AAATGGGATTTCAGAAATATGCTGCATGTGGTATAAAATCCAGGATTTTTTTAAAAAGAGGGCATTGTTCACAGGAGTATTAAAGTGATCATTTTTTTATACTTCAAAAGTATTTAAGACCTAAAGAAATATTGTGCCTTCCATTTCAGCTATAAAAAGTCCAAAAGG\",\n )\n self.assertEqual(\n alignment[5],\n \"CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATTT------------------------------------------------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[6].seq), 170899992)\n self.assertEqual(\n alignment.sequences[6].seq[155028517 : 155028517 + 169],\n \"AAATGAGATTTCAGAAATATGCTGCATGTGGTATAAAATCCAGGATTTTTTTTAAAAAGAGGGCATTGTTCACAGGAGTATTAAAGTGATCATTTTTTTATACTTCAAAAGTATTTAAGACCTAAAGAAATATTGTGCCTTCCATTTCAGCTATAAAAAGTCCAAAAGG\",\n )\n self.assertEqual(\n alignment[6],\n \"CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTT------------------------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[7].seq), 133105)\n self.assertEqual(\n alignment.sequences[7].seq[6404 : 6404 + 223],\n \"TCTTTTGTATTTTTTTATAGCTGAAAAGGAAGGCACACTGTCTCTTTAGGTCTTAAATACGTTTGAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCCTCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATTTCCTTTCCTGGCAGGTTTATTAATAGCAAGTTCTCTCTCTTATTTATTTATTT\",\n )\n self.assertEqual(\n alignment[7],\n \"TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGTCTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCCTCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATTTCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT------------ATTT\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[8].seq), 359464)\n self.assertEqual(\n alignment.sequences[8].seq[174925 : 174925 + 222],\n \"GAGAAAAAGAAGAAGAAAGCCGGAGAGAACTTGCTAACAAACCCGCCAAAAAGGAAATGAGATTTTGGAAATATGCTGGATCTGGTATAAAATCCAAGATTTTTTTAAATGAGGGCATTGTTCACAGGAACAGTAAAGTAATCGTTTTATTATACTTCAAAAGGATTTAAGTCCTAAAAAAACAGTGTGCCTTTCATTTCACCCATAAAAAAGCCCAAAATA\",\n )\n self.assertEqual(\n alignment[8],\n \"TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCCTCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATTT-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT------------TCTC\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"999999999999999999999999999999999799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"ornAna1.chr2\")\n self.assertEqual(len(alignment.sequences[9].seq), 54797317)\n self.assertEqual(\n alignment.sequences[9].seq[40046122 : 40046122 + 201],\n \"AAAGAGAGAACGGTTAATACAATGCACCCAAAAAGGAACTAAGATTTTGGAAATGGGCTGTATGTCGTTAAAATACAAAGATATTTTAATGAGGGCTTTGTTAGCGGGGAAATGAAGATCATAATTACAATACACTTTTAAAAAGGCTTAAGATAGAAAGAAAACAATGAGCCTTTCACTTTTGCAGTAACATTTCCAAGG\",\n )\n self.assertEqual(\n alignment[9],\n \"--CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTATCTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCCTCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGTTCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT----------------\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 5690)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 10)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3014842, 3014843, 3014843, 3014843, 3014849, 3014849,\n 3014849, 3014851, 3014852, 3014874, 3014874, 3014875,\n 3014875, 3014899, 3014899, 3014951, 3014951, 3014951,\n 3014951, 3014951, 3014969, 3014970, 3014981, 3014981,\n 3014988, 3014988, 3014996, 3014997, 3014998, 3014999,\n 3015005, 3015005, 3015009, 3015009, 3015012, 3015012,\n 3015012, 3015012, 3015012, 3015012, 3015024, 3015024,\n 3015028],\n [ 9203, 9202, 9201, 9200, 9194, 9186,\n 9185, 9183, 9182, 9160, 9156, 9155,\n 9155, 9131, 9131, 9079, 9079, 9078,\n 9077, 9076, 9058, 9057, 9046, 9045,\n 9038, 9033, 9025, 9024, 9023, 9023,\n 9017, 9013, 9009, 9009, 9006, 9006,\n 9002, 8993, 8992, 8986, 8974, 8962,\n 8958],\n [ 2184, 2184, 2184, 2184, 2178, 2178,\n 2178, 2176, 2176, 2154, 2150, 2149,\n 2149, 2125, 2125, 2073, 2073, 2073,\n 2073, 2073, 2055, 2054, 2043, 2042,\n 2035, 2030, 2022, 2021, 2020, 2019,\n 2013, 2009, 2005, 2005, 2002, 2002,\n 2002, 2002, 2002, 2002, 1990, 1990,\n 1986],\n [ 326906, 326905, 326904, 326903, 326897, 326897,\n 326897, 326895, 326894, 326872, 326868, 326867,\n 326867, 326843, 326843, 326791, 326791, 326791,\n 326791, 326790, 326772, 326771, 326760, 326759,\n 326752, 326747, 326739, 326738, 326737, 326737,\n 326731, 326727, 326723, 326723, 326720, 326720,\n 326716, 326707, 326707, 326707, 326695, 326695,\n 326691],\n [158040919, 158040918, 158040917, 158040916, 158040910, 158040910,\n 158040910, 158040908, 158040907, 158040885, 158040881, 158040880,\n 158040880, 158040856, 158040856, 158040804, 158040804, 158040804,\n 158040804, 158040803, 158040785, 158040784, 158040773, 158040772,\n 158040765, 158040760, 158040752, 158040751, 158040750, 158040750,\n 158040744, 158040740, 158040736, 158040736, 158040733, 158040730,\n 158040726, 158040717, 158040716, 158040716, 158040704, 158040704,\n 158040700],\n [157518738, 157518737, 157518736, 157518735, 157518729, 157518729,\n 157518729, 157518727, 157518726, 157518704, 157518700, 157518699,\n 157518699, 157518675, 157518675, 157518623, 157518622, 157518622,\n 157518622, 157518621, 157518603, 157518602, 157518591, 157518590,\n 157518583, 157518578, 157518570, 157518570, 157518570, 157518570,\n 157518570, 157518570, 157518570, 157518570, 157518570, 157518570,\n 157518570, 157518570, 157518570, 157518570, 157518570, 157518570,\n 157518570],\n [155028686, 155028685, 155028684, 155028683, 155028677, 155028677,\n 155028677, 155028675, 155028674, 155028652, 155028648, 155028647,\n 155028647, 155028623, 155028623, 155028571, 155028570, 155028570,\n 155028569, 155028568, 155028550, 155028549, 155028538, 155028537,\n 155028530, 155028525, 155028517, 155028517, 155028517, 155028517,\n 155028517, 155028517, 155028517, 155028517, 155028517, 155028517,\n 155028517, 155028517, 155028517, 155028517, 155028517, 155028517,\n 155028517],\n [ 6404, 6405, 6406, 6407, 6413, 6413,\n 6414, 6416, 6417, 6439, 6443, 6444,\n 6444, 6468, 6468, 6520, 6521, 6522,\n 6523, 6524, 6542, 6543, 6554, 6555,\n 6562, 6567, 6575, 6576, 6577, 6577,\n 6583, 6587, 6591, 6591, 6594, 6597,\n 6601, 6610, 6611, 6611, 6623, 6623,\n 6627],\n [ 175147, 175146, 175145, 175144, 175138, 175138,\n 175137, 175135, 175134, 175112, 175108, 175107,\n 175107, 175083, 175083, 175031, 175031, 175031,\n 175031, 175030, 175012, 175011, 175000, 174999,\n 174992, 174987, 174979, 174979, 174978, 174978,\n 174972, 174968, 174964, 174964, 174961, 174961,\n 174957, 174948, 174947, 174941, 174929, 174929,\n 174925],\n [ 40046323, 40046323, 40046323, 40046322, 40046316, 40046316,\n 40046316, 40046314, 40046313, 40046291, 40046287, 40046286,\n 40046285, 40046261, 40046260, 40046208, 40046208, 40046208,\n 40046208, 40046208, 40046190, 40046190, 40046179, 40046178,\n 40046171, 40046166, 40046158, 40046157, 40046156, 40046156,\n 40046150, 40046146, 40046142, 40046141, 40046138, 40046138,\n 40046134, 40046134, 40046134, 40046134, 40046122, 40046122,\n 40046122],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014842 C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGAT\nloxAfr1.s 9203 tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGC\ncavPor2.s 2184 ---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGA\ntupBel1.s 326906 CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGT\nponAbe2.c 158040919 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGT\npanTro2.c 157518738 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGT\nhg18.chr6 155028686 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGT\ncalJac1.C 6404 TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGT\notoGar1.s 175147 TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGA\nornAna1.c 40046323 --CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTAT\n\nmm9.chr10 3014886 CTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCT\nloxAfr1.s 9144 CATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCC\ncavPor2.s 2138 CTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCC\ntupBel1.s 326856 CTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCC\nponAbe2.c 158040869 CTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCC\npanTro2.c 157518688 CTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCC\nhg18.chr6 155028636 CTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCC\ncalJac1.C 6455 CTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCC\notoGar1.s 175096 CTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCC\nornAna1.c 40046274 CTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCC\n\nmm9.chr10 3014945 TCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtt\nloxAfr1.s 9085 TCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATT\ncavPor2.s 2079 TCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATT\ntupBel1.s 326797 TCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATT\nponAbe2.c 158040810 TCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATT\npanTro2.c 157518629 TCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATT\nhg18.chr6 155028577 TCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATT\ncalJac1.C 6514 TCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATT\notoGar1.s 175037 TCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATT\nornAna1.c 40046214 TCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGT\n\nmm9.chr10 3014995 tttatttttt----tatt-tat-----------------------ttattttttttt---\nloxAfr1.s 9026 CCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGAC\ncavPor2.s 2023 TCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt---\ntupBel1.s 326740 TCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG---\nponAbe2.c 158040753 TCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT---\npanTro2.c 157518571 T-----------------------------------------------------------\nhg18.chr6 155028518 T-----------------------------------------------------------\ncalJac1.C 6574 TCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT---\notoGar1.s 174980 T-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT---\nornAna1.c 40046159 TCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT---\n\nmm9.chr10 3015024 ---------cttt 3015028\nloxAfr1.s 8971 TTTGGCCAAATCT 8958\ncavPor2.s 1990 ---------ctct 1986\ntupBel1.s 326695 ---------ACTT 326691\nponAbe2.c 158040704 ---------ACTT 158040700\npanTro2.c 157518570 ------------- 157518570\nhg18.chr6 155028517 ------------- 155028517\ncalJac1.C 6623 ---------ATTT 6627\notoGar1.s 174929 ---------TCTC 174925\nornAna1.c 40046122 ------------- 40046122\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=320596.000000\ns mm9.chr10 3014842 186 + 129993255 C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGATCTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCTTCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtttttatttttt----tatt-tat-----------------------ttattttttttt------------cttt\ns loxAfr1.scaffold_75566 1371 245 - 10574 tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGCCATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCCTCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATTCCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGACTTTGGCCAAATCT\nq loxAfr1.scaffold_75566 999999999999999999999999999999999999999999999999-999999999999999999999999-9999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999-99999999999999-999---999999999999999999999999999999999999999999999999\ni loxAfr1.scaffold_75566 C 0 C 0\ns cavPor2.scaffold_216473 7842 198 - 10026 ---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCCTCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATTTCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt------------ctct\nq cavPor2.scaffold_216473 ---610137---------77-200195531236266876425368858-778987956887868956898956-8988778987788768588885664786777656586678636299978766----89979789936989956687867689995888978886997659897789899998996778899997-989-----------------------998799999777------------9899\ni cavPor2.scaffold_216473 C 0 C 0\ns tupBel1.scaffold_114895.1-498454 171548 215 - 498454 CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGTCTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCCTCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATTTCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG------------ACTT\nq tupBel1.scaffold_114895.1-498454 989999999---------899999998999999999999999999999-999999999999999999999999-9999998999999999999999999999999999899999999999999999---998899999999973999999998999999999999999979999999999999-99999997699849-999---9999999999999-------999999999999------------9999\ni tupBel1.scaffold_114895.1-498454 C 0 C 0\ns ponAbe2.chr6 16169512 219 - 174210431 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCCTCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTTCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT------------ACTT\ni ponAbe2.chr6 C 0 C 0\ns panTro2.chr6 16389874 168 - 173908612 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATTT------------------------------------------------------------------------\nq panTro2.chr6 999999999---------999999999999999999999999999999-999999999999999999999999-99999999999999999999999999999999999999999999999999999--9999999999999999999999999999999999999999999999999999------------------------------------------------------------------------\ni panTro2.chr6 C 0 C 0\ns hg18.chr6 15871306 169 - 170899992 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTT------------------------------------------------------------------------\ni hg18.chr6 C 0 C 0\ns calJac1.Contig6394 6404 223 + 133105 TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGTCTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCCTCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATTTCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT------------ATTT\ni calJac1.Contig6394 C 0 C 0\ns otoGar1.scaffold_334.1-359464 184317 222 - 359464 TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCCTCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATTT-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT------------TCTC\nq otoGar1.scaffold_334.1-359464 999999999--------9999999999999999999999997999999-999999999999999999999999-9999999999999999999999999999999999999999999999999999---9999999999999999999999999999999999999999999999999999-9-99999999999999-999---99999999999999999999999999999999------------9999\ni otoGar1.scaffold_334.1-359464 C 0 C 0\ns ornAna1.chr2 14750994 201 - 54797317 --CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTATCTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCCTCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGTTCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT----------------\ni ornAna1.chr2 N 0 I 5690\ne echTel1.scaffold_288249 87661 7564 + 100002 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, -36127)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3015028 : 3015028 + 58],\n \"ccattttttattaggtatttagctcatttacatttccaatgctataccaaaagtcccc\",\n )\n self.assertEqual(\n alignment[0],\n \"ccatttt----------ttattaggtatttagctcatttacatttccaatgctatac----caaaagtcccc\",\n )\n self.assertEqual(alignment.sequences[1].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[1].seq), 10574)\n self.assertEqual(\n alignment.sequences[1].seq[8925 : 8925 + 33],\n \"GAGAACTTTTGTAAGGAATGGAGGTAGAAGTGA\",\n )\n self.assertEqual(\n alignment[1],\n \"TCACTTCTA---------------------------------------CCTCCATTCCTTACAAAAGTTCTC\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[2].seq), 10026)\n self.assertEqual(alignment.sequences[2].seq[1978 : 1978 + 8], \"agacacag\")\n self.assertEqual(\n alignment[2],\n \"ctgtgtc----------t------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"quality\"], \"67889899\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 1372)\n self.assertEqual(alignment.sequences[3].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[3].seq), 498454)\n self.assertEqual(alignment.sequences[3].seq[326690 : 326690 + 1], \"A\")\n self.assertEqual(\n alignment[3],\n \"T-----------------------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"quality\"], \"9\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 2374)\n self.assertEqual(alignment.sequences[4].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 174210431)\n self.assertEqual(\n alignment.sequences[4].seq[158040688 : 158040688 + 12], \"GAAAAGGCAAAA\"\n )\n self.assertEqual(\n alignment[4],\n \"TTTTGCCTTTTC------------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 75)\n self.assertEqual(alignment.sequences[5].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[5].seq), 133105)\n self.assertEqual(\n alignment.sequences[5].seq[6627 : 6627 + 22], \"TGCTTTTTCTCAAATCTCCACT\"\n )\n self.assertEqual(\n alignment[5],\n \"TGCTTTTTCTCAAATCTCCACT--------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 3479)\n self.assertEqual(alignment.sequences[6].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[6].seq), 359464)\n self.assertEqual(\n alignment.sequences[6].seq[174889 : 174889 + 36],\n \"TGGAAGTGAATATTTGGCAAAAGTCAATAGAAAAAA\",\n )\n self.assertEqual(\n alignment[6],\n \"TTTTTTCTATT------------GACTTTTGCCAAATATTCACTTCCA------------------------\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 137)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028517, 155028517))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518570, 157518570))\n self.assertEqual(status, \"C\")\n self.assertEqual(len(alignment.sequences), 7)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 4)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3015028, 3015029, 3015035, 3015035, 3015035, 3015035,\n 3015035, 3015036, 3015040, 3015041, 3015066, 3015075,\n 3015075, 3015086],\n [ 8958, 8957, 8951, 8949, 8949, 8949,\n 8949, 8949, 8949, 8949, 8949, 8940,\n 8936, 8925],\n [ 1986, 1985, 1979, 1979, 1979, 1979,\n 1979, 1978, 1978, 1978, 1978, 1978,\n 1978, 1978],\n [ 326691, 326690, 326690, 326690, 326690, 326690,\n 326690, 326690, 326690, 326690, 326690, 326690,\n 326690, 326690],\n [158040700, 158040699, 158040693, 158040691, 158040689, 158040688,\n 158040688, 158040688, 158040688, 158040688, 158040688, 158040688,\n 158040688, 158040688],\n [ 6627, 6628, 6634, 6636, 6638, 6639,\n 6644, 6645, 6649, 6649, 6649, 6649,\n 6649, 6649],\n [ 174925, 174924, 174918, 174916, 174914, 174914,\n 174914, 174914, 174914, 174914, 174889, 174889,\n 174889, 174889],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3015028 ccatttt----------ttattaggtatttagctcatttacatttccaatgctatac---\nloxAfr1.s 8958 TCACTTCTA---------------------------------------CCTCCATTCCTT\ncavPor2.s 1986 ctgtgtc----------t------------------------------------------\ntupBel1.s 326691 T-----------------------------------------------------------\nponAbe2.c 158040700 TTTTGCCTTTTC------------------------------------------------\ncalJac1.C 6627 TGCTTTTTCTCAAATCTCCACT--------------------------------------\notoGar1.s 174925 TTTTTTCTATT------------GACTTTTGCCAAATATTCACTTCCA------------\n\nmm9.chr10 3015075 -caaaagtcccc 3015086\nloxAfr1.s 8937 ACAAAAGTTCTC 8925\ncavPor2.s 1978 ------------ 1978\ntupBel1.s 326690 ------------ 326690\nponAbe2.c 158040688 ------------ 158040688\ncalJac1.C 6649 ------------ 6649\notoGar1.s 174889 ------------ 174889\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=-36127.000000\ns mm9.chr10 3015028 58 + 129993255 ccatttt----------ttattaggtatttagctcatttacatttccaatgctatac----caaaagtcccc\ns loxAfr1.scaffold_75566 1616 33 - 10574 TCACTTCTA---------------------------------------CCTCCATTCCTTACAAAAGTTCTC\nq loxAfr1.scaffold_75566 999999999---------------------------------------999999999999999999999999\ni loxAfr1.scaffold_75566 C 0 N 0\ns cavPor2.scaffold_216473 8040 8 - 10026 ctgtgtc----------t------------------------------------------------------\nq cavPor2.scaffold_216473 6788989----------9------------------------------------------------------\ni cavPor2.scaffold_216473 C 0 I 1372\ns tupBel1.scaffold_114895.1-498454 171763 1 - 498454 T-----------------------------------------------------------------------\nq tupBel1.scaffold_114895.1-498454 9-----------------------------------------------------------------------\ni tupBel1.scaffold_114895.1-498454 C 0 I 2374\ns ponAbe2.chr6 16169731 12 - 174210431 TTTTGCCTTTTC------------------------------------------------------------\ni ponAbe2.chr6 C 0 I 75\ns calJac1.Contig6394 6627 22 + 133105 TGCTTTTTCTCAAATCTCCACT--------------------------------------------------\ni calJac1.Contig6394 C 0 I 3479\ns otoGar1.scaffold_334.1-359464 184539 36 - 359464 TTTTTTCTATT------------GACTTTTGCCAAATATTCACTTCCA------------------------\nq otoGar1.scaffold_334.1-359464 99999999999------------9999999999999999999999999------------------------\ni otoGar1.scaffold_334.1-359464 C 0 I 137\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne hg18.chr6 155028517 0 + 170899992 C\ne panTro2.chr6 157518570 0 + 173908612 C\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['c', 'c', 'a', 't', 't', 't', 't', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 't', 't', 'a', 't', 't', 'a', 'g', 'g', 't',\n 'a', 't', 't', 't', 'a', 'g', 'c', 't', 'c', 'a', 't', 't', 't',\n 'a', 'c', 'a', 't', 't', 't', 'c', 'c', 'a', 'a', 't', 'g', 'c',\n 't', 'a', 't', 'a', 'c', '-', '-', '-', '-', 'c', 'a', 'a', 'a',\n 'a', 'g', 't', 'c', 'c', 'c', 'c'],\n ['T', 'C', 'A', 'C', 'T', 'T', 'C', 'T', 'A', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'T', 'C',\n 'C', 'A', 'T', 'T', 'C', 'C', 'T', 'T', 'A', 'C', 'A', 'A', 'A',\n 'A', 'G', 'T', 'T', 'C', 'T', 'C'],\n ['c', 't', 'g', 't', 'g', 't', 'c', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 't', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-'],\n ['T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-'],\n ['T', 'T', 'T', 'T', 'G', 'C', 'C', 'T', 'T', 'T', 'T', 'C', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-'],\n ['T', 'G', 'C', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C', 'A', 'A',\n 'A', 'T', 'C', 'T', 'C', 'C', 'A', 'C', 'T', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-'],\n ['T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'T', 'T', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'A', 'C',\n 'T', 'T', 'T', 'T', 'G', 'C', 'C', 'A', 'A', 'A', 'T', 'A', 'T',\n 'T', 'C', 'A', 'C', 'T', 'T', 'C', 'C', 'A', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3015086 : 3015086 + 2572],\n \"catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcccctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccgactaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagttcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctctagctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctgtgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataagatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccctggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgtaactccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcagtcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcctaggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaatgtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataaattaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgtatccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataaggctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatatatgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaaccgccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtgttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagccattctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgattaaggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaattctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccaccttcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaagatcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcagaaactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattgctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttctcctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttgaccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagttgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctcccttgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattccattggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgtagtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagagtttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaattcgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttggcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttccatcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagatctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgagaagggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggccattgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggtttaggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaagtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaattgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagccttgtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttggctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG\",\n )\n self.assertEqual(\n alignment[0],\n \"catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcccctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccgactaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagttcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctctagctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctgtgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataagatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccctggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgtaactccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcagtcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcctaggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaatgtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataaattaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgtatccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataaggctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatatatgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaaccgccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtgttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagccattctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgattaaggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaattctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccaccttcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaagatcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcagaaactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattgctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttctcctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttgaccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagttgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctcccttgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattccattggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgtagtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagagtttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaattcgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttggcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttccatcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagatctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgagaagggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggccattgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggtttaggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaagtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaattgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagccttgtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttggctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174889, 174752))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028517, 155028517))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518570, 157518570))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040688, 158040613))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3015086, 3017658]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3015086 catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcc\n\nmm9.chr10 3015146 cctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccg\n\nmm9.chr10 3015206 actaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagt\n\nmm9.chr10 3015266 tcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctct\n\nmm9.chr10 3015326 agctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctg\n\nmm9.chr10 3015386 tgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataa\n\nmm9.chr10 3015446 gatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccct\n\nmm9.chr10 3015506 ggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgta\n\nmm9.chr10 3015566 actccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcag\n\nmm9.chr10 3015626 tcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcct\n\nmm9.chr10 3015686 aggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaat\n\nmm9.chr10 3015746 gtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataa\n\nmm9.chr10 3015806 attaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgta\n\nmm9.chr10 3015866 tccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataagg\n\nmm9.chr10 3015926 ctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatata\n\nmm9.chr10 3015986 tgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaacc\n\nmm9.chr10 3016046 gccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtg\n\nmm9.chr10 3016106 ttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagcca\n\nmm9.chr10 3016166 ttctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgatta\n\nmm9.chr10 3016226 aggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaatt\n\nmm9.chr10 3016286 ctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccacct\n\nmm9.chr10 3016346 tcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaaga\n\nmm9.chr10 3016406 tcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcaga\n\nmm9.chr10 3016466 aactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattg\n\nmm9.chr10 3016526 ctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttct\n\nmm9.chr10 3016586 cctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttga\n\nmm9.chr10 3016646 ccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagt\n\nmm9.chr10 3016706 tgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctccct\n\nmm9.chr10 3016766 tgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattcc\n\nmm9.chr10 3016826 attggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgt\n\nmm9.chr10 3016886 agtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagag\n\nmm9.chr10 3016946 tttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaatt\n\nmm9.chr10 3017006 cgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttg\n\nmm9.chr10 3017066 gcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttcc\n\nmm9.chr10 3017126 atcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagat\n\nmm9.chr10 3017186 ctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgaga\n\nmm9.chr10 3017246 agggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggcca\n\nmm9.chr10 3017306 ttgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggttta\n\nmm9.chr10 3017366 ggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaa\n\nmm9.chr10 3017426 gtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaa\n\nmm9.chr10 3017486 ttgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagcctt\n\nmm9.chr10 3017546 gtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttgg\n\nmm9.chr10 3017606 ctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG 3017658\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3015086 2572 + 129993255 catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcccctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccgactaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagttcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctctagctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctgtgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataagatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccctggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgtaactccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcagtcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcctaggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaatgtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataaattaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgtatccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataaggctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatatatgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaaccgccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtgttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagccattctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgattaaggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaattctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccaccttcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaagatcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcagaaactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattgctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttctcctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttgaccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagttgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctcccttgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattccattggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgtagtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagagtttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaattcgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttggcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttccatcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagatctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgagaagggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggccattgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggtttaggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaagtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaattgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagccttgtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttggctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184575 137 - 359464 I\ne hg18.chr6 155028517 0 + 170899992 C\ne panTro2.chr6 157518570 0 + 173908612 C\ne ponAbe2.chr6 16169743 75 - 174210431 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 12170)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3017658 : 3017658 + 85],\n \"TTTTTATTTGCAGGTTTCTTTACAGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTGTTGACCTTTATCAGATTTCTGCTTTAACC\",\n )\n self.assertEqual(\n alignment[0],\n \"TTTTTATTTGCAGGTTTCTTTAC----AGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTGTTGACCTTTATCAGATTTCTGCTTTAACC\",\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155028434 : 155028434 + 83],\n \"GGTGGAAGTGGAGATTTGGGAAAAGGCAAAAAAATAAATAAGAGAGAGAGATAACTTGCTATAAATAACCCTGCCAAGAAAGG\",\n )\n self.assertEqual(\n alignment[1],\n \"CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 53)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157518487 : 157518487 + 83],\n \"GGTGGAAGTGGAGATTTGGGAAAAGGCAAAAAAATAAATAAGAGAGAGAGATAACTTGCTATAAATAACCCTGCCAAGAAAGG\",\n )\n self.assertEqual(\n alignment[2],\n \"CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 53)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174889, 174752))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040688, 158040613))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 3)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 7)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3017658, 3017681, 3017681, 3017699, 3017705, 3017743],\n [155028517, 155028494, 155028490, 155028472, 155028472, 155028434],\n [157518570, 157518547, 157518543, 157518525, 157518525, 157518487],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3017658 TTTTTATTTGCAGGTTTCTTTAC----AGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTG\nhg18.chr6 155028517 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTT\npanTro2.c 157518570 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTT\n\nmm9.chr10 3017714 TTGACCTTTATCAGATTTCTGCTTTAACC 3017743\nhg18.chr6 155028463 TTGCCTTTTCCCAAATCTCCACTTCCACC 155028434\npanTro2.c 157518516 TTGCCTTTTCCCAAATCTCCACTTCCACC 157518487\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=12170.000000\ns mm9.chr10 3017658 85 + 129993255 TTTTTATTTGCAGGTTTCTTTAC----AGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTGTTGACCTTTATCAGATTTCTGCTTTAACC\ns hg18.chr6 15871475 83 - 170899992 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC\ni hg18.chr6 C 0 I 53\ns panTro2.chr6 16390042 83 - 173908612 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC\nq panTro2.chr6 999999999999999999999999999999999999999999999------99999999999999999999999999999999999999\ni panTro2.chr6 C 0 I 53\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184575 137 - 359464 I\ne ponAbe2.chr6 16169743 75 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'T', 'G', 'C', 'A', 'G',\n 'G', 'T', 'T', 'T', 'C', 'T', 'T', 'T', 'A', 'C', '-', '-', '-',\n '-', 'A', 'G', 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'A',\n 'T', 'T', 'C', 'T', 'T', 'C', 'T', 'C', 'C', 'T', 'C', 'T', 'T',\n 'T', 'T', 'C', 'T', 'T', 'C', 'T', 'G', 'T', 'T', 'G', 'A', 'C',\n 'C', 'T', 'T', 'T', 'A', 'T', 'C', 'A', 'G', 'A', 'T', 'T', 'T',\n 'C', 'T', 'G', 'C', 'T', 'T', 'T', 'A', 'A', 'C', 'C'],\n ['C', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'G', 'G', 'C', 'A', 'G',\n 'G', 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'T', 'A', 'G', 'C',\n 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'C', 'T', 'C', 'T', 'C', 'T',\n 'C', 'T', 'C', 'T', 'T', 'A', '-', '-', '-', '-', '-', '-', 'T',\n 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'G', 'C', 'C',\n 'T', 'T', 'T', 'T', 'C', 'C', 'C', 'A', 'A', 'A', 'T', 'C', 'T',\n 'C', 'C', 'A', 'C', 'T', 'T', 'C', 'C', 'A', 'C', 'C'],\n ['C', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'G', 'G', 'C', 'A', 'G',\n 'G', 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'T', 'A', 'G', 'C',\n 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'C', 'T', 'C', 'T', 'C', 'T',\n 'C', 'T', 'C', 'T', 'T', 'A', '-', '-', '-', '-', '-', '-', 'T',\n 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'G', 'C', 'C',\n 'T', 'T', 'T', 'T', 'C', 'C', 'C', 'A', 'A', 'A', 'T', 'C', 'T',\n 'C', 'C', 'A', 'C', 'T', 'T', 'C', 'C', 'A', 'C', 'C']],\n dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3017743 : 3017743 + 418],\n \"ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggctgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaattagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaagagagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgccagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaatctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggagacctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca\",\n )\n self.assertEqual(\n alignment[0],\n \"ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggctgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaattagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaagagagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgccagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaatctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggagacctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174889, 174752))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028434, 155028381))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518487, 157518434))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040688, 158040613))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3017743, 3018161]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3017743 ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggc\n\nmm9.chr10 3017803 tgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaa\n\nmm9.chr10 3017863 ttagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaag\n\nmm9.chr10 3017923 agagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgc\n\nmm9.chr10 3017983 cagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaat\n\nmm9.chr10 3018043 ctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggaga\n\nmm9.chr10 3018103 cctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca\n\nmm9.chr10 3018161\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3017743 418 + 129993255 ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggctgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaattagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaagagagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgccagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaatctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggagacctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184575 137 - 359464 I\ne hg18.chr6 15871558 53 - 170899992 I\ne panTro2.chr6 16390125 53 - 173908612 I\ne ponAbe2.chr6 16169743 75 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'C', 'C', 'A', 'C', 'A', 'G', 'A', 'C', 'C', 'T', 'T', 'C',\n 'T', 'G', 'T', 'T', 'T', 'A', 'G', 'T', 'C', 'C', 'A', 'A', 'A',\n 'G', 'G', 'A', 'C', 'G', 'C', 'A', 'A', 'A', 'T', 'T', 'A', 'T',\n 'G', 'T', 'A', 'T', 'C', 'C', 'A', 'C', 'T', 'T', 't', 'a', 'g',\n 't', 'a', 'g', 'g', 'a', 'g', 'g', 'c', 't', 'g', 'a', 'c', 'c',\n 'c', 'g', 'c', 'a', 'g', 'c', 'c', 't', 'a', 'c', 'a', 't', 'g',\n 'a', 'a', 'c', 'c', 'a', 'g', 'g', 't', 'a', 't', 't', 't', 'c',\n 't', 'g', 'g', 'a', 'a', 'g', 'g', 'c', 'a', 'g', 'g', 'c', 't',\n 'g', 'g', 'g', 'g', 't', 't', 'g', 'a', 'a', 'a', 'g', 'a', 'g',\n 'a', 'a', 'a', 't', 't', 'a', 'g', 'a', 't', 'g', 'g', 't', 'g',\n 'a', 'g', 'a', 'a', 'a', 'a', 'g', 'a', 'a', 't', 'a', 'a', 't',\n 'g', 'a', 'g', 'g', 'c', 'c', 'a', 'a', 'g', 'a', 'c', 'a', 'a',\n 'a', 't', 't', 't', 't', 't', 'c', 't', 'c', 't', 't', 'a', 't',\n 'c', 'a', 'a', 'g', 'g', 'c', 'c', 'c', 'a', 'a', 'g', 'a', 'g',\n 'a', 'g', 't', 't', 't', 'a', 'c', 't', 'a', 'a', 'g', 'a', 'g',\n 'a', 'c', 't', 'a', 't', 'g', 'c', 't', 't', 'a', 'a', 'a', 'a',\n 'g', 'g', 'g', 'g', 'g', 'a', 'a', 'g', 'g', 'c', 'c', 'c', 'a',\n 't', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c',\n 't', 'c', 'g', 'c', 'g', 'c', 'c', 'a', 'g', 't', 'c', 't', 'a',\n 't', 'c', 'c', 't', 't', 'g', 'g', 't', 'g', 'c', 't', 't', 't',\n 'g', 't', 'c', 'a', 'c', 'c', 'a', 't', 'g', 'c', 'c', 'a', 't',\n 'c', 'a', 'g', 'c', 'a', 'c', 't', 't', 'g', 'g', 't', 'c', 'g',\n 'g', 'c', 'a', 'g', 'g', 't', 'a', 'g', 'c', 'a', 'g', 'a', 'a',\n 't', 'c', 't', 'c', 'a', 'g', 'g', 'g', 'c', 'a', 'g', 't', 't',\n 'g', 'a', 'c', 'a', 'c', 't', 't', 'c', 'a', 'a', 'a', 'a', 'g',\n 'a', 'a', 'a', 'c', 'c', 'a', 'g', 'c', 'c', 'a', 'a', 'g', 't',\n 'c', 'a', 'g', 'a', 'a', 'a', 'g', 'c', 't', 'g', 'c', 'a', 'c',\n 't', 'g', 'c', 'a', 'g', 'g', 'a', 'g', 'a', 'c', 'c', 't', 'g',\n 'c', 'a', 'c', 't', 'c', 'a', 'g', 't', 'g', 'g', 't', 'g', 'a',\n 'c', 'a', 'a', 'g', 'g', 't', 'c', 't', 'g', 't', 'a', 'c', 'c',\n 'a', 'g', 'c', 'c', 't', 'g', 'c', 't', 't', 'c', 'a', 'g', 'g',\n 'c', 't', 'g', 'g', 'g', 'g', 'g', 'a', 'g', 'g', 'c', 't', 'a',\n 'c', 'a']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 22499)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018161 : 3018161 + 69],\n \"ATCCACAAAAGAGACAAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAATTCCATTTTATTGA\",\n )\n self.assertEqual(\n alignment[0],\n \"ATCCACAAAAGAGAC-----AAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAATTCCATTTTATTGA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 173908612)\n self.assertEqual(\n alignment.sequences[1].seq[157518369 : 157518369 + 65],\n \"TCAATAAAATAAAATTGTTTTATGGTACAAACTTTTCTTATGGTTAATTGTTTTCCTTTGTAGGT\",\n )\n self.assertEqual(\n alignment[1],\n \"ACCTACAAAGG---------AAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 53)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 170899992)\n self.assertEqual(\n alignment.sequences[2].seq[155028316 : 155028316 + 65],\n \"TCAATAAAATAAAATTGTTTTATGGTACAAACTTTTCTTGTGGTTAATTGTTTTCCTTTGTAGGT\",\n )\n self.assertEqual(\n alignment[2],\n \"ACCTACAAAGG---------AAAACAATTAACCACAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 53)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158040552 : 158040552 + 61],\n \"TCAATAAAATAAAATTGTTTTATGGTACAAACTTTTCTTATGGTTAATTGTTTTCCTTTGT\",\n )\n self.assertEqual(\n alignment[3],\n \"-------------ACAAAGGAAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 75)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 97)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174889, 174752))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 4)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3018161, 3018172, 3018174, 3018176, 3018176, 3018230],\n [157518434, 157518423, 157518423, 157518423, 157518423, 157518369],\n [155028381, 155028370, 155028370, 155028370, 155028370, 155028316],\n [158040613, 158040613, 158040613, 158040611, 158040606, 158040552],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018161 ATCCACAAAAGAGAC-----AAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAA\npanTro2.c 157518434 ACCTACAAAGG---------AAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAA\nhg18.chr6 155028381 ACCTACAAAGG---------AAAACAATTAACCACAAGAAAAGTTTGTACCATAAAACAA\nponAbe2.c 158040613 -------------ACAAAGGAAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAA\n\nmm9.chr10 3018216 TTCCATTTTATTGA 3018230\npanTro2.c 157518383 TTTTATTTTATTGA 157518369\nhg18.chr6 155028330 TTTTATTTTATTGA 155028316\nponAbe2.c 158040566 TTTTATTTTATTGA 158040552\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=22499.000000\ns mm9.chr10 3018161 69 + 129993255 ATCCACAAAAGAGAC-----AAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAATTCCATTTTATTGA\ns panTro2.chr6 16390178 65 - 173908612 ACCTACAAAGG---------AAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\nq panTro2.chr6 99999999999---------999999999999999999999999999999999999999999999999999999\ni panTro2.chr6 I 53 C 0\ns hg18.chr6 15871611 65 - 170899992 ACCTACAAAGG---------AAAACAATTAACCACAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\ni hg18.chr6 I 53 C 0\ns ponAbe2.chr6 16169818 61 - 174210431 -------------ACAAAGGAAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\ni ponAbe2.chr6 I 75 I 97\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184575 137 - 359464 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'T', 'C', 'C', 'A', 'C', 'A', 'A', 'A', 'A', 'G', 'A', 'G',\n 'A', 'C', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'G', 'A', 'A',\n 'G', 'A', 'A', 'A', 'A', 'C', 'C', 'A', 'A', 'A', 'A', 'G', 'A',\n 'A', 'A', 'A', 'G', 'A', 'T', 'T', 'G', 'T', 'A', 'G', 'C', 'T',\n 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'C', 'C', 'A',\n 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A'],\n ['A', 'C', 'C', 'T', 'A', 'C', 'A', 'A', 'A', 'G', 'G', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'A', 'C', 'A',\n 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'T', 'A', 'A', 'G', 'A',\n 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G', 'T', 'A', 'C', 'C', 'A',\n 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A'],\n ['A', 'C', 'C', 'T', 'A', 'C', 'A', 'A', 'A', 'G', 'G', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'A', 'C', 'A',\n 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'C', 'A', 'A', 'G', 'A',\n 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G', 'T', 'A', 'C', 'C', 'A',\n 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'A', 'C', 'A', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'C', 'A',\n 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'T', 'A', 'A', 'G', 'A',\n 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G', 'T', 'A', 'C', 'C', 'A',\n 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 4781)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018230 : 3018230 + 129],\n \"AGGACAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATGAATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTACAGCCCCAGC\",\n )\n self.assertEqual(\n alignment[0],\n \"AGGA-CAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATGAATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTA-CAGCCCCAGC\",\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155028221 : 155028221 + 95],\n \"CATATACCTAATAAATCTATATATGTGTAAATTCTTTTTCATAATGACTATCAGAACATTGGGAGCCAGGTTCTGATATATATTGATTGGATTAT\",\n )\n self.assertEqual(\n alignment[1],\n \"ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTATGAA----------AAAGAATTTACACATATATAGATTTATTAGGTATATG\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157518274 : 157518274 + 95],\n \"catatacctaataaatctatatatgtgtaaatTCTTTTTCACAATGACTATCAGAACATTGGGAGCCAGGTTCTGATATATATTGATTGGATTAT\",\n )\n self.assertEqual(\n alignment[2],\n \"ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTGTGAA----------AAAGAatttacacatatatagatttattaggtatatg\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174889, 174752))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040552, 158040455))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 3)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 7)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3018230, 3018234, 3018234, 3018249, 3018270, 3018289,\n 3018294, 3018313, 3018323, 3018349, 3018349, 3018359],\n [155028316, 155028312, 155028311, 155028296, 155028296, 155028277,\n 155028277, 155028258, 155028258, 155028232, 155028231, 155028221],\n [157518369, 157518365, 157518364, 157518349, 157518349, 157518330,\n 157518330, 157518311, 157518311, 157518285, 157518284, 157518274],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018230 AGGA-CAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATG\nhg18.chr6 155028316 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG\npanTro2.c 157518369 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG\n\nmm9.chr10 3018289 AATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTA\nhg18.chr6 155028277 -----TTCTGATAGTCATTATGAA----------AAAGAATTTACACATATATAGATTTA\npanTro2.c 157518330 -----TTCTGATAGTCATTGTGAA----------AAAGAatttacacatatatagattta\n\nmm9.chr10 3018349 -CAGCCCCAGC 3018359\nhg18.chr6 155028232 TTAGGTATATG 155028221\npanTro2.c 157518285 ttaggtatatg 157518274\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=4781.000000\ns mm9.chr10 3018230 129 + 129993255 AGGA-CAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATGAATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTA-CAGCCCCAGC\ns hg18.chr6 15871676 95 - 170899992 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTATGAA----------AAAGAATTTACACATATATAGATTTATTAGGTATATG\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16390243 95 - 173908612 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTGTGAA----------AAAGAatttacacatatatagatttattaggtatatg\nq panTro2.chr6 99999999999999999999---------------------9999999999999999999-----9999999999999999999----------9999999999999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184575 137 - 359464 I\ne ponAbe2.chr6 16169879 97 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'G', 'G', 'A', '-', 'C', 'A', 'A', 'A', 'A', 'T', 'A', 'A',\n 'T', 'A', 'C', 'A', 'G', 'A', 't', 't', 't', 't', 't', 't', 't',\n 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't',\n 't', 'G', 'C', 'A', 'G', 'T', 'A', 'C', 'T', 'G', 'G', 'A', 'A',\n 'A', 'T', 'G', 'G', 'A', 'A', 'T', 'G', 'A', 'A', 'T', 'G', 'T',\n 'C', 'C', 'C', 'T', 'C', 'A', 'C', 'A', 'A', 'T', 'C', 'A', 'C',\n 'T', 'A', 'T', 'C', 'A', 'A', 'G', 'G', 'T', 'C', 'C', 'C', 'T',\n 'A', 'T', 'C', 'A', 'A', 'G', 'G', 'C', 'A', 'A', 'T', 'C', 'A',\n 'C', 'T', 'C', 'T', 'G', 'T', 'C', 'A', 'C', 'C', 'G', 'A', 'G',\n 'C', 'T', 'A', '-', 'C', 'A', 'G', 'C', 'C', 'C', 'C', 'A', 'G',\n 'C'],\n ['A', 'T', 'A', 'A', 'T', 'C', 'C', 'A', 'A', 'T', 'C', 'A', 'A',\n 'T', 'A', 'T', 'A', 'T', 'A', 'T', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'C', 'A', 'G', 'A', 'A', 'C', 'C', 'T', 'G', 'G', 'C',\n 'T', 'C', 'C', 'C', 'A', 'A', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'T', 'C', 'T', 'G', 'A', 'T', 'A', 'G', 'T', 'C', 'A', 'T',\n 'T', 'A', 'T', 'G', 'A', 'A', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', 'A', 'A', 'A', 'G', 'A', 'A', 'T', 'T', 'T', 'A',\n 'C', 'A', 'C', 'A', 'T', 'A', 'T', 'A', 'T', 'A', 'G', 'A', 'T',\n 'T', 'T', 'A', 'T', 'T', 'A', 'G', 'G', 'T', 'A', 'T', 'A', 'T',\n 'G'],\n ['A', 'T', 'A', 'A', 'T', 'C', 'C', 'A', 'A', 'T', 'C', 'A', 'A',\n 'T', 'A', 'T', 'A', 'T', 'A', 'T', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'C', 'A', 'G', 'A', 'A', 'C', 'C', 'T', 'G', 'G', 'C',\n 'T', 'C', 'C', 'C', 'A', 'A', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'T', 'C', 'T', 'G', 'A', 'T', 'A', 'G', 'T', 'C', 'A', 'T',\n 'T', 'G', 'T', 'G', 'A', 'A', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', 'A', 'A', 'A', 'G', 'A', 'a', 't', 't', 't', 'a',\n 'c', 'a', 'c', 'a', 't', 'a', 't', 'a', 't', 'a', 'g', 'a', 't',\n 't', 't', 'a', 't', 't', 'a', 'g', 'g', 't', 'a', 't', 'a', 't',\n 'g']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 61520)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018359 : 3018359 + 123],\n \"TTCAAACATGCATACATGCATTCATGTCTCATAATAATTATTAACATTGTCTTAGGCCAGAGGCTCGACTGCCCCAAAGCAATCCACTTAAACTGTCCCTGAGAAAGTCAttcctctccctaa\",\n )\n self.assertEqual(\n alignment[0],\n \"TT-CAAACATGCATACATGCATTCATGTCTCATAA-TAATTATTAACA-TTGTCTTAGGCCAGAGGCTCGACTGCCCCAAAGCAATCCACT-------TAAACTGTCCCTGAGAA-AGTCAttcctctccctaa\",\n )\n self.assertEqual(alignment.sequences[1].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 173908612)\n self.assertEqual(\n alignment.sequences[1].seq[157518143 : 157518143 + 131],\n \"AAAGAAAAGGATGACCCTTCCCGGAGAGAATATAAAATATGGATGGCTTAGTTTGTATCACTCAGGCCACTGACCTAAGATGACTGTTAATAATTATTTATGAGacatacacatatatttgtacatttata\",\n )\n self.assertEqual(\n alignment[1],\n \"-tataaatgtacaaatatatgtgtatgtCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 2400)\n self.assertEqual(alignment.sequences[2].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 170899992)\n self.assertEqual(\n alignment.sequences[2].seq[155028090 : 155028090 + 131],\n \"AAAGAAAAGGATGACCCTTCCCGGAGAGAATATAAAATATGGATGGCTTAGTTTGTATCATTCAGGCCACTGACCTAAGATGACTGTTAATAATTATTTATGAGACATACACATATATTTGTACGTTTATA\",\n )\n self.assertEqual(\n alignment[2],\n \"-TATAAACGTACAAATATATGTGTATGTCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAATGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 2402)\n self.assertEqual(alignment.sequences[3].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[3].seq), 359464)\n self.assertEqual(\n alignment.sequences[3].seq[174625 : 174625 + 127],\n \"TCAGAAGAAAGGATGACCCTTCACACAGGGAGGATAGGATGGGTTAGCTTGTGTCACTCGGGCCTCTAACCTAAGACAAATGTTAATAATTACTTACAGGACCTACATTTACACATACATGTATAAA\",\n )\n self.assertEqual(\n alignment[3],\n \"TT-TATACATGTATGTGTAAATGTAGGTCCTGTAAGTAATTATTAACATTTGTCTTAGGTTAGAGGCCCGAGTGACACAAGCTAACCCATCC------TATCCTCCCTGTGTGAAGGGTCATCCTTTCTTCTGA\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999667736999999999999999999999999999995666677755798899998999967967999999999589\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 137)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 2731)\n self.assertEqual(alignment.sequences[4].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 174210431)\n self.assertEqual(\n alignment.sequences[4].seq[158040326 : 158040326 + 129],\n \"AAAGAAAAGGATGACCCTTCCCAGAGAGAATATAAAATATGGATGGCTTAGTTTCTATCACTCAGGCCACTGACCTAAGATGACTGTTAATAATtatttatgacacatacacatatatttgtacattta\",\n )\n self.assertEqual(\n alignment[4],\n \"---taaatgtacaaatatatgtgtatgtgtcataaataATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATAGAAACTAAGCCATCCATATTTTATATTCTCTCTGGGAAGGGTCATCCTTTTCTTT--\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 97)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 2523)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 5)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 5)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3018359, 3018360, 3018361, 3018361, 3018393, 3018393,\n 3018405, 3018405, 3018447, 3018447, 3018447, 3018464,\n 3018464, 3018480, 3018482],\n [157518274, 157518274, 157518273, 157518272, 157518240, 157518239,\n 157518227, 157518226, 157518184, 157518183, 157518177, 157518160,\n 157518159, 157518143, 157518143],\n [155028221, 155028221, 155028220, 155028219, 155028187, 155028186,\n 155028174, 155028173, 155028131, 155028130, 155028124, 155028107,\n 155028106, 155028090, 155028090],\n [ 174752, 174751, 174750, 174750, 174718, 174717,\n 174705, 174704, 174662, 174661, 174661, 174644,\n 174643, 174627, 174625],\n [158040455, 158040455, 158040455, 158040455, 158040423, 158040422,\n 158040410, 158040409, 158040367, 158040366, 158040360, 158040343,\n 158040342, 158040326, 158040326],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018359 TT-CAAACATGCATACATGCATTCATGTCTCATAA-TAATTATTAACA-TTGTCTTAGGC\npanTro2.c 157518274 -tataaatgtacaaatatatgtgtatgtCTCATAAATAATTATTAACAGTCATCTTAGGT\nhg18.chr6 155028221 -TATAAACGTACAAATATATGTGTATGTCTCATAAATAATTATTAACAGTCATCTTAGGT\notoGar1.s 174752 TT-TATACATGTATGTGTAAATGTAGGTCCTGTAAGTAATTATTAACATTTGTCTTAGGT\nponAbe2.c 158040455 ---taaatgtacaaatatatgtgtatgtgtcataaataATTATTAACAGTCATCTTAGGT\n\nmm9.chr10 3018416 CAGAGGCTCGACTGCCCCAAAGCAATCCACT-------TAAACTGTCCCTGAGAA-AGTC\npanTro2.c 157518215 CAGTGGCCTGAGTGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTC\nhg18.chr6 155028162 CAGTGGCCTGAATGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTC\notoGar1.s 174693 TAGAGGCCCGAGTGACACAAGCTAACCCATCC------TATCCTCCCTGTGTGAAGGGTC\nponAbe2.c 158040398 CAGTGGCCTGAGTGATAGAAACTAAGCCATCCATATTTTATATTCTCTCTGGGAAGGGTC\n\nmm9.chr10 3018468 Attcctctccctaa 3018482\npanTro2.c 157518155 ATCCTTTTCTTT-- 157518143\nhg18.chr6 155028102 ATCCTTTTCTTT-- 155028090\notoGar1.s 174639 ATCCTTTCTTCTGA 174625\nponAbe2.c 158040338 ATCCTTTTCTTT-- 158040326\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=61520.000000\ns mm9.chr10 3018359 123 + 129993255 TT-CAAACATGCATACATGCATTCATGTCTCATAA-TAATTATTAACA-TTGTCTTAGGCCAGAGGCTCGACTGCCCCAAAGCAATCCACT-------TAAACTGTCCCTGAGAA-AGTCAttcctctccctaa\ns panTro2.chr6 16390338 131 - 173908612 -tataaatgtacaaatatatgtgtatgtCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--\nq panTro2.chr6 -99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--\ni panTro2.chr6 C 0 I 2400\ns hg18.chr6 15871771 131 - 170899992 -TATAAACGTACAAATATATGTGTATGTCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAATGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--\ni hg18.chr6 C 0 I 2402\ns otoGar1.scaffold_334.1-359464 184712 127 - 359464 TT-TATACATGTATGTGTAAATGTAGGTCCTGTAAGTAATTATTAACATTTGTCTTAGGTTAGAGGCCCGAGTGACACAAGCTAACCCATCC------TATCCTCCCTGTGTGAAGGGTCATCCTTTCTTCTGA\nq otoGar1.scaffold_334.1-359464 99-99999999999999999999999999999999999999999999999999667736999999999999999999999999999995666------677755798899998999967967999999999589\ni otoGar1.scaffold_334.1-359464 I 137 I 2731\ns ponAbe2.chr6 16169976 129 - 174210431 ---taaatgtacaaatatatgtgtatgtgtcataaataATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATAGAAACTAAGCCATCCATATTTTATATTCTCTCTGGGAAGGGTCATCCTTTTCTTT--\ni ponAbe2.chr6 I 97 I 2523\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'T', '-', 'C', 'A', 'A', 'A', 'C', 'A', 'T', 'G', 'C', 'A',\n 'T', 'A', 'C', 'A', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T',\n 'G', 'T', 'C', 'T', 'C', 'A', 'T', 'A', 'A', '-', 'T', 'A', 'A',\n 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', '-', 'T', 'T', 'G',\n 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'C', 'C', 'A', 'G', 'A', 'G',\n 'G', 'C', 'T', 'C', 'G', 'A', 'C', 'T', 'G', 'C', 'C', 'C', 'C',\n 'A', 'A', 'A', 'G', 'C', 'A', 'A', 'T', 'C', 'C', 'A', 'C', 'T',\n '-', '-', '-', '-', '-', '-', '-', 'T', 'A', 'A', 'A', 'C', 'T',\n 'G', 'T', 'C', 'C', 'C', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'A',\n 'G', 'T', 'C', 'A', 't', 't', 'c', 'c', 't', 'c', 't', 'c', 'c',\n 'c', 't', 'a', 'a'],\n ['-', 't', 'a', 't', 'a', 'a', 'a', 't', 'g', 't', 'a', 'c', 'a',\n 'a', 'a', 't', 'a', 't', 'a', 't', 'g', 't', 'g', 't', 'a', 't',\n 'g', 't', 'C', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'T', 'A', 'A',\n 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'G', 'T', 'C', 'A',\n 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'T', 'G',\n 'G', 'C', 'C', 'T', 'G', 'A', 'G', 'T', 'G', 'A', 'T', 'A', 'C',\n 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'G', 'C', 'C', 'A', 'T', 'C',\n 'C', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'T', 'T',\n 'C', 'T', 'C', 'T', 'C', 'C', 'G', 'G', 'G', 'A', 'A', 'G', 'G',\n 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', '-', '-'],\n ['-', 'T', 'A', 'T', 'A', 'A', 'A', 'C', 'G', 'T', 'A', 'C', 'A',\n 'A', 'A', 'T', 'A', 'T', 'A', 'T', 'G', 'T', 'G', 'T', 'A', 'T',\n 'G', 'T', 'C', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'T', 'A', 'A',\n 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'G', 'T', 'C', 'A',\n 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'T', 'G',\n 'G', 'C', 'C', 'T', 'G', 'A', 'A', 'T', 'G', 'A', 'T', 'A', 'C',\n 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'G', 'C', 'C', 'A', 'T', 'C',\n 'C', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'T', 'T',\n 'C', 'T', 'C', 'T', 'C', 'C', 'G', 'G', 'G', 'A', 'A', 'G', 'G',\n 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', '-', '-'],\n ['T', 'T', '-', 'T', 'A', 'T', 'A', 'C', 'A', 'T', 'G', 'T', 'A',\n 'T', 'G', 'T', 'G', 'T', 'A', 'A', 'A', 'T', 'G', 'T', 'A', 'G',\n 'G', 'T', 'C', 'C', 'T', 'G', 'T', 'A', 'A', 'G', 'T', 'A', 'A',\n 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'T', 'T', 'T', 'G',\n 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'T', 'A', 'G', 'A', 'G',\n 'G', 'C', 'C', 'C', 'G', 'A', 'G', 'T', 'G', 'A', 'C', 'A', 'C',\n 'A', 'A', 'G', 'C', 'T', 'A', 'A', 'C', 'C', 'C', 'A', 'T', 'C',\n 'C', '-', '-', '-', '-', '-', '-', 'T', 'A', 'T', 'C', 'C', 'T',\n 'C', 'C', 'C', 'T', 'G', 'T', 'G', 'T', 'G', 'A', 'A', 'G', 'G',\n 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'C', 'T', 'T',\n 'C', 'T', 'G', 'A'],\n ['-', '-', '-', 't', 'a', 'a', 'a', 't', 'g', 't', 'a', 'c', 'a',\n 'a', 'a', 't', 'a', 't', 'a', 't', 'g', 't', 'g', 't', 'a', 't',\n 'g', 't', 'g', 't', 'c', 'a', 't', 'a', 'a', 'a', 't', 'a', 'A',\n 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'G', 'T', 'C', 'A',\n 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'T', 'G',\n 'G', 'C', 'C', 'T', 'G', 'A', 'G', 'T', 'G', 'A', 'T', 'A', 'G',\n 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'G', 'C', 'C', 'A', 'T', 'C',\n 'C', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'T', 'T',\n 'C', 'T', 'C', 'T', 'C', 'T', 'G', 'G', 'G', 'A', 'A', 'G', 'G',\n 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', '-', '-']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018482 : 3018482 + 162],\n \"tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtccttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatggggagaggaggaaaggaggagaggggaggagaggaggggagGTAT\",\n )\n self.assertEqual(\n alignment[0],\n \"tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtccttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatggggagaggaggaaaggaggagaggggaggagaggaggggagGTAT\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3018482, 3018644]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018482 tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtcc\n\nmm9.chr10 3018542 ttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatgggg\n\nmm9.chr10 3018602 agaggaggaaaggaggagaggggaggagaggaggggagGTAT 3018644\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3018482 162 + 129993255 tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtccttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatggggagaggaggaaaggaggagaggggaggagaggaggggagGTAT\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['t', 'c', 't', 't', 'c', 'a', 't', 'c', 't', 'c', 'c', 't', 'c',\n 't', 't', 't', 't', 'c', 'c', 't', 'c', 'c', 't', 't', 't', 't',\n 't', 't', 't', 't', 't', 't', 'c', 't', 'c', 'a', 't', 't', 't',\n 'c', 't', 'c', 't', 't', 't', 'c', 't', 'c', 't', 't', 't', 'c',\n 't', 't', 't', 't', 'g', 't', 'c', 'c', 't', 't', 't', 't', 'c',\n 'c', 't', 't', 'T', 'A', 'T', 'A', 'G', 'C', 'A', 'A', 'G', 'C',\n 'A', 'A', 'G', 'G', 'C', 'A', 'A', 'G', 'T', 'A', 'G', 'T', 'C',\n 'T', 'C', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'A', 'A', 'G', 'G',\n 'C', 'A', 'T', 'g', 'g', 'a', 'g', 'a', 'g', 'a', 'a', 't', 'g',\n 'g', 'g', 'g', 'a', 'g', 'a', 'g', 'g', 'a', 'g', 'g', 'a', 'a',\n 'a', 'g', 'g', 'a', 'g', 'g', 'a', 'g', 'a', 'g', 'g', 'g', 'g',\n 'a', 'g', 'g', 'a', 'g', 'a', 'g', 'g', 'a', 'g', 'g', 'g', 'g',\n 'a', 'g', 'G', 'T', 'A', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 1520)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018644 : 3018644 + 178],\n \"AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTCTGAGTGTCAGTGATGTTCATGAGATTATCACCAGCAAGGATGGCTGACGGGAACTGCAAGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATGCACTGTTTCAGCATCT\",\n )\n self.assertEqual(\n alignment[0],\n \"AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTC---TGAGTGTCAGTGATGTTCA-TGAGATTATCACCAGCAAGGATG--GCTGACGGGAACTG---CAAGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATG--------------------------CACTGTTTCAGCATCT\",\n )\n self.assertEqual(alignment.sequences[1].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[1].seq), 125616256)\n self.assertEqual(\n alignment.sequences[1].seq[47545632 : 47545632 + 204],\n \"AAATTCTTCAATAGGGAAATTTTATATTTCATATTACAATTCTATTCTATCCATGATCTTTCCTCTCATTTTAGAGTTCTGGCTGGTGGTATTTGCTTCTGATTCCATCAACCGCATCCTTAGGAGAGGATCTCAGTATCCATCACTTACACGCATGTGAATAAACTCAATGTGCTATCCCTCCCAGGGGCATTTGCCTTTTCT\",\n )\n self.assertEqual(\n alignment[1],\n \"AGAAAAGGCAAATGCCCCTGGGAGGGA-----TAGCACATTGA--GTTTATTCACATGCGTGTAAGTGATGGATACTGAGATCCTCTCC--TAAGGATGCGGTTGATGGAATCAGAAGCAAATACCACCAGCCAGAACTCTAAAATGAGAGGAAAGATCATGGATAGAATAGAATTGTAATATGAAATATAAAATTTCCCTATTGAAGAATTT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 160)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 2)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3018644, 3018671, 3018676, 3018687, 3018689, 3018697,\n 3018697, 3018716, 3018716, 3018729, 3018731, 3018739,\n 3018739, 3018753, 3018753, 3018806, 3018806, 3018822],\n [47545836, 47545809, 47545809, 47545798, 47545798, 47545790,\n 47545787, 47545768, 47545767, 47545754, 47545754, 47545746,\n 47545744, 47545730, 47545727, 47545674, 47545648, 47545632],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018644 AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTC---TGAG\n 0 ||...||||.||...||.|||||.|.|-----|.|.|.|.|||--||.|.|||---||.|\ncanFam2.c 47545836 AGAAAAGGCAAATGCCCCTGGGAGGGA-----TAGCACATTGA--GTTTATTCACATGCG\n\nmm9.chr10 3018701 TGTCAGTGATGTTCA-TGAGATTATCACCAGCAAGGATG--GCTGACGGGAACTG---CA\n 60 |||.|||||||...|-||||||..||.||--.|||||||--|.|||.||.|.|.|---||\ncanFam2.c 47545783 TGTAAGTGATGGATACTGAGATCCTCTCC--TAAGGATGCGGTTGATGGAATCAGAAGCA\n\nmm9.chr10 3018755 AGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATG---------\n 120 |....||....||.||..||||||......|||||..|||..||.||.||.---------\ncanFam2.c 47545725 AATACCACCAGCCAGAACTCTAAAATGAGAGGAAAGATCATGGATAGAATAGAATTGTAA\n\nmm9.chr10 3018806 -----------------CACTGTTTCAGCATCT 3018822\n 180 -----------------|.||.||..||.||.| 213\ncanFam2.c 47545665 TATGAAATATAAAATTTCCCTATTGAAGAATTT 47545632\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=1520.000000\ns mm9.chr10 3018644 178 + 129993255 AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTC---TGAGTGTCAGTGATGTTCA-TGAGATTATCACCAGCAAGGATG--GCTGACGGGAACTG---CAAGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATG--------------------------CACTGTTTCAGCATCT\ns canFam2.chr1 78070420 204 - 125616256 AGAAAAGGCAAATGCCCCTGGGAGGGA-----TAGCACATTGA--GTTTATTCACATGCGTGTAAGTGATGGATACTGAGATCCTCTCC--TAAGGATGCGGTTGATGGAATCAGAAGCAAATACCACCAGCCAGAACTCTAAAATGAGAGGAAAGATCATGGATAGAATAGAATTGTAATATGAAATATAAAATTTCCCTATTGAAGAATTT\nq canFam2.chr1 999999999999999999999999999-----99999999999--99999999999999999999999999999999999999999999--99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni canFam2.chr1 N 0 I 160\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'G', 'G', 'G', 'T', 'A', 'G', 'G', 'C', 'C', 'A', 'A', 'G',\n 'T', 'G', 'C', 'C', 'T', 'T', 'G', 'G', 'G', 'A', 'A', 'G', 'T',\n 'A', 'G', 'T', 'T', 'G', 'T', 'T', 'G', 'G', 'T', 'A', 'G', 'A',\n 'C', 'T', 'G', 'A', 'A', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'T',\n 'C', '-', '-', '-', 'T', 'G', 'A', 'G', 'T', 'G', 'T', 'C', 'A',\n 'G', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'C', 'A', '-', 'T', 'G',\n 'A', 'G', 'A', 'T', 'T', 'A', 'T', 'C', 'A', 'C', 'C', 'A', 'G',\n 'C', 'A', 'A', 'G', 'G', 'A', 'T', 'G', '-', '-', 'G', 'C', 'T',\n 'G', 'A', 'C', 'G', 'G', 'G', 'A', 'A', 'C', 'T', 'G', '-', '-',\n '-', 'C', 'A', 'A', 'G', 'A', 'G', 'G', 'C', 'A', 'T', 'A', 'G',\n 'C', 'C', 'C', 'T', 'G', 'A', 'G', 'T', 'T', 'C', 'T', 'A', 'A',\n 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'G', 'A', 'A', 'A', 'C',\n 'G', 'T', 'C', 'A', 'C', 'A', 'G', 'A', 'A', 'A', 'G', 'G', 'A',\n 'T', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'C', 'A', 'C', 'T', 'G', 'T', 'T', 'T', 'C', 'A', 'G',\n 'C', 'A', 'T', 'C', 'T'],\n ['A', 'G', 'A', 'A', 'A', 'A', 'G', 'G', 'C', 'A', 'A', 'A', 'T',\n 'G', 'C', 'C', 'C', 'C', 'T', 'G', 'G', 'G', 'A', 'G', 'G', 'G',\n 'A', '-', '-', '-', '-', '-', 'T', 'A', 'G', 'C', 'A', 'C', 'A',\n 'T', 'T', 'G', 'A', '-', '-', 'G', 'T', 'T', 'T', 'A', 'T', 'T',\n 'C', 'A', 'C', 'A', 'T', 'G', 'C', 'G', 'T', 'G', 'T', 'A', 'A',\n 'G', 'T', 'G', 'A', 'T', 'G', 'G', 'A', 'T', 'A', 'C', 'T', 'G',\n 'A', 'G', 'A', 'T', 'C', 'C', 'T', 'C', 'T', 'C', 'C', '-', '-',\n 'T', 'A', 'A', 'G', 'G', 'A', 'T', 'G', 'C', 'G', 'G', 'T', 'T',\n 'G', 'A', 'T', 'G', 'G', 'A', 'A', 'T', 'C', 'A', 'G', 'A', 'A',\n 'G', 'C', 'A', 'A', 'A', 'T', 'A', 'C', 'C', 'A', 'C', 'C', 'A',\n 'G', 'C', 'C', 'A', 'G', 'A', 'A', 'C', 'T', 'C', 'T', 'A', 'A',\n 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'A', 'A', 'G',\n 'A', 'T', 'C', 'A', 'T', 'G', 'G', 'A', 'T', 'A', 'G', 'A', 'A',\n 'T', 'A', 'G', 'A', 'A', 'T', 'T', 'G', 'T', 'A', 'A', 'T', 'A',\n 'T', 'G', 'A', 'A', 'A', 'T', 'A', 'T', 'A', 'A', 'A', 'A', 'T',\n 'T', 'T', 'C', 'C', 'C', 'T', 'A', 'T', 'T', 'G', 'A', 'A', 'G',\n 'A', 'A', 'T', 'T', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 1986)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018822 : 3018822 + 110],\n \"CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACAGAAGAGAACCTAACTTGCTTAGGAGCATATGTACAGTTAATCAAGACAAAAATAAGAATGGAGACt\",\n )\n self.assertEqual(\n alignment[0],\n \"CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACA----GAAGAGAACCTAACTTG-CTTAGGAGCATATGTACAGTTAATCAAGAC-----AAAAATAAGAATGGAGACt\",\n )\n self.assertEqual(alignment.sequences[1].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[1].seq), 125616256)\n self.assertEqual(\n alignment.sequences[1].seq[47545353 : 47545353 + 119],\n \"ATTTTCCATACTTATTTTTAGTTGATCTTGCTAAATTGTGTGCATCTCTAGAAGTCGATTTGAATTCCCTTTACAATGTGGAGAATTTTAAGTGAGTAATAATGGGCAGGGAAAAAAAG\",\n )\n self.assertEqual(\n alignment[1],\n \"CTTTTTTTCCCTGCCCATTATTACTCACTTAAAATTCTCC-ACATTGTAAAGGGAATTCAAATCGACTTCTAGAGATGCACACAATTTAGCAAGATCAACTAAAAATAAGTATGGAAAAT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 160)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 2)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3018822, 3018862, 3018863, 3018866, 3018866, 3018883,\n 3018883, 3018913, 3018913, 3018932],\n [47545472, 47545432, 47545432, 47545429, 47545425, 47545408,\n 47545407, 47545377, 47545372, 47545353],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018822 CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACA----GAAGAGAACCTA\n 0 ||...||.|..|.|...|||.|..|||||||.||..||||-|||----.|||.|||...|\ncanFam2.c 47545472 CTTTTTTTCCCTGCCCATTATTACTCACTTAAAATTCTCC-ACATTGTAAAGGGAATTCA\n\nmm9.chr10 3018878 ACTTG-CTTAGGAGCATATGTACAGTTAATCAAGAC-----AAAAATAAGAATGGAGACt\n 60 |.|.|-|||......||....|||.||.|.|||||.-----|||||||||.|||||.|..\ncanFam2.c 47545413 AATCGACTTCTAGAGATGCACACAATTTAGCAAGATCAACTAAAAATAAGTATGGAAAAT\n\nmm9.chr10 3018932 \n 120 \ncanFam2.c 47545353 \n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=1986.000000\ns mm9.chr10 3018822 110 + 129993255 CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACA----GAAGAGAACCTAACTTG-CTTAGGAGCATATGTACAGTTAATCAAGAC-----AAAAATAAGAATGGAGACt\ns canFam2.chr1 78070784 119 - 125616256 CTTTTTTTCCCTGCCCATTATTACTCACTTAAAATTCTCC-ACATTGTAAAGGGAATTCAAATCGACTTCTAGAGATGCACACAATTTAGCAAGATCAACTAAAAATAAGTATGGAAAAT\nq canFam2.chr1 9999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999\ni canFam2.chr1 I 160 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'T', 'G', 'C', 'C', 'T', 'T', 'C', 'C', 'A', 'T', 'T', 'A',\n 'C', 'G', 'A', 'T', 'T', 'T', 'A', 'C', 'T', 'G', 'A', 'T', 'C',\n 'A', 'C', 'T', 'T', 'A', 'C', 'A', 'A', 'C', 'C', 'C', 'T', 'C',\n 'C', 'C', 'A', 'C', 'A', '-', '-', '-', '-', 'G', 'A', 'A', 'G',\n 'A', 'G', 'A', 'A', 'C', 'C', 'T', 'A', 'A', 'C', 'T', 'T', 'G',\n '-', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'G', 'C', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'C', 'A', 'G', 'T', 'T', 'A', 'A', 'T', 'C',\n 'A', 'A', 'G', 'A', 'C', '-', '-', '-', '-', '-', 'A', 'A', 'A',\n 'A', 'A', 'T', 'A', 'A', 'G', 'A', 'A', 'T', 'G', 'G', 'A', 'G',\n 'A', 'C', 't'],\n ['C', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'C', 'C', 'T', 'G',\n 'C', 'C', 'C', 'A', 'T', 'T', 'A', 'T', 'T', 'A', 'C', 'T', 'C',\n 'A', 'C', 'T', 'T', 'A', 'A', 'A', 'A', 'T', 'T', 'C', 'T', 'C',\n 'C', '-', 'A', 'C', 'A', 'T', 'T', 'G', 'T', 'A', 'A', 'A', 'G',\n 'G', 'G', 'A', 'A', 'T', 'T', 'C', 'A', 'A', 'A', 'T', 'C', 'G',\n 'A', 'C', 'T', 'T', 'C', 'T', 'A', 'G', 'A', 'G', 'A', 'T', 'G',\n 'C', 'A', 'C', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'A', 'G', 'C',\n 'A', 'A', 'G', 'A', 'T', 'C', 'A', 'A', 'C', 'T', 'A', 'A', 'A',\n 'A', 'A', 'T', 'A', 'A', 'G', 'T', 'A', 'T', 'G', 'G', 'A', 'A',\n 'A', 'A', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018932 : 3018932 + 339],\n \"gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaaaaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtgggggcatggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatccaaaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacccacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaatggcaccactcctggtccaagaatatacaaaccatgaca\",\n )\n self.assertEqual(\n alignment[0],\n \"gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaaaaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtgggggcatggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatccaaaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacccacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaatggcaccactcctggtccaagaatatacaaaccatgaca\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47545353, 47545353))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][9]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 10)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3018932, 3019271]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018932 gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaa\n\nmm9.chr10 3018992 aaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtggggg\n\nmm9.chr10 3019052 catggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatcca\n\nmm9.chr10 3019112 aaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacc\n\nmm9.chr10 3019172 cacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaa\n\nmm9.chr10 3019232 tggcaccactcctggtccaagaatatacaaaccatgaca 3019271\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3018932 339 + 129993255 gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaaaaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtgggggcatggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatccaaaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacccacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaatggcaccactcctggtccaagaatatacaaaccatgaca\ne canFam2.chr1 47545353 0 + 125616256 C\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['g', 't', 'c', 't', 'g', 'a', 'g', 't', 't', 'a', 'g', 'g', 'g',\n 't', 't', 't', 't', 'a', 'c', 't', 'g', 'c', 't', 'g', 't', 'g',\n 'a', 'a', 'c', 'a', 'g', 'a', 'c', 'a', 'c', 'c', 'a', 't', 'g',\n 'a', 'c', 'c', 'a', 'a', 'g', 'g', 'c', 'a', 't', 'g', 't', 'c',\n 't', 't', 'a', 't', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 't',\n 't', 't', 'a', 'a', 't', 't', 'a', 'g', 'g', 'g', 'c', 't', 'g',\n 'g', 'c', 't', 't', 'a', 'c', 'a', 'g', 'a', 't', 't', 'c', 'a',\n 'g', 'a', 'g', 'g', 't', 't', 'c', 'a', 'g', 't', 'g', 'g', 'g',\n 'a', 'g', 'c', 'a', 't', 'c', 'a', 'a', 'g', 'g', 't', 'g', 'g',\n 'g', 'g', 'g', 'c', 'a', 't', 'g', 'g', 'c', 'a', 'g', 'c', 'a',\n 't', 'c', 'c', 'a', 'g', 'g', 'c', 'a', 'g', 'g', 'c', 'a', 't',\n 'g', 'g', 't', 'g', 'c', 'a', 'g', 'g', 'c', 'a', 'g', 'a', 'g',\n 'c', 't', 'g', 'a', 'g', 'a', 'g', 't', 't', 'c', 't', 'a', 'c',\n 'a', 't', 'c', 't', 't', 'c', 'a', 't', 'c', 'c', 'a', 'a', 'a',\n 'g', 'g', 'c', 't', 't', 'c', 't', 'a', 'g', 't', 'g', 'g', 'a',\n 'a', 'g', 'a', 'c', 't', 'g', 'a', 'c', 't', 't', 'c', 'c', 'a',\n 'g', 'g', 'c', 'a', 'c', 'c', 't', 'a', 'g', 'g', 'g', 't', 'g',\n 'a', 'g', 'g', 'g', 't', 'c', 't', 't', 'a', 'a', 'g', 'c', 'c',\n 'c', 'a', 'c', 'a', 'c', 'c', 'c', 'a', 'c', 'a', 'g', 't', 'g',\n 'a', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'a', 't', 't', 'c', 'c',\n 'a', 'a', 'c', 'c', 'a', 'g', 'g', 't', 'c', 'a', 'c', 'a', 'c',\n 'c', 't', 'a', 't', 't', 'c', 'c', 'a', 'a', 'c', 'a', 'a', 'g',\n 'g', 'c', 'c', 'a', 't', 'a', 'c', 'c', 't', 'c', 'c', 'a', 'a',\n 'a', 't', 'g', 'g', 'c', 'a', 'c', 'c', 'a', 'c', 't', 'c', 'c',\n 't', 'g', 'g', 't', 'c', 'c', 'a', 'a', 'g', 'a', 'a', 't', 'a',\n 't', 'a', 'c', 'a', 'a', 'a', 'c', 'c', 'a', 't', 'g', 'a', 'c',\n 'a']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 228)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019271 : 3019271 + 106],\n \"GAGACCAAATGTGGCGCTCACGTGAGGCCAGGAGTAAATCGCACACACAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG\",\n )\n self.assertEqual(\n alignment[0],\n \"GAGACCAAATG------------TGGCGCTCACG-TGAGGCCAGGAGTAAATCGCACACACAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[1].seq), 125616256)\n self.assertEqual(\n alignment.sequences[1].seq[47545247 : 47545247 + 106],\n \"CCAGGTTTGGGACCTATGTGTGTCAAGTGAATAGAAGCAGGTGGGACAGCATGTGCGTCACACATGGACACAGCCTGGACATCGTGGGGCATTTTCCATTTGCCTC\",\n )\n self.assertEqual(\n alignment[1],\n \"GAGGC-AAATGGAAAATGCCCCACGATGTCCAGGCTGTGTCCATGTGTGA--CGCACATGCTGTCC----------CACCTGCTTCTATTCACTTGACACACATAGGTCCCAAACCTGG\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 2)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019271, 3019276, 3019277, 3019282, 3019282, 3019293,\n 3019293, 3019308, 3019310, 3019324, 3019334, 3019377],\n [47545353, 47545348, 47545348, 47545343, 47545331, 47545320,\n 47545319, 47545304, 47545304, 47545290, 47545290, 47545247],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019271 GAGACCAAATG------------TGGCGCTCACG-TGAGGCCAGGAGTAAATCGCACACA\n 0 |||.|-|||||------------.|..|..||.|-||.|.|||.|.||.|--||||||..\ncanFam2.c 47545353 GAGGC-AAATGGAAAATGCCCCACGATGTCCAGGCTGTGTCCATGTGTGA--CGCACATG\n\nmm9.chr10 3019318 CAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG\n 60 |.|.||----------||.|||||....|.|.||.||.......|||...|.|||||||\ncanFam2.c 47545296 CTGTCC----------CACCTGCTTCTATTCACTTGACACACATAGGTCCCAAACCTGG\n\nmm9.chr10 3019377\n 119\ncanFam2.c 47545247\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=228.000000\ns mm9.chr10 3019271 106 + 129993255 GAGACCAAATG------------TGGCGCTCACG-TGAGGCCAGGAGTAAATCGCACACACAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG\ns canFam2.chr1 78070903 106 - 125616256 GAGGC-AAATGGAAAATGCCCCACGATGTCCAGGCTGTGTCCATGTGTGA--CGCACATGCTGTCC----------CACCTGCTTCTATTCACTTGACACACATAGGTCCCAAACCTGG\nq canFam2.chr1 99999-99999999999999999999999999999999999999999999--99999999999999----------9999999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['G', 'A', 'G', 'A', 'C', 'C', 'A', 'A', 'A', 'T', 'G', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'G', 'G',\n 'C', 'G', 'C', 'T', 'C', 'A', 'C', 'G', '-', 'T', 'G', 'A', 'G',\n 'G', 'C', 'C', 'A', 'G', 'G', 'A', 'G', 'T', 'A', 'A', 'A', 'T',\n 'C', 'G', 'C', 'A', 'C', 'A', 'C', 'A', 'C', 'A', 'G', 'C', 'C',\n 'C', 'A', 'T', 'G', 'C', 'T', 'T', 'T', 'C', 'A', 'C', 'C', 'A',\n 'T', 'C', 'T', 'G', 'C', 'T', 'A', 'G', 'G', 'G', 'T', 'G', 'C',\n 'T', 'C', 'T', 'G', 'G', 'A', 'G', 'C', 'A', 'G', 'G', 'G', 'C',\n 'A', 'G', 'G', 'C', 'T', 'T', 'C', 'T', 'A', 'A', 'C', 'C', 'T',\n 'G', 'G'],\n ['G', 'A', 'G', 'G', 'C', '-', 'A', 'A', 'A', 'T', 'G', 'G', 'A',\n 'A', 'A', 'A', 'T', 'G', 'C', 'C', 'C', 'C', 'A', 'C', 'G', 'A',\n 'T', 'G', 'T', 'C', 'C', 'A', 'G', 'G', 'C', 'T', 'G', 'T', 'G',\n 'T', 'C', 'C', 'A', 'T', 'G', 'T', 'G', 'T', 'G', 'A', '-', '-',\n 'C', 'G', 'C', 'A', 'C', 'A', 'T', 'G', 'C', 'T', 'G', 'T', 'C',\n 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A',\n 'C', 'C', 'T', 'G', 'C', 'T', 'T', 'C', 'T', 'A', 'T', 'T', 'C',\n 'A', 'C', 'T', 'T', 'G', 'A', 'C', 'A', 'C', 'A', 'C', 'A', 'T',\n 'A', 'G', 'G', 'T', 'C', 'C', 'C', 'A', 'A', 'A', 'C', 'C', 'T',\n 'G', 'G']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 10938)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019377 : 3019377 + 88],\n \"CCCCAGCATTCTGGCAGACACAGTGAAAAGAGACAGATGGTCACTAATAAAATCTGTATAAATTAGATCTCAGAGGATGGATGGACCA\",\n )\n self.assertEqual(\n alignment[0],\n \"CCCCAGCATTCTGGCAGACACAGTG-AAAAGAGACAGATGGTCACTAATAAAATCTGT-ATAAATTAG-ATCTCAGAGGATGGATGGACCA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[1].seq), 119354)\n self.assertEqual(\n alignment.sequences[1].seq[46757 : 46757 + 88],\n \"GAGTCCCATCCTCTGAGATTCTAGTTCACCACAAAGCTTACTGGTGGGCACATGCTTCTTTTTCACATTAGCTATCAGAACACTTGGG\",\n )\n self.assertEqual(\n alignment[1],\n \"CCCAAGTGTTCTGATAGCTAATGTGAAAAAGAAGCATGTGCCCACCAGTAAGCTTTGTGGTGAACTAGAATCTCAGAGGATG---GGACTC\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[2].seq), 125616256)\n self.assertEqual(\n alignment.sequences[2].seq[47545159 : 47545159 + 88],\n \"gagtcccatcctctgagattctaggtcattgcaaatctTATTAGCGGGCCCATGTTTCTTTTTCACAGAGGCAATCAGAACACTTGGG\",\n )\n self.assertEqual(\n alignment[2],\n \"CCCAAGTGTTCTGATTGCCTCTGTGAAAAAGAAACATGGGCCCGCTAATAagatttgcaatgacctagaatctcagaggatg---ggactc\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 3)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019377, 3019402, 3019402, 3019434, 3019434, 3019443,\n 3019443, 3019456, 3019459, 3019465],\n [ 46845, 46820, 46819, 46787, 46786, 46777,\n 46776, 46763, 46763, 46757],\n [47545247, 47545222, 47545221, 47545189, 47545188, 47545179,\n 47545178, 47545165, 47545165, 47545159],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019377 CCCCAGCATTCTGGCAGACACAGTG-AAAAGAGACAGATGGTCACTAATAAAATCTGT-A\nfelCat3.s 46845 CCCAAGTGTTCTGATAGCTAATGTGAAAAAGAAGCATGTGCCCACCAGTAAGCTTTGTGG\ncanFam2.c 47545247 CCCAAGTGTTCTGATTGCCTCTGTGAAAAAGAAACATGGGCCCGCTAATAagatttgcaa\n\nmm9.chr10 3019435 TAAATTAG-ATCTCAGAGGATGGATGGACCA 3019465\nfelCat3.s 46785 TGAACTAGAATCTCAGAGGATG---GGACTC 46757\ncanFam2.c 47545187 tgacctagaatctcagaggatg---ggactc 47545159\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=10938.000000\ns mm9.chr10 3019377 88 + 129993255 CCCCAGCATTCTGGCAGACACAGTG-AAAAGAGACAGATGGTCACTAATAAAATCTGT-ATAAATTAG-ATCTCAGAGGATGGATGGACCA\ns felCat3.scaffold_205680 72509 88 - 119354 CCCAAGTGTTCTGATAGCTAATGTGAAAAAGAAGCATGTGCCCACCAGTAAGCTTTGTGGTGAACTAGAATCTCAGAGGATG---GGACTC\nq felCat3.scaffold_205680 9999999999999999999999999999999999999999999999999999999999999999999999999999999999---999999\ni felCat3.scaffold_205680 N 0 C 0\ns canFam2.chr1 78071009 88 - 125616256 CCCAAGTGTTCTGATTGCCTCTGTGAAAAAGAAACATGGGCCCGCTAATAagatttgcaatgacctagaatctcagaggatg---ggactc\nq canFam2.chr1 9999999999999999999999999999999999999999999999999999999999999999999999999999999999---999999\ni canFam2.chr1 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'C', 'C', 'C', 'A', 'G', 'C', 'A', 'T', 'T', 'C', 'T', 'G',\n 'G', 'C', 'A', 'G', 'A', 'C', 'A', 'C', 'A', 'G', 'T', 'G', '-',\n 'A', 'A', 'A', 'A', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'A', 'T',\n 'G', 'G', 'T', 'C', 'A', 'C', 'T', 'A', 'A', 'T', 'A', 'A', 'A',\n 'A', 'T', 'C', 'T', 'G', 'T', '-', 'A', 'T', 'A', 'A', 'A', 'T',\n 'T', 'A', 'G', '-', 'A', 'T', 'C', 'T', 'C', 'A', 'G', 'A', 'G',\n 'G', 'A', 'T', 'G', 'G', 'A', 'T', 'G', 'G', 'A', 'C', 'C', 'A'],\n ['C', 'C', 'C', 'A', 'A', 'G', 'T', 'G', 'T', 'T', 'C', 'T', 'G',\n 'A', 'T', 'A', 'G', 'C', 'T', 'A', 'A', 'T', 'G', 'T', 'G', 'A',\n 'A', 'A', 'A', 'A', 'G', 'A', 'A', 'G', 'C', 'A', 'T', 'G', 'T',\n 'G', 'C', 'C', 'C', 'A', 'C', 'C', 'A', 'G', 'T', 'A', 'A', 'G',\n 'C', 'T', 'T', 'T', 'G', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'C',\n 'T', 'A', 'G', 'A', 'A', 'T', 'C', 'T', 'C', 'A', 'G', 'A', 'G',\n 'G', 'A', 'T', 'G', '-', '-', '-', 'G', 'G', 'A', 'C', 'T', 'C'],\n ['C', 'C', 'C', 'A', 'A', 'G', 'T', 'G', 'T', 'T', 'C', 'T', 'G',\n 'A', 'T', 'T', 'G', 'C', 'C', 'T', 'C', 'T', 'G', 'T', 'G', 'A',\n 'A', 'A', 'A', 'A', 'G', 'A', 'A', 'A', 'C', 'A', 'T', 'G', 'G',\n 'G', 'C', 'C', 'C', 'G', 'C', 'T', 'A', 'A', 'T', 'A', 'a', 'g',\n 'a', 't', 't', 't', 'g', 'c', 'a', 'a', 't', 'g', 'a', 'c', 'c',\n 't', 'a', 'g', 'a', 'a', 't', 'c', 't', 'c', 'a', 'g', 'a', 'g',\n 'g', 'a', 't', 'g', '-', '-', '-', 'g', 'g', 'a', 'c', 't', 'c']],\n dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 36924)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019465 : 3019465 + 47],\n \"AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT\",\n )\n self.assertEqual(\n alignment[0], \"AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT\"\n )\n self.assertEqual(alignment.sequences[1].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[1].seq), 133105)\n self.assertEqual(\n alignment.sequences[1].seq[10128 : 10128 + 47],\n \"aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC\",\n )\n self.assertEqual(\n alignment[1], \"aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC\"\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 3479)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157515703 : 157515703 + 40],\n \"AAAACAcatcagaataacatgaaaagccatttcaaaatat\",\n )\n self.assertEqual(\n alignment[2], \"-------atattttgaaatggcttttcatgttattctgatgTGTTTT\"\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 2400)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155025648 : 155025648 + 40],\n \"AAAACAcatcagaataacatgaaaagccatttcaaaatat\",\n )\n self.assertEqual(\n alignment[3], \"-------atattttgaaatggcttttcatgttattctgatgTGTTTT\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 2402)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[4].seq), 125616256)\n self.assertEqual(\n alignment.sequences[4].seq[47545115 : 47545115 + 44],\n \"aacacacattagaacaacatgaagagctatttttaaatatacct\",\n )\n self.assertEqual(\n alignment[4], \"---aggtatatttaaaaatagctcttcatgttgttctaatgtgtgtt\"\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[5].seq), 119354)\n self.assertEqual(\n alignment.sequences[5].seq[46714 : 46714 + 43],\n \"AACACACATCAGAACAACATGAAAACTATTTTTAAAAACACGT\",\n )\n self.assertEqual(\n alignment[5], \"---ACGTGTTTTTAAAAATAG-TTTTCATGTTGTTCTGATGTGTGTT\"\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 193)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 6)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019465, 3019468, 3019472, 3019486, 3019487, 3019512],\n [ 10128, 10131, 10135, 10149, 10150, 10175],\n [157515743, 157515743, 157515743, 157515729, 157515728, 157515703],\n [155025688, 155025688, 155025688, 155025674, 155025673, 155025648],\n [ 47545159, 47545159, 47545155, 47545141, 47545140, 47545115],\n [ 46757, 46757, 46753, 46739, 46739, 46714],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019465 AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT 3019512\ncalJac1.C 10128 aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC 10175\npanTro2.c 157515743 -------atattttgaaatggcttttcatgttattctgatgTGTTTT 157515703\nhg18.chr6 155025688 -------atattttgaaatggcttttcatgttattctgatgTGTTTT 155025648\ncanFam2.c 47545159 ---aggtatatttaaaaatagctcttcatgttgttctaatgtgtgtt 47545115\nfelCat3.s 46757 ---ACGTGTTTTTAAAAATAG-TTTTCATGTTGTTCTGATGTGTGTT 46714\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=36924.000000\ns mm9.chr10 3019465 47 + 129993255 AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT\ns calJac1.Contig6394 10128 47 + 133105 aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC\ni calJac1.Contig6394 I 3479 C 0\ns panTro2.chr6 16392869 40 - 173908612 -------atattttgaaatggcttttcatgttattctgatgTGTTTT\nq panTro2.chr6 -------9999999999999999999999999999999999999999\ni panTro2.chr6 I 2400 C 0\ns hg18.chr6 15874304 40 - 170899992 -------atattttgaaatggcttttcatgttattctgatgTGTTTT\ni hg18.chr6 I 2402 C 0\ns canFam2.chr1 78071097 44 - 125616256 ---aggtatatttaaaaatagctcttcatgttgttctaatgtgtgtt\nq canFam2.chr1 ---99999999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ns felCat3.scaffold_205680 72597 43 - 119354 ---ACGTGTTTTTAAAAATAG-TTTTCATGTTGTTCTGATGTGTGTT\nq felCat3.scaffold_205680 ---999999999999999999-9999999999999999999999999\ni felCat3.scaffold_205680 C 0 I 193\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'A', 'G', 'A', 'T', 'A', 'G', 'A', 'T', 'A', 'T', 'T', 'T',\n 'A', 'G', 'A', 'A', 'G', 'T', 'A', 'G', 'C', 'T', 'T', 'T', 'T',\n 'T', 'A', 'T', 'G', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'G', 'A',\n 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'T'],\n ['a', 'a', 'c', 'a', 'T', 'C', 'T', 'A', 'T', 'A', 'T', 'T', 'T',\n 'T', 'G', 'A', 'A', 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'T', 'T',\n 'C', 'A', 'T', 'G', 'T', 'T', 'A', 'C', 'T', 'C', 'T', 'G', 'A',\n 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'C'],\n ['-', '-', '-', '-', '-', '-', '-', 'a', 't', 'a', 't', 't', 't',\n 't', 'g', 'a', 'a', 'a', 't', 'g', 'g', 'c', 't', 't', 't', 't',\n 'c', 'a', 't', 'g', 't', 't', 'a', 't', 't', 'c', 't', 'g', 'a',\n 't', 'g', 'T', 'G', 'T', 'T', 'T', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', 'a', 't', 'a', 't', 't', 't',\n 't', 'g', 'a', 'a', 'a', 't', 'g', 'g', 'c', 't', 't', 't', 't',\n 'c', 'a', 't', 'g', 't', 't', 'a', 't', 't', 'c', 't', 'g', 'a',\n 't', 'g', 'T', 'G', 'T', 'T', 'T', 'T'],\n ['-', '-', '-', 'a', 'g', 'g', 't', 'a', 't', 'a', 't', 't', 't',\n 'a', 'a', 'a', 'a', 'a', 't', 'a', 'g', 'c', 't', 'c', 't', 't',\n 'c', 'a', 't', 'g', 't', 't', 'g', 't', 't', 'c', 't', 'a', 'a',\n 't', 'g', 't', 'g', 't', 'g', 't', 't'],\n ['-', '-', '-', 'A', 'C', 'G', 'T', 'G', 'T', 'T', 'T', 'T', 'T',\n 'A', 'A', 'A', 'A', 'A', 'T', 'A', 'G', '-', 'T', 'T', 'T', 'T',\n 'C', 'A', 'T', 'G', 'T', 'T', 'G', 'T', 'T', 'C', 'T', 'G', 'A',\n 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 20303)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019512 : 3019512 + 92],\n \"TGCATCATTAAGACTAGAGTTCCTTTCTGTCTTTGCTTTCTTGACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg\",\n )\n self.assertEqual(\n alignment[0],\n \"TGCATCATTAAGACTAGAGTTCCT---------------TTCTGTCTT---TGCTTTCTTG--------ACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg\",\n )\n self.assertEqual(alignment.sequences[1].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[1].seq), 133105)\n self.assertEqual(\n alignment.sequences[1].seq[10175 : 10175 + 86],\n \"CCTCATGAAGGCCCAAGTTCCTAAAACATTAATTCTCTTCCTATTTCCTAGCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC\",\n )\n self.assertEqual(\n alignment[1],\n \"--CCTCATGAAGGCCCAAGTTCCTAAA-----ACATTAATTCTCTTCC---TATTTCCTAGCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC----------------------\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157515610 : 157515610 + 93],\n \"CCAATACCCATGTGGGAATTGCTGGCGGGCAAGACCTCTTTTCTAGAAAAGAGGAAGAGAATGAATGTTTTAGGAACTTGGGCCTTAATGAAG\",\n )\n self.assertEqual(\n alignment[2],\n \"--CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155025555 : 155025555 + 93],\n \"CCAATACCCATGTGGGAATTGCTGGCGGGCAAGACCTCTTTTCTAGAAAAGAGGAAGAGAATGAATGTTTTAGGAACTTGGGCCTTAATGAAG\",\n )\n self.assertEqual(\n alignment[3],\n \"--CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[4].seq), 125616256)\n self.assertEqual(\n alignment.sequences[4].seq[47545018 : 47545018 + 97],\n \"CCGAACAAAGTAGGAATGACTGGCAGGCAAGACACTGATGAGGAAGGGTTGAAGAAAGAAAAAATATAAGCCTGTAAGAACCTGGGTTTAGATGAGG\",\n )\n self.assertEqual(\n alignment[4],\n \"--CCTCATCTAAACCCAGGTTCTTACAGGCTTATATTTTTTCTTTCTTCAACCCTTCCTCA--------TCAGTGTCTTGCCTGCCAGTCATTCCTAC-----------TTTGTTCGG\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (46714, 46521))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 5)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 7)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019512, 3019514, 3019536, 3019536, 3019536, 3019536,\n 3019545, 3019545, 3019555, 3019555, 3019555, 3019582,\n 3019584, 3019595, 3019604],\n [ 10175, 10175, 10197, 10200, 10200, 10207,\n 10216, 10216, 10226, 10232, 10234, 10261,\n 10261, 10261, 10261],\n [157515703, 157515703, 157515681, 157515678, 157515678, 157515671,\n 157515662, 157515662, 157515652, 157515652, 157515650, 157515623,\n 157515621, 157515610, 157515610],\n [155025648, 155025648, 155025626, 155025623, 155025623, 155025616,\n 155025607, 155025607, 155025597, 155025597, 155025595, 155025568,\n 155025566, 155025555, 155025555],\n [ 47545115, 47545115, 47545093, 47545090, 47545085, 47545078,\n 47545069, 47545066, 47545056, 47545056, 47545056, 47545029,\n 47545027, 47545027, 47545018],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019512 TGCATCATTAAGACTAGAGTTCCT---------------TTCTGTCTT---TGCTTTCTT\ncalJac1.C 10175 --CCTCATGAAGGCCCAAGTTCCTAAA-----ACATTAATTCTCTTCC---TATTTCCTA\npanTro2.c 157515703 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTA\nhg18.chr6 155025648 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTA\ncanFam2.c 47545115 --CCTCATCTAAACCCAGGTTCTTACAGGCTTATATTTTTTCTTTCTTCAACCCTTCCTC\n\nmm9.chr10 3019554 G--------ACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg\ncalJac1.C 10225 GCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC----------------------\npanTro2.c 157515653 G------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\nhg18.chr6 155025598 G------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\ncanFam2.c 47545057 A--------TCAGTGTCTTGCCTGCCAGTCATTCCTAC-----------TTTGTTCGG\n\nmm9.chr10 3019604\ncalJac1.C 10261\npanTro2.c 157515610\nhg18.chr6 155025555\ncanFam2.c 47545018\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=20303.000000\ns mm9.chr10 3019512 92 + 129993255 TGCATCATTAAGACTAGAGTTCCT---------------TTCTGTCTT---TGCTTTCTTG--------ACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg\ns calJac1.Contig6394 10175 86 + 133105 --CCTCATGAAGGCCCAAGTTCCTAAA-----ACATTAATTCTCTTCC---TATTTCCTAGCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC----------------------\ni calJac1.Contig6394 C 0 C 0\ns panTro2.chr6 16392909 93 - 173908612 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\nq panTro2.chr6 --9999999999999999999999999-----9999999999999999---9999999999------999999999999999999999999999999999999999999---------\ni panTro2.chr6 C 0 C 0\ns hg18.chr6 15874344 93 - 170899992 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\ni hg18.chr6 C 0 C 0\ns canFam2.chr1 78071141 97 - 125616256 --CCTCATCTAAACCCAGGTTCTTACAGGCTTATATTTTTTCTTTCTTCAACCCTTCCTCA--------TCAGTGTCTTGCCTGCCAGTCATTCCTAC-----------TTTGTTCGG\nq canFam2.chr1 --99999999999999999999999999999999999999999999999999999999999--------99999999999999999999999999999-----------999999999\ni canFam2.chr1 C 0 C 0\ne felCat3.scaffold_205680 72640 193 - 119354 I\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'G', 'C', 'A', 'T', 'C', 'A', 'T', 'T', 'A', 'A', 'G', 'A',\n 'C', 'T', 'A', 'G', 'A', 'G', 'T', 'T', 'C', 'C', 'T', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'T', 'T', 'C', 'T', 'G', 'T', 'C', 'T', 'T', '-', '-', '-', 'T',\n 'G', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'G', '-', '-', '-', '-',\n '-', '-', '-', '-', 'A', 'C', 'A', 'G', 'G', 'G', 'C', 'C', 'A',\n 'T', 'G', 'C', 'T', 'C', 'G', 'G', 'C', 'A', 'G', 'T', 'C', 'A',\n 'T', 'T', 'C', 'T', 'T', 'A', 'G', 'A', 'C', 'T', 'G', 'C', 'T',\n 'T', 'T', 'T', 'T', 'G', 'T', 'T', 'T', 'g', 't', 't', 't', 'g',\n 'g'],\n ['-', '-', 'C', 'C', 'T', 'C', 'A', 'T', 'G', 'A', 'A', 'G', 'G',\n 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'A', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'T', 'T', 'A', 'A',\n 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'C', 'C', '-', '-', '-', 'T',\n 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'G', 'C', 'T', 'G', 'T',\n 'C', 'T', 'C', 'G', 'C', 'C', 'T', 'A', 'G', 'G', 'C', 'C', 'T',\n 'T', 'G', 'C', 'C', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A',\n 'T', 'T', 'C', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-'],\n ['-', '-', 'C', 'T', 'T', 'C', 'A', 'T', 'T', 'A', 'A', 'G', 'G',\n 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'A', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'T', 'T', 'C', 'A',\n 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'C', 'C', '-', '-', '-', 'T',\n 'C', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'G', '-', '-', '-', '-',\n '-', '-', 'A', 'A', 'A', 'A', 'G', 'A', 'G', 'G', 'T', 'C', 'T',\n 'T', 'G', 'C', 'C', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A',\n 'T', 'T', 'C', 'C', 'C', 'A', 'C', 'A', 'T', 'G', 'G', 'G', 'T',\n 'A', 'T', 'T', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-',\n '-'],\n ['-', '-', 'C', 'T', 'T', 'C', 'A', 'T', 'T', 'A', 'A', 'G', 'G',\n 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'A', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'T', 'T', 'C', 'A',\n 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'C', 'C', '-', '-', '-', 'T',\n 'C', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'G', '-', '-', '-', '-',\n '-', '-', 'A', 'A', 'A', 'A', 'G', 'A', 'G', 'G', 'T', 'C', 'T',\n 'T', 'G', 'C', 'C', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A',\n 'T', 'T', 'C', 'C', 'C', 'A', 'C', 'A', 'T', 'G', 'G', 'G', 'T',\n 'A', 'T', 'T', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-',\n '-'],\n ['-', '-', 'C', 'C', 'T', 'C', 'A', 'T', 'C', 'T', 'A', 'A', 'A',\n 'C', 'C', 'C', 'A', 'G', 'G', 'T', 'T', 'C', 'T', 'T', 'A', 'C',\n 'A', 'G', 'G', 'C', 'T', 'T', 'A', 'T', 'A', 'T', 'T', 'T', 'T',\n 'T', 'T', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'C', 'A', 'A', 'C',\n 'C', 'C', 'T', 'T', 'C', 'C', 'T', 'C', 'A', '-', '-', '-', '-',\n '-', '-', '-', '-', 'T', 'C', 'A', 'G', 'T', 'G', 'T', 'C', 'T',\n 'T', 'G', 'C', 'C', 'T', 'G', 'C', 'C', 'A', 'G', 'T', 'C', 'A',\n 'T', 'T', 'C', 'C', 'T', 'A', 'C', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'T', 'T', 'T', 'G', 'T', 'T', 'C', 'G',\n 'G']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019604 : 3019604 + 98],\n \"tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctggaactcactttgtagaccagactggccttgaactcagaaa\",\n )\n self.assertEqual(\n alignment[0],\n \"tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctggaactcactttgtagaccagactggccttgaactcagaaa\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (46714, 46521))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47545018, 47545018))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (10261, 10261))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155025555, 155025555))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][9]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157515610, 157515610))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][10]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 11)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3019604, 3019702]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019604 tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctgga\n\nmm9.chr10 3019664 actcactttgtagaccagactggccttgaactcagaaa 3019702\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3019604 98 + 129993255 tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctggaactcactttgtagaccagactggccttgaactcagaaa\ne felCat3.scaffold_205680 72640 193 - 119354 I\ne canFam2.chr1 47545018 0 + 125616256 C\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 10261 0 + 133105 C\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 155025555 0 + 170899992 C\ne panTro2.chr6 157515610 0 + 173908612 C\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['t', 't', 't', 'g', 'g', 't', 't', 't', 'g', 'g', 't', 't', 't',\n 'g', 'g', 't', 't', 't', 't', 't', 't', 'c', 'a', 'a', 'g', 'a',\n 'c', 'a', 'g', 'g', 'g', 't', 't', 't', 'c', 't', 't', 't', 'g',\n 't', 'a', 't', 'a', 'g', 't', 'c', 'c', 't', 'a', 'g', 'c', 't',\n 'g', 't', 'c', 'c', 't', 'g', 'g', 'a', 'a', 'c', 't', 'c', 'a',\n 'c', 't', 't', 't', 'g', 't', 'a', 'g', 'a', 'c', 'c', 'a', 'g',\n 'a', 'c', 't', 'g', 'g', 'c', 'c', 't', 't', 'g', 'a', 'a', 'c',\n 't', 'c', 'a', 'g', 'a', 'a', 'a']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 45)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019702 : 3019702 + 42],\n \"tctgcctgcctctgcctcccaagtcctgggattaaaggcgtg\",\n )\n self.assertEqual(\n alignment[0],\n \"tctgcctgcctctgcctcccaag--------------------------------tcctgggattaaaggcgtg\",\n )\n self.assertEqual(alignment.sequences[1].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[1].seq), 119354)\n self.assertEqual(\n alignment.sequences[1].seq[46447 : 46447 + 74],\n \"TAAACCTTTAAGAACTTGAGTTTGTTTGTTTGGttttttttaatgtttatttttgagagagagagagagacaga\",\n )\n self.assertEqual(\n alignment[1],\n \"tctgtctctctctctctctcaaaaataaacattaaaaaaaaCCAAACAAACAAACTCAAGTTCTTAAAGGTTTA\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 193)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47545018, 47545018))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (10261, 10261))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155025555, 155025555))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157515610, 157515610))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][9]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 2)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 10)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n # fmt: off\n np.array([[3019702, 3019725, 3019725, 3019744],\n [ 46521, 46498, 46466, 46447],\n ])\n # fmt: on\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019702 tctgcctgcctctgcctcccaag--------------------------------tcctg\n 0 ||||.||..||||..|||.|||.--------------------------------.....\nfelCat3.s 46521 tctgtctctctctctctctcaaaaataaacattaaaaaaaaCCAAACAAACAAACTCAAG\n\nmm9.chr10 3019730 ggattaaaggcgtg 3019744\n 60 .............. 74\nfelCat3.s 46461 TTCTTAAAGGTTTA 46447\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=45.000000\ns mm9.chr10 3019702 42 + 129993255 tctgcctgcctctgcctcccaag--------------------------------tcctgggattaaaggcgtg\ns felCat3.scaffold_205680 72833 74 - 119354 tctgtctctctctctctctcaaaaataaacattaaaaaaaaCCAAACAAACAAACTCAAGTTCTTAAAGGTTTA\nq felCat3.scaffold_205680 99999999999999999999999999999999999999999999999999999999999999999999999999\ni felCat3.scaffold_205680 I 193 C 0\ne canFam2.chr1 47545018 0 + 125616256 C\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 10261 0 + 133105 C\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 155025555 0 + 170899992 C\ne panTro2.chr6 157515610 0 + 173908612 C\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['t', 'c', 't', 'g', 'c', 'c', 't', 'g', 'c', 'c', 't', 'c', 't',\n 'g', 'c', 'c', 't', 'c', 'c', 'c', 'a', 'a', 'g', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', 't', 'c', 'c', 't', 'g', 'g', 'g', 'a', 't', 't',\n 'a', 'a', 'a', 'g', 'g', 'c', 'g', 't', 'g'],\n ['t', 'c', 't', 'g', 't', 'c', 't', 'c', 't', 'c', 't', 'c', 't',\n 'c', 't', 'c', 't', 'c', 't', 'c', 'a', 'a', 'a', 'a', 'a', 't',\n 'a', 'a', 'a', 'c', 'a', 't', 't', 'a', 'a', 'a', 'a', 'a', 'a',\n 'a', 'a', 'C', 'C', 'A', 'A', 'A', 'C', 'A', 'A', 'A', 'C', 'A',\n 'A', 'A', 'C', 'T', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'T', 'T',\n 'A', 'A', 'A', 'G', 'G', 'T', 'T', 'T', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, -16865)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019744 : 3019744 + 33],\n \"cgccaccactgccctgcCTTAAACTGCTCTTAA\",\n )\n self.assertEqual(\n alignment[0],\n \"-----------------cgccaccactgccctgcCT------------TAAACTGCTCTTAA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 174210431)\n self.assertEqual(\n alignment.sequences[1].seq[158037776 : 158037776 + 27],\n \"CCAATACCCATGTGGGAATTGCTGGCG\",\n )\n self.assertEqual(\n alignment[1],\n \"-----------------CGCCAGCAATTCC------------------CACATGGGTATTGG\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 2523)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[2].seq), 498454)\n self.assertEqual(alignment.sequences[2].seq[324312 : 324312 + 4], \"TCAA\")\n self.assertEqual(\n alignment[2],\n \"----------------------------------------------------------TTGA\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"quality\"], \"9999\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 2374)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[3].seq), 133105)\n self.assertEqual(\n alignment.sequences[3].seq[10261 : 10261 + 13], \"ACATGGCTACTGG\"\n )\n self.assertEqual(\n alignment[3],\n \"-------------------------------------------------ACATGGCTACTGG\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[4].seq), 359464)\n self.assertEqual(\n alignment.sequences[4].seq[171883 : 171883 + 11], \"TCAACACCAAT\"\n )\n self.assertEqual(\n alignment[4],\n \"---------------------------------------------------ATTGGTGTTGA\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"quality\"], \"87784564678\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 2731)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[5].seq), 4726)\n self.assertEqual(\n alignment.sequences[5].seq[4493 : 4493 + 41],\n \"TCAACACCCCTATGGGACCTGAGACAGGCAAGACAATGGTG\",\n )\n self.assertEqual(\n alignment[5],\n \"--------------------CACCATTGTCTTGCCTGTC-TCAGGTCCCATAGGGGTGTTGA\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[6].seq), 119354)\n self.assertEqual(\n alignment.sequences[6].seq[46385 : 46385 + 62],\n \"TCTACACCAATGTGGGAATGACTGAAAGACAAGACACTGATGAGTAAGAGAAAGAGAAATCA\",\n )\n self.assertEqual(\n alignment[6],\n \"TGATTTCTCTTTCTCTTACTCATCAGTGTCTTGTCTTTCAGTCATTCCCACATTGGTGTAGA\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47545018, 47545018))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155025555, 155025555))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157515610, 157515610))\n self.assertEqual(status, \"C\")\n self.assertEqual(len(alignment.sequences), 7)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019744, 3019744, 3019747, 3019757, 3019763, 3019763,\n 3019763, 3019763, 3019764, 3019766, 3019773, 3019777],\n [158037803, 158037803, 158037800, 158037790, 158037790, 158037790,\n 158037790, 158037790, 158037789, 158037787, 158037780, 158037776],\n [ 324316, 324316, 324316, 324316, 324316, 324316,\n 324316, 324316, 324316, 324316, 324316, 324312],\n [ 10261, 10261, 10261, 10261, 10261, 10261,\n 10261, 10261, 10261, 10263, 10270, 10274],\n [ 171894, 171894, 171894, 171894, 171894, 171894,\n 171894, 171894, 171894, 171894, 171887, 171883],\n [ 4534, 4534, 4534, 4524, 4518, 4515,\n 4515, 4507, 4506, 4504, 4497, 4493],\n [ 46447, 46430, 46427, 46417, 46411, 46408,\n 46407, 46399, 46398, 46396, 46389, 46385],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019744 -----------------cgccaccactgccctgcCT------------TAAACTGCTCTT\nponAbe2.c 158037803 -----------------CGCCAGCAATTCC------------------CACATGGGTATT\ntupBel1.s 324316 ----------------------------------------------------------TT\ncalJac1.C 10261 -------------------------------------------------ACATGGCTACT\notoGar1.s 171894 ---------------------------------------------------ATTGGTGTT\noryCun1.s 4534 --------------------CACCATTGTCTTGCCTGTC-TCAGGTCCCATAGGGGTGTT\nfelCat3.s 46447 TGATTTCTCTTTCTCTTACTCATCAGTGTCTTGTCTTTCAGTCATTCCCACATTGGTGTA\n\nmm9.chr10 3019775 AA 3019777\nponAbe2.c 158037778 GG 158037776\ntupBel1.s 324314 GA 324312\ncalJac1.C 10272 GG 10274\notoGar1.s 171885 GA 171883\noryCun1.s 4495 GA 4493\nfelCat3.s 46387 GA 46385\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=-16865.000000\ns mm9.chr10 3019744 33 + 129993255 -----------------cgccaccactgccctgcCT------------TAAACTGCTCTTAA\ns ponAbe2.chr6 16172628 27 - 174210431 -----------------CGCCAGCAATTCC------------------CACATGGGTATTGG\ni ponAbe2.chr6 I 2523 C 0\ns tupBel1.scaffold_114895.1-498454 174138 4 - 498454 ----------------------------------------------------------TTGA\nq tupBel1.scaffold_114895.1-498454 ----------------------------------------------------------9999\ni tupBel1.scaffold_114895.1-498454 I 2374 C 0\ns calJac1.Contig6394 10261 13 + 133105 -------------------------------------------------ACATGGCTACTGG\ni calJac1.Contig6394 C 0 C 0\ns otoGar1.scaffold_334.1-359464 187570 11 - 359464 ---------------------------------------------------ATTGGTGTTGA\nq otoGar1.scaffold_334.1-359464 ---------------------------------------------------87784564678\ni otoGar1.scaffold_334.1-359464 I 2731 C 0\ns oryCun1.scaffold_156751 192 41 - 4726 --------------------CACCATTGTCTTGCCTGTC-TCAGGTCCCATAGGGGTGTTGA\nq oryCun1.scaffold_156751 --------------------9999999999999999999-9999999999999999999999\ni oryCun1.scaffold_156751 N 0 C 0\ns felCat3.scaffold_205680 72907 62 - 119354 TGATTTCTCTTTCTCTTACTCATCAGTGTCTTGTCTTTCAGTCATTCCCACATTGGTGTAGA\nq felCat3.scaffold_205680 99999999999999999999999999999999999999999999999999999999999999\ni felCat3.scaffold_205680 C 0 C 0\ne canFam2.chr1 47545018 0 + 125616256 C\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne hg18.chr6 155025555 0 + 170899992 C\ne panTro2.chr6 157515610 0 + 173908612 C\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'c', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c',\n 't', 'g', 'c', 'c', 'c', 't', 'g', 'c', 'C', 'T', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'A', 'A', 'A',\n 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'A', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A',\n 'T', 'T', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'C', 'A',\n 'T', 'G', 'G', 'G', 'T', 'A', 'T', 'T', 'G', 'G'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', 'T', 'T', 'G', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'C', 'A',\n 'T', 'G', 'G', 'C', 'T', 'A', 'C', 'T', 'G', 'G'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A',\n 'T', 'T', 'G', 'G', 'T', 'G', 'T', 'T', 'G', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'C', 'C', 'A', 'T',\n 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'C', 'C', 'T', 'G', 'T', 'C',\n '-', 'T', 'C', 'A', 'G', 'G', 'T', 'C', 'C', 'C', 'A', 'T', 'A',\n 'G', 'G', 'G', 'G', 'T', 'G', 'T', 'T', 'G', 'A'],\n ['T', 'G', 'A', 'T', 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'T', 'C',\n 'T', 'C', 'T', 'T', 'A', 'C', 'T', 'C', 'A', 'T', 'C', 'A', 'G',\n 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'T', 'C', 'T', 'T', 'T', 'C',\n 'A', 'G', 'T', 'C', 'A', 'T', 'T', 'C', 'C', 'C', 'A', 'C', 'A',\n 'T', 'T', 'G', 'G', 'T', 'G', 'T', 'A', 'G', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 367532)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019777 : 3019777 + 183],\n \"GGCAATGTCAGGCTATGCGTTCTAGACAGGGCACAAGAAAAGCTTTTAGCAGCAGAATAAACTTTTAAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGATACAGTGGAAAGAGGCCTTTGAGAATGCATGAGAGAATATTTCCTGTAAGAGTTGAACAATTTAGAATTTACc\",\n )\n self.assertEqual(\n alignment[0],\n \"GGCAATGTCA-GGCTATGCGT------TCTAGACAGGGCACAAGAAAAGCTTTTAGCAGCAGAATAAACTTTT-AAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGA-TACAGT------GGAAAG-----A----------GGCCTTTGAGAAT---GCATGAGAGAATAT---TTCCTGTA------AGAGTTGAACAATTTAGAATTTACc\",\n )\n self.assertEqual(alignment.sequences[1].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[1].seq), 4726)\n self.assertEqual(\n alignment.sequences[1].seq[4300 : 4300 + 193],\n \"AATCCTAAACTATTTAGCTCTGAGAAATAGGGGAAGTAATATTATTCCATCCTGATTCCCAAAAGGCTTTTTTTTTCTTTGTTGTATCACTTTGAACACTTGATTACTAGCAAGGGAAGCAGTTTCCTCTAAAGGCTTATTCTACTGGAAAAAGCTTTTCCTGTCCCTTAGAACATAAGGTCATGATGTTGCC\",\n )\n self.assertEqual(\n alignment[1],\n \"GGCAACATCATGACCTTATGT------TCTAA----GGGACAGGAAAAGCTTTTTCCAGTAGAATAAGCCTTT-AGAGGAAACTGCTTCCCTTGCTAGTAATCAAGTGTTCAAAGTGA-TACAACAAAGAAAAAAAA-----A----------GCCTTTTGGGAAT-CAGGATGGAATAATATTACTTCCCCTATTTCTCAGAGCTAAATAGTTTAGGATT----\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999899999999989999999999999999999999999999999999999999999999999999898999999989979999999999999997999999998978998999999999999999978999999979689999999999999999979\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 37)\n self.assertEqual(alignment.sequences[2].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 170899992)\n self.assertEqual(\n alignment.sequences[2].seq[155025365 : 155025365 + 190],\n \"AATCCTAAATTGTTTAACTCTTAGAAATAAGGGAAATAATATTATTCTATCCTGCATTCTCAAAAAAATTTTTCTTCATCTCACTTTGGTGACCTGATTGCTATCAAGGAAAGCAATTCCCTTTAACATTTTATTCCACTGCAAAAAGCTTTTCCTGTACTTTATCTTGAATATGTATCATGGTGTTGCC\",\n )\n self.assertEqual(\n alignment[2],\n \"GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGGAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A----------TTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 173908612)\n self.assertEqual(\n alignment.sequences[3].seq[157515419 : 157515419 + 191],\n \"AATCCTAAATTGTTTAACTCTTAGAAATAAGGGAAATAATATTATTCTATCCTGCATTCTCAAAAAAAATTTTTCTTCATCTCACTTTGGTGACCTGATTGCTATCAAGGAAAGCAATTTCCTTTAACATTTTATTCCACTGCAAAAAGCTTTTCCTGTACTTTATCTTGAATATGTATCATGGTGTTGCC\",\n )\n self.assertEqual(\n alignment[3],\n \"GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 174210431)\n self.assertEqual(\n alignment.sequences[4].seq[158037586 : 158037586 + 190],\n \"AATCCTAAATTGTTTAACTCTAGAAATAAGGGAAATAATATTATTCTGTGCTGCATTCTCAAAAAGAATTTTTCTTCATCTCACTTTGGTGACCTGATTGCTATCAAGGAAAGCAATTTCCTTTAACATTTTATTCCACCGCAAAAAGCTTTTCCTGTACTTTATCTTGAATATGTATCATGGTGTTGCC\",\n )\n self.assertEqual(\n alignment[4],\n \"GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCGGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTCTTTTTGAGAATGCAGCACAGAATAATATTATTTCCCTTATTTCT-AGAGTTAAACAATTTAGGATT----\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 21)\n self.assertEqual(alignment.sequences[5].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[5].seq), 133105)\n self.assertEqual(\n alignment.sequences[5].seq[10274 : 10274 + 187],\n \"GGCAACACCGTGATACATATCCGAGATAAAGTACAGGAAAAGCTTTTGCAGTGGACGAAAATGTTGAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGAGATGAAGAAAGTTTTTTGAGAATGTGGGATAGAATAATATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT\",\n )\n self.assertEqual(\n alignment[5],\n \"GGCAACACCGTGA-TACATAT------CCGAGATAAAGTACAGGAAAAGC-TTTTGCAGTGGACGAAAATGTT-GAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAA-----------------GTTTTTTGAGAATGTGGGATAGAATAATATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT----\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 21)\n self.assertEqual(alignment.sequences[6].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[6].seq), 359464)\n self.assertEqual(\n alignment.sequences[6].seq[171686 : 171686 + 197],\n \"AATCCTGAATTATTTAACTCTGAAATGGAGGGTGGATAAAATTATTCTTTCCAGCATTCTCAAAACATTTTTTCTTTATAATCACTTTGGTCACCTGATTGCTATCAAGAAAAGCAATTTCCTTTAACCTTTTATTCTACCGTAAAGGGCTTTTCCTGCACTTTGTCTTTATCTACAGCAAGGATCACGGCGTTGCC\",\n )\n self.assertEqual(\n alignment[6],\n \"GGCAACGCCGTGA-TCCTTGCTGTAGATAAAGACAAAGTGCAGGAAAAGCCCTTTACGGTAGAATAAAAGGTT-AAAGGAAATTGCTTTTCTTGATAGCAATCAGGTGACCAAAGTGATTATAA-------AGAAAA-----A----------ATGTTTTGAGAATGCTGGAAAGAATAATTTTATCCACCCTCCATTTCAGAGTTAAATAATTCAGGATT----\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"54667653455648997776896979788699699955776666776867789776453646557877552667697777697779896767576676677696675376877786786858478887756858859779666569356677477759968759378767656876769557597655596536566\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 358)\n self.assertEqual(alignment.sequences[7].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[7].seq), 498454)\n self.assertEqual(\n alignment.sequences[7].seq[324116 : 324116 + 196],\n \"AAGCCCAAGTTATTTAACTTAGACATAGGGAAAATAATATGCTTCTATACTGCATCCACAAAAGTTTGTTTTTGTTTTTTTTTTCAGTATGACTTTGGTCACCTGATTGCTGTCAAGGAAGGCAATTTCCTTTAAAAGTTTATCCTACTGCAAAAAGCTTTTCCTGTACTTTATCTAGAACATTCATGACATTGCC\",\n )\n self.assertEqual(\n alignment[7],\n \"GGCAATGTCATGA----ATGT------TCTAGATAAAGTACAGGAAAAGCTTTTTGCAGTAGGATAAACTTTT-AAAGGAAATTGCCTTCCTTGACAGCAATCAGGTGACCAAAGTCATACTGA-------AAAAAA-----AAACAAAAACAAACTTTTGTGGATGCAGTATAGAAGCATATTATTTTCCCTATGTCT--AAGTTAAATAACTTGGGCTT----\",\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 623)\n self.assertEqual(alignment.sequences[8].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[8].seq), 119354)\n self.assertEqual(\n alignment.sequences[8].seq[46199 : 46199 + 186],\n \"aattttaaattatttaaCTCTTAGATGTAGGGGAAATAATATTATTGTATCCTGTATTCTCAAAAAAAATTCCCTTTATATTACTTTAATCACCTAATGTCTCTTGAAGAAAGCAATTTCCTACAACATTTTATTCTACTCAAAATGCTTTTCCTGCACTTTATCTAGAATGTACTTTATGATGTC\",\n )\n self.assertEqual(\n alignment[8],\n \"GACATC---ATAA-AGTACAT------TCTAGATAAAGTGCAGGAAAAGCATTTTG-AGTAGAATAAAATGTT-GTAGGAAATTGCTTTCTTCAAGAGACATTAGGTGATTAAAGTAA-TATAA-------AGGGAA-----T----------TTTTTTTGAGAATACAGGATACAATAATATTATTTCCCCTACATCTAAGAGttaaataatttaaaatt----\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 27)\n self.assertEqual(alignment.sequences[9].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[9].seq), 125616256)\n self.assertEqual(\n alignment.sequences[9].seq[47544825 : 47544825 + 193],\n \"attaaattttaaattatttaaCTCTTAGAAGTAAGGGAAACAATATTATTCTAACTTGGATTCACTGAACTTTGTTTTTTCCCTTTATATTCCTTCAATCACCTGATTGCTCTCAAAGAAAGTAATTTCCTATTAACATTTTATCCTGTTCAAAATCCTTTTGTTGTACTTTACCCGGAATTTACATCATGAT\",\n )\n self.assertEqual(\n alignment[9],\n \"------ATCATGA-TGTAAAT------TCCGGGTAAAGTACAACAAAAGGATTTTG-AACAGGATAAAATGTTAATAGGAAATTACTTTCTTTGAGAGCAATCAGGTGATTGAAGGAA-TATAA-------AGGGAAAAAACA----------AAGTTCAGTGAATCCAAGTTAGAATAATATTGTTTCCCTTACTTCTAAGAGttaaataatttaaaatttaat\",\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 10)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 3)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019777, 3019783, 3019786, 3019787, 3019787, 3019789,\n 3019790, 3019793, 3019797, 3019797, 3019802, 3019806,\n 3019820, 3019821, 3019826, 3019827, 3019843, 3019843,\n 3019887, 3019887, 3019892, 3019893, 3019893, 3019898,\n 3019899, 3019899, 3019900, 3019900, 3019900, 3019913,\n 3019913, 3019913, 3019927, 3019927, 3019935, 3019935,\n 3019935, 3019936, 3019956, 3019960],\n [ 4493, 4487, 4484, 4483, 4482, 4480,\n 4479, 4476, 4472, 4472, 4467, 4467,\n 4453, 4452, 4447, 4446, 4430, 4430,\n 4386, 4386, 4381, 4380, 4374, 4369,\n 4368, 4368, 4367, 4367, 4367, 4354,\n 4354, 4352, 4338, 4335, 4327, 4322,\n 4321, 4320, 4300, 4300],\n [155025555, 155025549, 155025546, 155025545, 155025544, 155025542,\n 155025542, 155025539, 155025535, 155025535, 155025530, 155025526,\n 155025512, 155025511, 155025506, 155025505, 155025489, 155025489,\n 155025445, 155025445, 155025440, 155025440, 155025440, 155025435,\n 155025434, 155025434, 155025433, 155025433, 155025433, 155025420,\n 155025419, 155025417, 155025403, 155025400, 155025392, 155025387,\n 155025386, 155025385, 155025365, 155025365],\n [157515610, 157515604, 157515601, 157515600, 157515599, 157515597,\n 157515597, 157515594, 157515590, 157515590, 157515585, 157515581,\n 157515567, 157515566, 157515561, 157515560, 157515544, 157515544,\n 157515500, 157515500, 157515495, 157515495, 157515495, 157515490,\n 157515489, 157515489, 157515488, 157515488, 157515487, 157515474,\n 157515473, 157515471, 157515457, 157515454, 157515446, 157515441,\n 157515440, 157515439, 157515419, 157515419],\n [158037776, 158037770, 158037767, 158037766, 158037765, 158037763,\n 158037763, 158037760, 158037756, 158037756, 158037751, 158037747,\n 158037733, 158037732, 158037727, 158037726, 158037710, 158037710,\n 158037666, 158037666, 158037661, 158037661, 158037661, 158037656,\n 158037655, 158037655, 158037654, 158037654, 158037653, 158037640,\n 158037639, 158037637, 158037623, 158037620, 158037612, 158037607,\n 158037607, 158037606, 158037586, 158037586],\n [ 10274, 10280, 10283, 10284, 10285, 10287,\n 10287, 10290, 10294, 10294, 10299, 10303,\n 10317, 10317, 10322, 10323, 10339, 10339,\n 10383, 10383, 10388, 10388, 10388, 10393,\n 10393, 10393, 10393, 10393, 10393, 10406,\n 10407, 10409, 10423, 10426, 10434, 10439,\n 10440, 10441, 10461, 10461],\n [ 171883, 171877, 171874, 171873, 171872, 171870,\n 171870, 171867, 171863, 171857, 171852, 171848,\n 171834, 171833, 171828, 171827, 171811, 171811,\n 171767, 171766, 171761, 171761, 171761, 171756,\n 171755, 171755, 171754, 171754, 171754, 171741,\n 171740, 171738, 171724, 171721, 171713, 171708,\n 171707, 171706, 171686, 171686],\n [ 324312, 324306, 324303, 324302, 324301, 324299,\n 324299, 324299, 324295, 324295, 324290, 324286,\n 324272, 324271, 324266, 324265, 324249, 324249,\n 324205, 324204, 324199, 324199, 324199, 324194,\n 324193, 324193, 324192, 324183, 324182, 324169,\n 324168, 324166, 324152, 324149, 324141, 324136,\n 324136, 324136, 324116, 324116],\n [ 46385, 46379, 46379, 46378, 46377, 46375,\n 46375, 46372, 46368, 46368, 46363, 46359,\n 46345, 46344, 46339, 46339, 46323, 46323,\n 46279, 46279, 46274, 46274, 46274, 46269,\n 46268, 46268, 46267, 46267, 46267, 46254,\n 46253, 46251, 46237, 46234, 46226, 46221,\n 46220, 46219, 46199, 46199],\n [ 47545018, 47545018, 47545015, 47545014, 47545013, 47545011,\n 47545011, 47545008, 47545004, 47545004, 47544999, 47544995,\n 47544981, 47544980, 47544975, 47544975, 47544959, 47544958,\n 47544914, 47544914, 47544909, 47544909, 47544909, 47544904,\n 47544903, 47544898, 47544897, 47544897, 47544897, 47544884,\n 47544883, 47544881, 47544867, 47544864, 47544856, 47544851,\n 47544850, 47544849, 47544829, 47544825],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019777 GGCAATGTCA-GGCTATGCGT------TCTAGACAGGGCACAAGAAAAGCTTTTAGCAGC\noryCun1.s 4493 GGCAACATCATGACCTTATGT------TCTAA----GGGACAGGAAAAGCTTTTTCCAGT\nhg18.chr6 155025555 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGT\npanTro2.c 157515610 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGT\nponAbe2.c 158037776 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCGGT\ncalJac1.C 10274 GGCAACACCGTGA-TACATAT------CCGAGATAAAGTACAGGAAAAGC-TTTTGCAGT\notoGar1.s 171883 GGCAACGCCGTGA-TCCTTGCTGTAGATAAAGACAAAGTGCAGGAAAAGCCCTTTACGGT\ntupBel1.s 324312 GGCAATGTCATGA----ATGT------TCTAGATAAAGTACAGGAAAAGCTTTTTGCAGT\nfelCat3.s 46385 GACATC---ATAA-AGTACAT------TCTAGATAAAGTGCAGGAAAAGCATTTTG-AGT\ncanFam2.c 47545018 ------ATCATGA-TGTAAAT------TCCGGGTAAAGTACAACAAAAGGATTTTG-AAC\n\nmm9.chr10 3019830 AGAATAAACTTTT-AAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGA-T\noryCun1.s 4443 AGAATAAGCCTTT-AGAGGAAACTGCTTCCCTTGCTAGTAATCAAGTGTTCAAAGTGA-T\nhg18.chr6 155025502 GGAATAAAATGTT-AAAGGGAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-G\npanTro2.c 157515557 GGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-G\nponAbe2.c 158037723 GGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-G\ncalJac1.C 10326 GGACGAAAATGTT-GAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGA-G\notoGar1.s 171824 AGAATAAAAGGTT-AAAGGAAATTGCTTTTCTTGATAGCAATCAGGTGACCAAAGTGATT\ntupBel1.s 324262 AGGATAAACTTTT-AAAGGAAATTGCCTTCCTTGACAGCAATCAGGTGACCAAAGTCATA\nfelCat3.s 46336 AGAATAAAATGTT-GTAGGAAATTGCTTTCTTCAAGAGACATTAGGTGATTAAAGTAA-T\ncanFam2.c 47544972 AGGATAAAATGTTAATAGGAAATTACTTTCTTTGAGAGCAATCAGGTGATTGAAGGAA-T\n\nmm9.chr10 3019888 ACAGT------GGAAAG-----A----------GGCCTTTGAGAAT---GCATGAGAGAA\noryCun1.s 4385 ACAACAAAGAAAAAAAA-----A----------GCCTTTTGGGAAT-CAGGATGGAATAA\nhg18.chr6 155025444 ATGA-------AGAAAA-----A----------TTTTTTTGAGAATGCAGGATAGAATAA\npanTro2.c 157515499 ATGA-------AGAAAA-----A---------TTTTTTTTGAGAATGCAGGATAGAATAA\nponAbe2.c 158037665 ATGA-------AGAAAA-----A---------TTCTTTTTGAGAATGCAGCACAGAATAA\ncalJac1.C 10384 ATGA-------AGAAA-----------------GTTTTTTGAGAATGTGGGATAGAATAA\notoGar1.s 171765 ATAA-------AGAAAA-----A----------ATGTTTTGAGAATGCTGGAAAGAATAA\ntupBel1.s 324203 CTGA-------AAAAAA-----AAACAAAAACAAACTTTTGTGGATGCAGTATAGAAGCA\nfelCat3.s 46278 ATAA-------AGGGAA-----T----------TTTTTTTGAGAATACAGGATACAATAA\ncanFam2.c 47544913 ATAA-------AGGGAAAAAACA----------AAGTTCAGTGAATCCAAGTTAGAATAA\n\nmm9.chr10 3019924 TAT---TTCCTGTA------AGAGTTGAACAATTTAGAATTTACc 3019960\noryCun1.s 4341 TATTACTTCCCCTATTTCTCAGAGCTAAATAGTTTAGGATT---- 4300\nhg18.chr6 155025406 TATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT---- 155025365\npanTro2.c 157515460 TATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT---- 157515419\nponAbe2.c 158037626 TATTATTTCCCTTATTTCT-AGAGTTAAACAATTTAGGATT---- 158037586\ncalJac1.C 10420 TATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT---- 10461\notoGar1.s 171727 TTTTATCCACCCTCCATTTCAGAGTTAAATAATTCAGGATT---- 171686\ntupBel1.s 324155 TATTATTTTCCCTATGTCT--AAGTTAAATAACTTGGGCTT---- 324116\nfelCat3.s 46240 TATTATTTCCCCTACATCTAAGAGttaaataatttaaaatt---- 46199\ncanFam2.c 47544870 TATTGTTTCCCTTACTTCTAAGAGttaaataatttaaaatttaat 47544825\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=367532.000000\ns mm9.chr10 3019777 183 + 129993255 GGCAATGTCA-GGCTATGCGT------TCTAGACAGGGCACAAGAAAAGCTTTTAGCAGCAGAATAAACTTTT-AAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGA-TACAGT------GGAAAG-----A----------GGCCTTTGAGAAT---GCATGAGAGAATAT---TTCCTGTA------AGAGTTGAACAATTTAGAATTTACc\ns oryCun1.scaffold_156751 233 193 - 4726 GGCAACATCATGACCTTATGT------TCTAA----GGGACAGGAAAAGCTTTTTCCAGTAGAATAAGCCTTT-AGAGGAAACTGCTTCCCTTGCTAGTAATCAAGTGTTCAAAGTGA-TACAACAAAGAAAAAAAA-----A----------GCCTTTTGGGAAT-CAGGATGGAATAATATTACTTCCCCTATTTCTCAGAGCTAAATAGTTTAGGATT----\nq oryCun1.scaffold_156751 999999999999999999999------99999----9999999999989999999998999999999999999-99999999999999999999999999999999999998989999-999899799999999999-----9----------9997999999998-978998999999999999999978999999979689999999999999999979----\ni oryCun1.scaffold_156751 C 0 I 37\ns hg18.chr6 15874437 190 - 170899992 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGGAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A----------TTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16393002 191 - 173908612 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----\nq panTro2.chr6 9999999999999-9999999------9999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999-99999-------999999-----9---------999999999999999999999999999999999999999999999999999999999999999999999----\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16172655 190 - 174210431 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCGGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTCTTTTTGAGAATGCAGCACAGAATAATATTATTTCCCTTATTTCT-AGAGTTAAACAATTTAGGATT----\ni ponAbe2.chr6 C 0 I 21\ns calJac1.Contig6394 10274 187 + 133105 GGCAACACCGTGA-TACATAT------CCGAGATAAAGTACAGGAAAAGC-TTTTGCAGTGGACGAAAATGTT-GAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAA-----------------GTTTTTTGAGAATGTGGGATAGAATAATATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT----\ni calJac1.Contig6394 C 0 I 21\ns otoGar1.scaffold_334.1-359464 187581 197 - 359464 GGCAACGCCGTGA-TCCTTGCTGTAGATAAAGACAAAGTGCAGGAAAAGCCCTTTACGGTAGAATAAAAGGTT-AAAGGAAATTGCTTTTCTTGATAGCAATCAGGTGACCAAAGTGATTATAA-------AGAAAA-----A----------ATGTTTTGAGAATGCTGGAAAGAATAATTTTATCCACCCTCCATTTCAGAGTTAAATAATTCAGGATT----\nq otoGar1.scaffold_334.1-359464 5466765345564-89977768969797886996999557766667768677897764536465578775526-67697777697779896767576676677696675376877786786858-------478887-----7----------56858859779666569356677477759968759378767656876769557597655596536566----\ni otoGar1.scaffold_334.1-359464 C 0 I 358\ns tupBel1.scaffold_114895.1-498454 174142 196 - 498454 GGCAATGTCATGA----ATGT------TCTAGATAAAGTACAGGAAAAGCTTTTTGCAGTAGGATAAACTTTT-AAAGGAAATTGCCTTCCTTGACAGCAATCAGGTGACCAAAGTCATACTGA-------AAAAAA-----AAACAAAAACAAACTTTTGTGGATGCAGTATAGAAGCATATTATTTTCCCTATGTCT--AAGTTAAATAACTTGGGCTT----\nq tupBel1.scaffold_114895.1-498454 9999999999999----9999------9999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999-------999999-----999999999999999999999999999999999999999999999999999999999--99999999999999999999----\ni tupBel1.scaffold_114895.1-498454 C 0 I 623\ns felCat3.scaffold_205680 72969 186 - 119354 GACATC---ATAA-AGTACAT------TCTAGATAAAGTGCAGGAAAAGCATTTTG-AGTAGAATAAAATGTT-GTAGGAAATTGCTTTCTTCAAGAGACATTAGGTGATTAAAGTAA-TATAA-------AGGGAA-----T----------TTTTTTTGAGAATACAGGATACAATAATATTATTTCCCCTACATCTAAGAGttaaataatttaaaatt----\nq felCat3.scaffold_205680 999999---9999-9999999------99999999999999999999999999999-9999999999999999-99999999999999999999999999999999999999999999-99999-------999999-----9----------99999999999999999999999999999999999999999999999999999999999999999999----\ni felCat3.scaffold_205680 C 0 I 27\ns canFam2.chr1 78071238 193 - 125616256 ------ATCATGA-TGTAAAT------TCCGGGTAAAGTACAACAAAAGGATTTTG-AACAGGATAAAATGTTAATAGGAAATTACTTTCTTTGAGAGCAATCAGGTGATTGAAGGAA-TATAA-------AGGGAAAAAACA----------AAGTTCAGTGAATCCAAGTTAGAATAATATTGTTTCCCTTACTTCTAAGAGttaaataatttaaaatttaat\nq canFam2.chr1 ------9999999-9999999------99999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999-99999-------999999999999----------999999999999999999999999999999999999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019960 : 3019960 + 757],\n \"actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacagttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgagggatgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaatgcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactcaggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttgctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgcagatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggatggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccggggactaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagcagaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagagaaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccctcttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggagggagaacatttgaaatgtaaataaataaaataataaaaaa\",\n )\n self.assertEqual(\n alignment[0],\n \"actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacagttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgagggatgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaatgcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactcaggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttgctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgcagatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggatggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccggggactaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagcagaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagagaaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccctcttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggagggagaacatttgaaatgtaaataaataaaataataaaaaa\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (46199, 46172))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47544825, 47544825))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (10461, 10482))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171686, 171328))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155025365, 155025365))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][9]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157515419, 157515419))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][10]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158037586, 158037565))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][11]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(record.seq), 4726)\n self.assertEqual(segment, (4300, 4263))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 12)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3019960, 3020717]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019960 actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacag\n\nmm9.chr10 3020020 ttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgaggg\n\nmm9.chr10 3020080 atgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaat\n\nmm9.chr10 3020140 gcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactca\n\nmm9.chr10 3020200 ggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttg\n\nmm9.chr10 3020260 ctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgc\n\nmm9.chr10 3020320 agatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggat\n\nmm9.chr10 3020380 ggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccgggga\n\nmm9.chr10 3020440 ctaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagc\n\nmm9.chr10 3020500 agaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagag\n\nmm9.chr10 3020560 aaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccct\n\nmm9.chr10 3020620 cttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggaggga\n\nmm9.chr10 3020680 gaacatttgaaatgtaaataaataaaataataaaaaa 3020717\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3019960 757 + 129993255 actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacagttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgagggatgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaatgcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactcaggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttgctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgcagatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggatggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccggggactaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagcagaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagagaaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccctcttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggagggagaacatttgaaatgtaaataaataaaataataaaaaa\ne felCat3.scaffold_205680 73155 27 - 119354 I\ne canFam2.chr1 47544825 0 + 125616256 C\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 10461 21 + 133105 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 187778 358 - 359464 I\ne hg18.chr6 155025365 0 + 170899992 C\ne panTro2.chr6 157515419 0 + 173908612 C\ne ponAbe2.chr6 16172845 21 - 174210431 I\ne oryCun1.scaffold_156751 426 37 - 4726 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['a', 'c', 't', 'a', 'g', 'g', 'g', 'a', 't', 'g', 'g', 'g', 'a',\n 'g', 'a', 'g', 'g', 'c', 't', 'c', 'c', 'c', 'a', 'g', 'a', 'a',\n 'c', 'c', 'c', 'a', 'g', 't', 'a', 'a', 't', 'g', 'a', 't', 'g',\n 'a', 'c', 'a', 't', 't', 'a', 'a', 'g', 'a', 'a', 'a', 't', 'a',\n 'c', 'a', 'c', 'a', 'a', 'c', 'a', 'g', 't', 't', 'g', 'g', 'g',\n 'a', 'a', 'a', 't', 'g', 'g', 'a', 'a', 'c', 'c', 'c', 'a', 'a',\n 'a', 'g', 'a', 'g', 'a', 'a', 'c', 'a', 'c', 'c', 't', 'c', 'c',\n 'a', 'g', 't', 'a', 'g', 'a', 't', 'a', 'a', 'g', 'c', 'a', 't',\n 'g', 'a', 'c', 'c', 'c', 'c', 'c', 'a', 'g', 't', 't', 'g', 'a',\n 'g', 'g', 'g', 'a', 't', 'g', 'g', 'g', 'c', 'c', 'c', 'a', 't',\n 'g', 'c', 'a', 'c', 'c', 'c', 'a', 't', 'c', 't', 't', 'a', 'a',\n 'a', 'a', 't', 't', 't', 't', 'g', 'g', 'a', 'c', 'c', 'c', 'a',\n 'g', 'a', 'a', 't', 't', 'a', 't', 't', 'c', 't', 't', 'c', 't',\n 'c', 'a', 'a', 'a', 'a', 'g', 'g', 'a', 'a', 'a', 't', 'g', 'c',\n 'a', 'g', 'g', 'g', 'a', 't', 'g', 'a', 'a', 'a', 'a', 't', 'g',\n 'g', 'a', 'g', 'c', 'a', 'g', 'a', 'g', 'a', 'c', 't', 'g', 'g',\n 'a', 'a', 'g', 'a', 'a', 'a', 'g', 'g', 'c', 'c', 'a', 'a', 'c',\n 'c', 'a', 'g', 'a', 'g', 'a', 'c', 't', 'g', 'c', 'c', 'c', 't',\n 'a', 'a', 'c', 't', 'c', 'a', 'g', 'g', 'a', 't', 'c', 'c', 'a',\n 't', 'c', 'g', 'c', 'a', 't', 'g', 't', 'g', 'c', 'a', 'g', 'g',\n 'c', 'a', 'c', 'c', 'a', 'a', 'c', 'c', 'c', 'c', 'a', 'a', 'c',\n 'a', 'c', 't', 'a', 't', 't', 'g', 'c', 't', 'g', 'a', 't', 'g',\n 'c', 'c', 'a', 't', 'g', 't', 't', 'g', 't', 'a', 'c', 't', 't',\n 'g', 'c', 't', 'g', 'a', 't', 'g', 'g', 'a', 'a', 'g', 'c', 'c',\n 't', 'g', 'g', 'c', 'a', 't', 'g', 'g', 'c', 't', 'g', 't', 'c',\n 'c', 't', 'c', 't', 'g', 'a', 'g', 'a', 'g', 't', 'c', 't', 'c',\n 'a', 'a', 'a', 't', 'g', 'a', 'g', 'g', 'c', 'a', 'c', 'c', 't',\n 'g', 'a', 'c', 'a', 'g', 'a', 't', 'g', 'c', 'a', 'g', 'a', 't',\n 'a', 'c', 't', 't', 'a', 'c', 'a', 'g', 'c', 'c', 'a', 'a', 'c',\n 'c', 'a', 'a', 't', 'g', 'g', 'a', 'c', 't', 'g', 'a', 'g', 'c',\n 'c', 'c', 'c', 'g', 'g', 'g', 'a', 'c', 'c', 't', 'c', 'a', 'a',\n 't', 'a', 'a', 'a', 'a', 'g', 'a', 'a', 't', 'g', 'a', 'g', 'g',\n 'g', 'g', 'a', 't', 'g', 'g', 'c', 'a', 'a', 'c', 'c', 'c', 'c',\n 'a', 't', 'a', 'g', 'g', 'a', 'a', 'g', 'a', 'a', 'c', 'a', 'a',\n 'c', 'a', 'g', 't', 'a', 't', 'c', 'a', 'a', 'c', 't', 'c', 'c',\n 'c', 't', 'g', 'g', 'a', 'c', 't', 'c', 'c', 't', 'c', 'a', 'g',\n 'a', 'g', 'c', 't', 'c', 'c', 'c', 'g', 'g', 'g', 'g', 'a', 'c',\n 't', 'a', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'a', 'c', 't',\n 'a', 'a', 'a', 'g', 'a', 'g', 'c', 'a', 't', 'a', 'c', 'a', 't',\n 'a', 'g', 'g', 'c', 't', 'g', 'c', 't', 'c', 't', 'g', 'a', 'g',\n 'g', 'c', 'c', 'c', 'c', 'a', 'g', 'a', 't', 'a', 'c', 'a', 't',\n 'a', 't', 'g', 't', 'a', 'g', 'c', 'a', 'g', 'a', 'g', 'g', 'a',\n 'c', 't', 'g', 'c', 'c', 't', 'c', 'a', 'g', 't', 'g', 'g', 'g',\n 'a', 'g', 'g', 'g', 'g', 'a', 't', 'g', 't', 'g', 'c', 't', 't',\n 'g', 'g', 't', 'c', 't', 't', 'g', 't', 'g', 'a', 'a', 'g', 'g',\n 'c', 't', 't', 'g', 'a', 't', 'g', 'c', 't', 'c', 'c', 'a', 'g',\n 'a', 'g', 'a', 'a', 'g', 'g', 'a', 'g', 'g', 'a', 't', 'g', 'c',\n 't', 'a', 'g', 'a', 'g', 'g', 'g', 'g', 't', 'g', 'a', 'g', 'g',\n 't', 'g', 'g', 'g', 'a', 'g', 't', 'g', 'g', 'a', 't', 'g', 'g',\n 'g', 't', 'g', 'g', 'g', 't', 'g', 'g', 'g', 'c', 'a', 'g', 'g',\n 'g', 'g', 'a', 'g', 'c', 'a', 'c', 'c', 'c', 't', 'c', 't', 't',\n 'a', 'g', 'a', 'g', 'g', 'a', 'c', 'a', 'a', 'g', 'g', 'g', 'c',\n 't', 'c', 't', 'g', 'g', 'g', 'g', 't', 'g', 'g', 'g', 'g', 'g',\n 'a', 'g', 'c', 't', 'c', 'a', 't', 'g', 'g', 'a', 'g', 'g', 'g',\n 'g', 'g', 'a', 'a', 'c', 't', 'g', 'g', 'g', 'a', 'a', 'g', 'g',\n 'a', 'g', 'g', 'g', 'a', 'g', 'a', 'a', 'c', 'a', 't', 't', 't',\n 'g', 'a', 'a', 'a', 't', 'g', 't', 'a', 'a', 'a', 't', 'a', 'a',\n 'a', 't', 'a', 'a', 'a', 'a', 't', 'a', 'a', 't', 'a', 'a', 'a',\n 'a', 'a', 'a']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 8951)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3020717 : 3020717 + 44],\n \"TGTCAAACATGCATAAAGATATACTGAGGAGCCCATGAATTTTA\",\n )\n self.assertEqual(alignment[0], \"TGTCAAACATGCATAAAGATATACT-GAGGAGCCCATGAATTTTA\")\n self.assertEqual(alignment.sequences[1].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[1].seq), 125616256)\n self.assertEqual(\n alignment.sequences[1].seq[47544792 : 47544792 + 33],\n \"TAAAATTCATGGGCCCCTCTATTATGTTAAACa\",\n )\n self.assertEqual(alignment[1], \"tGTT------------TAACATAATAGAGGGGCCCATGAATTTTA\")\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157515381 : 157515381 + 38],\n \"TAAAATTCATGGACCCCTCTAGTATATTTAAAATTTTT\",\n )\n self.assertEqual(alignment[2], \"----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA\")\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 11)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155025327 : 155025327 + 38],\n \"TAAAATTCATGGACCCCTCTAGTATATTTAAAATTTTT\",\n )\n self.assertEqual(alignment[3], \"----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 11)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (46199, 46172))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (10461, 10482))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171686, 171328))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158037586, 158037565))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(record.seq), 4726)\n self.assertEqual(segment, (4300, 4263))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 4)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3020717, 3020721, 3020727, 3020730, 3020733, 3020742,\n 3020742, 3020761],\n [ 47544825, 47544821, 47544821, 47544821, 47544821, 47544812,\n 47544811, 47544792],\n [157515419, 157515419, 157515413, 157515413, 157515410, 157515401,\n 157515400, 157515381],\n [155025365, 155025365, 155025359, 155025359, 155025356, 155025347,\n 155025346, 155025327],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3020717 TGTCAAACATGCATAAAGATATACT-GAGGAGCCCATGAATTTTA 3020761\ncanFam2.c 47544825 tGTT------------TAACATAATAGAGGGGCCCATGAATTTTA 47544792\npanTro2.c 157515419 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA 157515381\nhg18.chr6 155025365 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA 155025327\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=8951.000000\ns mm9.chr10 3020717 44 + 129993255 TGTCAAACATGCATAAAGATATACT-GAGGAGCCCATGAATTTTA\ns canFam2.chr1 78071431 33 - 125616256 tGTT------------TAACATAATAGAGGGGCCCATGAATTTTA\nq canFam2.chr1 9999------------99999999999999999999999999999\ni canFam2.chr1 C 0 I 9\ns panTro2.chr6 16393193 38 - 173908612 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA\nq panTro2.chr6 ----999999---99999999999999999999999999999999\ni panTro2.chr6 C 0 I 11\ns hg18.chr6 15874627 38 - 170899992 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA\ni hg18.chr6 C 0 I 11\ne felCat3.scaffold_205680 73155 27 - 119354 I\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 10461 21 + 133105 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 187778 358 - 359464 I\ne ponAbe2.chr6 16172845 21 - 174210431 I\ne oryCun1.scaffold_156751 426 37 - 4726 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'G', 'T', 'C', 'A', 'A', 'A', 'C', 'A', 'T', 'G', 'C', 'A',\n 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'A', 'T', 'A', 'C', 'T', '-',\n 'G', 'A', 'G', 'G', 'A', 'G', 'C', 'C', 'C', 'A', 'T', 'G', 'A',\n 'A', 'T', 'T', 'T', 'T', 'A'],\n ['t', 'G', 'T', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', 'T', 'A', 'A', 'C', 'A', 'T', 'A', 'A', 'T', 'A',\n 'G', 'A', 'G', 'G', 'G', 'G', 'C', 'C', 'C', 'A', 'T', 'G', 'A',\n 'A', 'T', 'T', 'T', 'T', 'A'],\n ['-', '-', '-', '-', 'A', 'A', 'A', 'A', 'A', 'T', '-', '-', '-',\n 'T', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'A', 'C', 'T', 'A',\n 'G', 'A', 'G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A',\n 'A', 'T', 'T', 'T', 'T', 'A'],\n ['-', '-', '-', '-', 'A', 'A', 'A', 'A', 'A', 'T', '-', '-', '-',\n 'T', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'A', 'C', 'T', 'A',\n 'G', 'A', 'G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A',\n 'A', 'T', 'T', 'T', 'T', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3020761 : 3020761 + 157],\n \"TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaagattttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaagtgctgagatcatacctctgcaccatcctgcccACCT\",\n )\n self.assertEqual(\n alignment[0],\n \"TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaagattttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaagtgctgagatcatacctctgcaccatcctgcccACCT\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (46199, 46172))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47544792, 47544783))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (10461, 10482))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171686, 171328))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155025327, 155025316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][9]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157515381, 157515370))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][10]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158037586, 158037565))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][11]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(record.seq), 4726)\n self.assertEqual(segment, (4300, 4263))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 12)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3020761, 3020918]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3020761 TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaag\n\nmm9.chr10 3020821 attttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaa\n\nmm9.chr10 3020881 gtgctgagatcatacctctgcaccatcctgcccACCT 3020918\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3020761 157 + 129993255 TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaagattttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaagtgctgagatcatacctctgcaccatcctgcccACCT\ne felCat3.scaffold_205680 73155 27 - 119354 I\ne canFam2.chr1 78071464 9 - 125616256 I\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 10461 21 + 133105 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 187778 358 - 359464 I\ne hg18.chr6 15874665 11 - 170899992 I\ne panTro2.chr6 16393231 11 - 173908612 I\ne ponAbe2.chr6 16172845 21 - 174210431 I\ne oryCun1.scaffold_156751 426 37 - 4726 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'A', 'T', 'A', 'T', 'A', 'T', 'G', 'C', 'T', 'A', 'T', 'C',\n 'C', 'G', 'T', 'G', 'T', 'G', 'C', 'T', 'G', 'T', 'G', 'A', 'T',\n 'T', 'T', 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'A', 'A', 'T',\n 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'G', 'T', 'A',\n 'T', 'A', 'T', 'G', 'c', 'a', 'a', 'g', 'a', 't', 't', 't', 't',\n 'g', 'c', 'a', 't', 't', 'g', 't', 'a', 'g', 'c', 'a', 'g', 'a',\n 'a', 'g', 'g', 't', 'g', 'g', 'c', 't', 't', 'c', 'a', 'a', 'a',\n 'c', 't', 'c', 'a', 'c', 'g', 'a', 't', 'c', 'c', 't', 'c', 'c',\n 't', 'g', 'c', 'c', 't', 'c', 'a', 'g', 'c', 'c', 't', 't', 'c',\n 'c', 'a', 'a', 'g', 't', 'g', 'c', 't', 'g', 'a', 'g', 'a', 't',\n 'c', 'a', 't', 'a', 'c', 'c', 't', 'c', 't', 'g', 'c', 'a', 'c',\n 'c', 'a', 't', 'c', 'c', 't', 'g', 'c', 'c', 'c', 'A', 'C', 'C',\n 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 85471)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3020918 : 3020918 + 96],\n \"GAGGTTTGTGACTTTTAATACTGATTGTTATCTAACATCACAGAATTCTCAGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA\",\n )\n self.assertEqual(\n alignment[0],\n \"GAGGTTTGTGACTTTTAATA----------CTGATTGTTATCTAACATCACAGAATTCTCAGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155025243 : 155025243 + 73],\n \"TTGTCCTAAATAATTAATAAGTCAAACATGTTTTTCCTTAAAAGCTGAGGATTGTGCAGTATTAAATAACCAT\",\n )\n self.assertEqual(\n alignment[1],\n \"---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 11)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157515297 : 157515297 + 73],\n \"TTGTCCTAAATAATTAATAAGTCAAACATGTTTTTCCTTAAAAGCTGAGGATTGTGCAGTATTAAATAACCAT\",\n )\n self.assertEqual(\n alignment[2],\n \"---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 11)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[3].seq), 125616256)\n self.assertEqual(\n alignment.sequences[3].seq[47544708 : 47544708 + 75],\n \"TTGTCCTAAGTAATTAACAAATCACTTTTTCCTTAAGAGCTGAGAACTTCATAATGGTACAGAATTATTTTATTA\",\n )\n self.assertEqual(\n alignment[3],\n \"--------------------------TAATAAAATAATTCTGTACCATTATGAAGTTCTCAGCTCTTAAGGAAAAA-----GTGATTTGTTAATTACTTAGGACAA\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[4].seq), 119354)\n self.assertEqual(\n alignment.sequences[4].seq[46096 : 46096 + 76],\n \"TTGTCCTAAATAATTAATAAATTACTTTGTGATATTAAAGAATTATTTCATTACTTCACCATTAAAATTCATGGAC\",\n )\n self.assertEqual(\n alignment[4],\n \"---GTCCATGAATTTTAATGGTGAAGTAATGAAATAATTCTTTAATATCAC----------------------AAA-----GTAATTTATTAATTATTTAGGACAA\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"9999899999999999999999999999999999999999999999999999999999999999999999999769\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 27)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[5].seq), 10026)\n self.assertEqual(\n alignment.sequences[5].seq[524 : 524 + 82],\n \"tttaaaaaaatcacactttTTCCATCAGAACTGAAAACTTTGTAATATTAatcttcttttcctattaaaATTTGCAGAACTC\",\n )\n self.assertEqual(\n alignment[5],\n \"GAGTTCTGCAAATtttaata----------ggaaaagaagatTAATATTACAAAGTTTTCAGTTCTGATGGAAaaa----------gtgtgatttttttaaa----\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9967996679966856646585678288383465687882688656636765583677657766676965686997776684\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 1372)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 28)\n self.assertEqual(alignment.sequences[6].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[6].seq), 4726)\n self.assertEqual(\n alignment.sequences[6].seq[4161 : 4161 + 102],\n \"TCATCCCAAGTCATTAACAAGTCAAACACTTTTTTCCTTAAGACTTGAGGATTTTCCAACATTAAATAATTATCTCATTGCTTTATTAAAATTCATGGATCT\",\n )\n self.assertEqual(\n alignment[6],\n \"-AGATCCATGAATTTTAATA---AAGCAATGAGATAATTATTTAATGTTGGAAAATCCTCAAGTCTTAAGGAAAAAAGTGTTTGACTTGTTAATGACTTGGGATGA\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"999999799999999999999999999999999999999999999999999998677999969999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 37)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[7].seq), 133105)\n self.assertEqual(\n alignment.sequences[7].seq[10482 : 10482 + 100],\n \"GGGGTCCATGAATTTTAATAGTAACAAAATGGTTATTCAATATTGCAAAATCCTCAGCTTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA\",\n )\n self.assertEqual(\n alignment[7],\n \"GGGGTCCATGAATTTTAATA-----GTAACAAAATGGTTATTCAATATTGCAAAATCCTCAGC-TTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 21)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[8].seq), 174210431)\n self.assertEqual(\n alignment.sequences[8].seq[158037464 : 158037464 + 101],\n \"TTGTCCTAAATAATTAATAAGTCAAACACGTTTTTCCTTAAAAGCTGAGGATTTTGCAATATTAAATAACCATTTTATTACTATTAAAATTCATGGACCCC\",\n )\n self.assertEqual(\n alignment[8],\n \"GGGGTCCATGAATTTTAATA-----GTAATAAAATGGTTATTTAATATTGCAAAATCCTCAGCTTTTAAGGAAAAACGTGTTTGACTTATTAATTATTTAGGACAA\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 21)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171686, 171328))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 9)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 4)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3020918, 3020919, 3020921, 3020938, 3020938, 3020938,\n 3020938, 3020938, 3020941, 3020959, 3020971, 3020972,\n 3020981, 3020984, 3020989, 3020994, 3021010, 3021014],\n [155025316, 155025316, 155025316, 155025316, 155025316, 155025316,\n 155025316, 155025316, 155025316, 155025298, 155025286, 155025285,\n 155025276, 155025273, 155025268, 155025263, 155025247, 155025243],\n [157515370, 157515370, 157515370, 157515370, 157515370, 157515370,\n 157515370, 157515370, 157515370, 157515352, 157515340, 157515339,\n 157515330, 157515327, 157515322, 157515317, 157515301, 157515297],\n [ 47544783, 47544783, 47544783, 47544783, 47544783, 47544783,\n 47544783, 47544779, 47544776, 47544758, 47544746, 47544745,\n 47544736, 47544733, 47544733, 47544728, 47544712, 47544708],\n [ 46172, 46172, 46172, 46155, 46152, 46150,\n 46149, 46145, 46142, 46124, 46124, 46124,\n 46124, 46121, 46121, 46116, 46100, 46096],\n [ 606, 605, 603, 586, 586, 586,\n 586, 586, 583, 565, 553, 552,\n 543, 540, 540, 540, 524, 524],\n [ 4263, 4263, 4261, 4244, 4244, 4242,\n 4241, 4237, 4234, 4216, 4204, 4203,\n 4194, 4191, 4186, 4181, 4165, 4161],\n [ 10482, 10483, 10485, 10502, 10502, 10502,\n 10503, 10507, 10510, 10528, 10540, 10540,\n 10549, 10552, 10557, 10562, 10578, 10582],\n [158037565, 158037564, 158037562, 158037545, 158037545, 158037545,\n 158037544, 158037540, 158037537, 158037519, 158037507, 158037506,\n 158037497, 158037494, 158037489, 158037484, 158037468, 158037464],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3020918 GAGGTTTGTGACTTTTAATA----------CTGATTGTTATCTAACATCACAGAATTCTC\nhg18.chr6 155025316 ---------------------------------ATGGTTATTTAATACTGCACAATCCTC\npanTro2.c 157515370 ---------------------------------ATGGTTATTTAATACTGCACAATCCTC\ncanFam2.c 47544783 --------------------------TAATAAAATAATTCTGTACCATTATGAAGTTCTC\nfelCat3.s 46172 ---GTCCATGAATTTTAATGGTGAAGTAATGAAATAATTCTTTAATATCAC---------\ncavPor2.s 606 GAGTTCTGCAAATtttaata----------ggaaaagaagatTAATATTACAAAGTTTTC\noryCun1.s 4263 -AGATCCATGAATTTTAATA---AAGCAATGAGATAATTATTTAATGTTGGAAAATCCTC\ncalJac1.C 10482 GGGGTCCATGAATTTTAATA-----GTAACAAAATGGTTATTCAATATTGCAAAATCCTC\nponAbe2.c 158037565 GGGGTCCATGAATTTTAATA-----GTAATAAAATGGTTATTTAATATTGCAAAATCCTC\n\nmm9.chr10 3020968 AGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA 3021014\nhg18.chr6 155025289 AGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA 155025243\npanTro2.c 157515343 AGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA 157515297\ncanFam2.c 47544749 AGCTCTTAAGGAAAAA-----GTGATTTGTTAATTACTTAGGACAA 47544708\nfelCat3.s 46124 -------------AAA-----GTAATTTATTAATTATTTAGGACAA 46096\ncavPor2.s 556 AGTTCTGATGGAAaaa----------gtgtgatttttttaaa---- 524\noryCun1.s 4207 AAGTCTTAAGGAAAAAAGTGTTTGACTTGTTAATGACTTGGGATGA 4161\ncalJac1.C 10537 AGC-TTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA 10582\nponAbe2.c 158037510 AGCTTTTAAGGAAAAACGTGTTTGACTTATTAATTATTTAGGACAA 158037464\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=85471.000000\ns mm9.chr10 3020918 96 + 129993255 GAGGTTTGTGACTTTTAATA----------CTGATTGTTATCTAACATCACAGAATTCTCAGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA\ns hg18.chr6 15874676 73 - 170899992 ---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA\ni hg18.chr6 I 11 C 0\ns panTro2.chr6 16393242 73 - 173908612 ---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA\nq panTro2.chr6 ---------------------------------9999999999999999999999999999999999999999999999999999999999999999999999999\ni panTro2.chr6 I 11 C 0\ns canFam2.chr1 78071473 75 - 125616256 --------------------------TAATAAAATAATTCTGTACCATTATGAAGTTCTCAGCTCTTAAGGAAAAA-----GTGATTTGTTAATTACTTAGGACAA\nq canFam2.chr1 --------------------------99999999999999999999999999999999999999999999999999-----9999999999999999999999999\ni canFam2.chr1 I 9 C 0\ns felCat3.scaffold_205680 73182 76 - 119354 ---GTCCATGAATTTTAATGGTGAAGTAATGAAATAATTCTTTAATATCAC----------------------AAA-----GTAATTTATTAATTATTTAGGACAA\nq felCat3.scaffold_205680 ---999989999999999999999999999999999999999999999999----------------------999-----9999999999999999999999769\ni felCat3.scaffold_205680 I 27 C 0\ns cavPor2.scaffold_216473 9420 82 - 10026 GAGTTCTGCAAATtttaata----------ggaaaagaagatTAATATTACAAAGTTTTCAGTTCTGATGGAAaaa----------gtgtgatttttttaaa----\nq cavPor2.scaffold_216473 99679966799668566465----------8567828838346568788268865663676558367765776667----------6965686997776684----\ni cavPor2.scaffold_216473 I 1372 I 28\ns oryCun1.scaffold_156751 463 102 - 4726 -AGATCCATGAATTTTAATA---AAGCAATGAGATAATTATTTAATGTTGGAAAATCCTCAAGTCTTAAGGAAAAAAGTGTTTGACTTGTTAATGACTTGGGATGA\nq oryCun1.scaffold_156751 -9999997999999999999---99999999999999999999999999999999998677999969999999999999999999999999999999999999999\ni oryCun1.scaffold_156751 I 37 C 0\ns calJac1.Contig6394 10482 100 + 133105 GGGGTCCATGAATTTTAATA-----GTAACAAAATGGTTATTCAATATTGCAAAATCCTCAGC-TTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA\ni calJac1.Contig6394 I 21 C 0\ns ponAbe2.chr6 16172866 101 - 174210431 GGGGTCCATGAATTTTAATA-----GTAATAAAATGGTTATTTAATATTGCAAAATCCTCAGCTTTTAAGGAAAAACGTGTTTGACTTATTAATTATTTAGGACAA\ni ponAbe2.chr6 I 21 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 187778 358 - 359464 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['G', 'A', 'G', 'G', 'T', 'T', 'T', 'G', 'T', 'G', 'A', 'C', 'T',\n 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'C', 'T', 'G', 'A', 'T', 'T', 'G', 'T', 'T',\n 'A', 'T', 'C', 'T', 'A', 'A', 'C', 'A', 'T', 'C', 'A', 'C', 'A',\n 'G', 'A', 'A', 'T', 'T', 'C', 'T', 'C', 'A', 'G', 'T', 'T', 'C',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'C', 'A', 'A', 'T',\n 'T', 'G', 'T', 'T', 'C', 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'T',\n 'A', 'T', 'T', 'T', 'G', 'T', 'C', 'T', 'A', 'G', 'G', 'A', 'G',\n 'G', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', 'A', 'T', 'G', 'G', 'T', 'T',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'C', 'T', 'G', 'C', 'A',\n 'C', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'T',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'A',\n 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'A', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', 'A', 'T', 'G', 'G', 'T', 'T',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'C', 'T', 'G', 'C', 'A',\n 'C', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'T',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'A',\n 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'A', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'T', 'A', 'A', 'T', 'A', 'A', 'A', 'A', 'T', 'A', 'A', 'T', 'T',\n 'C', 'T', 'G', 'T', 'A', 'C', 'C', 'A', 'T', 'T', 'A', 'T', 'G',\n 'A', 'A', 'G', 'T', 'T', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'C',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', '-', '-',\n '-', '-', '-', 'G', 'T', 'G', 'A', 'T', 'T', 'T', 'G', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A'],\n ['-', '-', '-', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T',\n 'T', 'T', 'T', 'A', 'A', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G',\n 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'A', 'T', 'A', 'A', 'T', 'T',\n 'C', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'T', 'C', 'A', 'C', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', '-', '-',\n '-', '-', '-', 'G', 'T', 'A', 'A', 'T', 'T', 'T', 'A', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A'],\n ['G', 'A', 'G', 'T', 'T', 'C', 'T', 'G', 'C', 'A', 'A', 'A', 'T',\n 't', 't', 't', 'a', 'a', 't', 'a', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'g', 'g', 'a', 'a', 'a', 'a', 'g', 'a', 'a',\n 'g', 'a', 't', 'T', 'A', 'A', 'T', 'A', 'T', 'T', 'A', 'C', 'A',\n 'A', 'A', 'G', 'T', 'T', 'T', 'T', 'C', 'A', 'G', 'T', 'T', 'C',\n 'T', 'G', 'A', 'T', 'G', 'G', 'A', 'A', 'a', 'a', 'a', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', 'g', 't', 'g', 't', 'g',\n 'a', 't', 't', 't', 't', 't', 't', 't', 'a', 'a', 'a', '-', '-',\n '-', '-'],\n ['-', 'A', 'G', 'A', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T',\n 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', 'A', 'A', 'G',\n 'C', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T', 'A', 'A', 'T', 'T',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'G', 'T', 'T', 'G', 'G', 'A',\n 'A', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'A', 'G', 'T', 'C',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'A', 'G',\n 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'G', 'T', 'T',\n 'A', 'A', 'T', 'G', 'A', 'C', 'T', 'T', 'G', 'G', 'G', 'A', 'T',\n 'G', 'A'],\n ['G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T',\n 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-', 'G',\n 'T', 'A', 'A', 'C', 'A', 'A', 'A', 'A', 'T', 'G', 'G', 'T', 'T',\n 'A', 'T', 'T', 'C', 'A', 'A', 'T', 'A', 'T', 'T', 'G', 'C', 'A',\n 'A', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', '-', 'T',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'A',\n 'T', 'A', 'T', 'T', 'T', 'G', 'A', 'T', 'T', 'T', 'G', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A'],\n ['G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T',\n 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-', 'G',\n 'T', 'A', 'A', 'T', 'A', 'A', 'A', 'A', 'T', 'G', 'G', 'T', 'T',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'T', 'T', 'G', 'C', 'A',\n 'A', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'T',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'G',\n 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'A', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 105724)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021014 : 3021014 + 40],\n \"ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG\",\n )\n self.assertEqual(alignment[0], \"ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG\")\n self.assertEqual(alignment.sequences[1].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[1].seq), 4726)\n self.assertEqual(\n alignment.sequences[1].seq[4121 : 4121 + 40],\n \"AATTCCTAAATCATCCAAGTTGGAATGACTTCATCAAGAT\",\n )\n self.assertEqual(alignment[1], \"ATCTTGATGAAGTCATTCCAACTTGGATGATTTAGGAATT\")\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999969999699999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[2].seq), 359464)\n self.assertEqual(\n alignment.sequences[2].seq[171288 : 171288 + 40],\n \"CATTCCTAAATCACATAAATTGGAATAACTTCACCAAGAT\",\n )\n self.assertEqual(alignment[2], \"ATCTTGGTGAAGTTATTCCAATTTATGTGATTTAGGAATG\")\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 358)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[3].seq), 133105)\n self.assertEqual(\n alignment.sequences[3].seq[10582 : 10582 + 40],\n \"ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG\",\n )\n self.assertEqual(alignment[3], \"ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 170899992)\n self.assertEqual(\n alignment.sequences[4].seq[155025203 : 155025203 + 40],\n \"CATTCCTAAGCCATGCAAGTTGGAATAACTTCACCAAAAT\",\n )\n self.assertEqual(alignment[4], \"ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 173908612)\n self.assertEqual(\n alignment.sequences[5].seq[157515257 : 157515257 + 40],\n \"CATTCCTAAGCCATGCAAGTTGGAATAACTTCACCAAAAT\",\n )\n self.assertEqual(alignment[5], \"ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\")\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[6].seq), 174210431)\n self.assertEqual(\n alignment.sequences[6].seq[158037424 : 158037424 + 40],\n \"CATTCCTAAGCCATGCAAGTTGGAATAACTTCACCAAAAT\",\n )\n self.assertEqual(alignment[6], \"ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[7].seq), 125616256)\n self.assertEqual(\n alignment.sequences[7].seq[47544668 : 47544668 + 40],\n \"CATTCCTAAATCATGCGAGTCAGAATGACTTCACTGAGAT\",\n )\n self.assertEqual(alignment[7], \"ATCTCAGTGAAGTCATTCTGACTCGCATGATTTAGGAATG\")\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[8].seq), 119354)\n self.assertEqual(\n alignment.sequences[8].seq[46056 : 46056 + 40],\n \"CATACCTAAATCATGCAAGTCAGAATAACTTCACTGAGAT\",\n )\n self.assertEqual(alignment[8], \"ATCTCAGTGAAGTTATTCTGACTTGCATGATTTAGGTATG\")\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"9999989999989988999997999979997996167779\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[9].seq), 10470)\n self.assertEqual(\n alignment.sequences[9].seq[7314 : 7314 + 40],\n \"CATCGCTCAGTCATACGAGTCGGAATGATTTCACTGATGT\",\n )\n self.assertEqual(alignment[9], \"ACATCAGTGAAATCATTCCGACTCGTATGACTGAGCGATG\")\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"9759855999977756667495765475885678385647\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (524, 496))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 10)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 4)\n self.assertTrue(\n np.array_equal(\n # fmt: off\n alignment.coordinates, np.array([[ 3021014, 3021054],\n [ 4161, 4121],\n [ 171328, 171288],\n [ 10582, 10622],\n [155025243, 155025203],\n [157515297, 157515257],\n [158037464, 158037424],\n [ 47544708, 47544668],\n [ 46096, 46056],\n [ 7354, 7314],\n ])\n # fmt: on\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021014 ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG 3021054\noryCun1.s 4161 ATCTTGATGAAGTCATTCCAACTTGGATGATTTAGGAATT 4121\notoGar1.s 171328 ATCTTGGTGAAGTTATTCCAATTTATGTGATTTAGGAATG 171288\ncalJac1.C 10582 ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG 10622\nhg18.chr6 155025243 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG 155025203\npanTro2.c 157515297 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG 157515257\nponAbe2.c 158037464 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG 158037424\ncanFam2.c 47544708 ATCTCAGTGAAGTCATTCTGACTCGCATGATTTAGGAATG 47544668\nfelCat3.s 46096 ATCTCAGTGAAGTTATTCTGACTTGCATGATTTAGGTATG 46056\ndasNov1.s 7354 ACATCAGTGAAATCATTCCGACTCGTATGACTGAGCGATG 7314\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=105724.000000\ns mm9.chr10 3021014 40 + 129993255 ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG\ns oryCun1.scaffold_156751 565 40 - 4726 ATCTTGATGAAGTCATTCCAACTTGGATGATTTAGGAATT\nq oryCun1.scaffold_156751 9999999999999969999699999999999999999999\ni oryCun1.scaffold_156751 C 0 C 0\ns otoGar1.scaffold_334.1-359464 188136 40 - 359464 ATCTTGGTGAAGTTATTCCAATTTATGTGATTTAGGAATG\nq otoGar1.scaffold_334.1-359464 9999999999999999999999999999999999999999\ni otoGar1.scaffold_334.1-359464 I 358 C 0\ns calJac1.Contig6394 10582 40 + 133105 ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG\ni calJac1.Contig6394 C 0 C 0\ns hg18.chr6 15874749 40 - 170899992 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16393315 40 - 173908612 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\nq panTro2.chr6 9999999999999999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16172967 40 - 174210431 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\ni ponAbe2.chr6 C 0 C 0\ns canFam2.chr1 78071548 40 - 125616256 ATCTCAGTGAAGTCATTCTGACTCGCATGATTTAGGAATG\nq canFam2.chr1 9999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ns felCat3.scaffold_205680 73258 40 - 119354 ATCTCAGTGAAGTTATTCTGACTTGCATGATTTAGGTATG\nq felCat3.scaffold_205680 9999989999989988999997999979997996167779\ni felCat3.scaffold_205680 C 0 C 0\ns dasNov1.scaffold_56749 3116 40 - 10470 ACATCAGTGAAATCATTCCGACTCGTATGACTGAGCGATG\nq dasNov1.scaffold_56749 9759855999977756667495765475885678385647\ni dasNov1.scaffold_56749 N 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 9502 28 - 10026 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'C', 'C', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'C', 'G', 'C',\n 'C', 'A', 'C', 'T', 'G', 'G', 'A', 'T', 'T', 'T', 'T', 'G', 'T',\n 'A', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'A', 'T', 'A', 'C', 'T',\n 'G'],\n ['A', 'T', 'C', 'T', 'T', 'G', 'A', 'T', 'G', 'A', 'A', 'G', 'T',\n 'C', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'G',\n 'A', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'T'],\n ['A', 'T', 'C', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'T', 'T', 'T', 'A', 'T',\n 'G', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'T',\n 'G', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'C',\n 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'C',\n 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'C',\n 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'C', 'T', 'C', 'A', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'C', 'A', 'T', 'T', 'C', 'T', 'G', 'A', 'C', 'T', 'C', 'G', 'C',\n 'A', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'C', 'T', 'C', 'A', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'T', 'G', 'A', 'C', 'T', 'T', 'G', 'C',\n 'A', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'T', 'A', 'T',\n 'G'],\n ['A', 'C', 'A', 'T', 'C', 'A', 'G', 'T', 'G', 'A', 'A', 'A', 'T',\n 'C', 'A', 'T', 'T', 'C', 'C', 'G', 'A', 'C', 'T', 'C', 'G', 'T',\n 'A', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'G', 'C', 'G', 'A', 'T',\n 'G']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 115790)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021054 : 3021054 + 50],\n \"CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAGGACTTACATGCAG\",\n )\n self.assertEqual(\n alignment[0],\n \"CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAG--------------------GACTTACATGCAG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[458 : 458 + 38],\n \"TCACAAGTATTTATAGCAACTCTGAACTCCCAAATGAG\",\n )\n self.assertEqual(\n alignment[1],\n \"CTCATTTGGGAGTTCAGAGTT--------GCTATAAA--------------------TACTTGTGA----\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"78877766789884666566698766677876665669\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 28)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[4052 : 4052 + 69],\n \"ATACGTGTAATTAAGGAGGAAAAAAGAAGACTCCATTAGGCAGTTATAAAATGTAAGAGCCCAAATTAG\",\n )\n self.assertEqual(\n alignment[2],\n \"CTAATTTGGGCTCTTACATTTTATAACTGCCTAATGGAGTCTTCTTTTTTCCT-CCTTAATTACACGTAT\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"999999999999979997999999999999999999999997997999999979979999999495999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[3].seq), 359464)\n self.assertEqual(\n alignment.sequences[3].seq[171219 : 171219 + 69],\n \"GTACATAGAGTCTGGGGAAGGGACCAGTGGGCTCCATTAAGCCTTTATGAACCTGTGTCCCCAAGTTAG\",\n )\n self.assertEqual(\n alignment[3],\n \"CTAACTTGGGGACACAGG-TTCATAAAGGCTTAATGGAGCCCACTGGTCCCTTCCCCAGACTCTATGTAC\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"999999999999999999999999999999999999998999999689999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[4].seq), 133105)\n self.assertEqual(\n alignment.sequences[4].seq[10622 : 10622 + 70],\n \"CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGCCTATATGTAT\",\n )\n self.assertEqual(\n alignment[4],\n \"CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGCCTATATGTAT\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155025133 : 155025133 + 70],\n \"ATACATATAGTCTAGGGAAGGAAGGAGCAGACTTCATTAGGCAGTTAGGAAATGTAAATCCCCAAATTGT\",\n )\n self.assertEqual(\n alignment[5],\n \"ACAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCCTTCCTTCCCTAGACTATATGTAT\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[6].seq), 173908612)\n self.assertEqual(\n alignment.sequences[6].seq[157515187 : 157515187 + 70],\n \"ATACATATAGTCTAGGGAAGGAAAGAGCAGACTTCATTAGGCAGTTAGGAAATGTAAATCCCCAAATTGG\",\n )\n self.assertEqual(\n alignment[6],\n \"CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[7].seq), 174210431)\n self.assertEqual(\n alignment.sequences[7].seq[158037354 : 158037354 + 70],\n \"ATACATATAGTCTAGGGAAGGAAAGAGCAGACTTCATTAGGCAGTTAGGAAATGTAAATCCCCAAATTGG\",\n )\n self.assertEqual(\n alignment[7],\n \"CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[8].seq), 125616256)\n self.assertEqual(\n alignment.sequences[8].seq[47544598 : 47544598 + 70],\n \"ATACATATGGTGTAGGGAAGAAAACATCAGCTTTCATTAAGCAATTATGAAATTTGAGTCACCAAATTAG\",\n )\n self.assertEqual(\n alignment[8],\n \"CTAATTTGGTGACTCAAATTTCATAATTGCTTAATGAAAGCTGATGTTTTCTTCCCTACACCATATGTAT\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[9].seq), 119354)\n self.assertEqual(\n alignment.sequences[9].seq[45986 : 45986 + 70],\n \"ATGCATATAGTCTTGGGAAGGAAACAGCAGGCTTCCTTAAGCAATTATGAAATTCAAGTCACCAAATTAG\",\n )\n self.assertEqual(\n alignment[9],\n \"CTAATTTGGTGACTTGAATTTCATAATTGCTTAAGGAAGCCTGCTGTTTCCTTCCCAAGACTATATGCAT\",\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"9769999999975699868977669777966666596959759669595666758736585676666655\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[10].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[10].seq), 10470)\n self.assertEqual(\n alignment.sequences[10].seq[7244 : 7244 + 70],\n \"ATACTTATAGTCTAGAGAAGAAAACAGCAGGCTTCGGTTAGCAATTTTAAAATGTGAGTCCCCCAATTAG\",\n )\n self.assertEqual(\n alignment[10],\n \"CTAATTGGGGGACTCACATTTTAAAATTGCTAACCGAAGCCTGCTGTTTTCTTCTCTAGACTATAAGTAT\",\n )\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"],\n \"5556576999664654656985688667655565647767537567688856666555556565555656\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 11)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 3)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021054, 3021072, 3021073, 3021075, 3021083, 3021091,\n 3021091, 3021091, 3021091, 3021100, 3021104],\n [ 496, 478, 477, 475, 475, 467,\n 467, 467, 467, 458, 458],\n [ 4121, 4103, 4102, 4100, 4092, 4084,\n 4068, 4068, 4065, 4056, 4052],\n [ 171288, 171270, 171270, 171268, 171260, 171252,\n 171236, 171235, 171232, 171223, 171219],\n [ 10622, 10640, 10641, 10643, 10651, 10659,\n 10675, 10676, 10679, 10688, 10692],\n [155025203, 155025185, 155025184, 155025182, 155025174, 155025166,\n 155025150, 155025149, 155025146, 155025137, 155025133],\n [157515257, 157515239, 157515238, 157515236, 157515228, 157515220,\n 157515204, 157515203, 157515200, 157515191, 157515187],\n [158037424, 158037406, 158037405, 158037403, 158037395, 158037387,\n 158037371, 158037370, 158037367, 158037358, 158037354],\n [ 47544668, 47544650, 47544649, 47544647, 47544639, 47544631,\n 47544615, 47544614, 47544611, 47544602, 47544598],\n [ 46056, 46038, 46037, 46035, 46027, 46019,\n 46003, 46002, 45999, 45990, 45986],\n [ 7314, 7296, 7295, 7293, 7285, 7277,\n 7261, 7260, 7257, 7248, 7244],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021054 CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAG--------------------GAC\ncavPor2.s 496 CTCATTTGGGAGTTCAGAGTT--------GCTATAAA--------------------TAC\noryCun1.s 4121 CTAATTTGGGCTCTTACATTTTATAACTGCCTAATGGAGTCTTCTTTTTTCCT-CCTTAA\notoGar1.s 171288 CTAACTTGGGGACACAGG-TTCATAAAGGCTTAATGGAGCCCACTGGTCCCTTCCCCAGA\ncalJac1.C 10622 CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGC\nhg18.chr6 155025203 ACAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCCTTCCTTCCCTAGA\npanTro2.c 157515257 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGA\nponAbe2.c 158037424 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGA\ncanFam2.c 47544668 CTAATTTGGTGACTCAAATTTCATAATTGCTTAATGAAAGCTGATGTTTTCTTCCCTACA\nfelCat3.s 46056 CTAATTTGGTGACTTGAATTTCATAATTGCTTAAGGAAGCCTGCTGTTTCCTTCCCAAGA\ndasNov1.s 7314 CTAATTGGGGGACTCACATTTTAAAATTGCTAACCGAAGCCTGCTGTTTTCTTCTCTAGA\n\nmm9.chr10 3021094 TTACATGCAG 3021104\ncavPor2.s 464 TTGTGA---- 458\noryCun1.s 4062 TTACACGTAT 4052\notoGar1.s 171229 CTCTATGTAC 171219\ncalJac1.C 10682 CTATATGTAT 10692\nhg18.chr6 155025143 CTATATGTAT 155025133\npanTro2.c 157515197 CTATATGTAT 157515187\nponAbe2.c 158037364 CTATATGTAT 158037354\ncanFam2.c 47544608 CCATATGTAT 47544598\nfelCat3.s 45996 CTATATGCAT 45986\ndasNov1.s 7254 CTATAAGTAT 7244\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=115790.000000\ns mm9.chr10 3021054 50 + 129993255 CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAG--------------------GACTTACATGCAG\ns cavPor2.scaffold_216473 9530 38 - 10026 CTCATTTGGGAGTTCAGAGTT--------GCTATAAA--------------------TACTTGTGA----\nq cavPor2.scaffold_216473 788777667898846665666--------98766677--------------------876665669----\ni cavPor2.scaffold_216473 I 28 C 0\ns oryCun1.scaffold_156751 605 69 - 4726 CTAATTTGGGCTCTTACATTTTATAACTGCCTAATGGAGTCTTCTTTTTTCCT-CCTTAATTACACGTAT\nq oryCun1.scaffold_156751 99999999999997999799999999999999999999999799799999997-9979999999495999\ni oryCun1.scaffold_156751 C 0 C 0\ns otoGar1.scaffold_334.1-359464 188176 69 - 359464 CTAACTTGGGGACACAGG-TTCATAAAGGCTTAATGGAGCCCACTGGTCCCTTCCCCAGACTCTATGTAC\nq otoGar1.scaffold_334.1-359464 999999999999999999-999999999999999999998999999689999999999999999999999\ni otoGar1.scaffold_334.1-359464 C 0 C 0\ns calJac1.Contig6394 10622 70 + 133105 CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGCCTATATGTAT\ni calJac1.Contig6394 C 0 C 0\ns hg18.chr6 15874789 70 - 170899992 ACAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCCTTCCTTCCCTAGACTATATGTAT\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16393355 70 - 173908612 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT\nq panTro2.chr6 9999999999999999999999999999999999999999999999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16173007 70 - 174210431 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT\ni ponAbe2.chr6 C 0 C 0\ns canFam2.chr1 78071588 70 - 125616256 CTAATTTGGTGACTCAAATTTCATAATTGCTTAATGAAAGCTGATGTTTTCTTCCCTACACCATATGTAT\nq canFam2.chr1 9999999999999999999999999999999999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ns felCat3.scaffold_205680 73298 70 - 119354 CTAATTTGGTGACTTGAATTTCATAATTGCTTAAGGAAGCCTGCTGTTTCCTTCCCAAGACTATATGCAT\nq felCat3.scaffold_205680 9769999999975699868977669777966666596959759669595666758736585676666655\ni felCat3.scaffold_205680 C 0 C 0\ns dasNov1.scaffold_56749 3156 70 - 10470 CTAATTGGGGGACTCACATTTTAAAATTGCTAACCGAAGCCTGCTGTTTTCTTCTCTAGACTATAAGTAT\nq dasNov1.scaffold_56749 5556576999664654656985688667655565647767537567688856666555556565555656\ni dasNov1.scaffold_56749 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'T', 'C', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'A', 'A', 'C',\n 'T', 'T', 'A', 'C', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'C', 'A',\n 'A', 'A', 'G', 'G', 'C', 'T', 'T', 'C', 'C', 'A', 'G', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'G', 'A', 'C', 'T', 'T', 'A', 'C', 'A',\n 'T', 'G', 'C', 'A', 'G'],\n ['C', 'T', 'C', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'A', 'G', 'T',\n 'T', 'C', 'A', 'G', 'A', 'G', 'T', 'T', '-', '-', '-', '-', '-',\n '-', '-', '-', 'G', 'C', 'T', 'A', 'T', 'A', 'A', 'A', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'T', 'A', 'C', 'T', 'T', 'G', 'T', 'G',\n 'A', '-', '-', '-', '-'],\n ['C', 'T', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'C', 'T', 'C',\n 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'A',\n 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'G', 'A', 'G',\n 'T', 'C', 'T', 'T', 'C', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'C',\n 'T', '-', 'C', 'C', 'T', 'T', 'A', 'A', 'T', 'T', 'A', 'C', 'A',\n 'C', 'G', 'T', 'A', 'T'],\n ['C', 'T', 'A', 'A', 'C', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'C',\n 'A', 'C', 'A', 'G', 'G', '-', 'T', 'T', 'C', 'A', 'T', 'A', 'A',\n 'A', 'G', 'G', 'C', 'T', 'T', 'A', 'A', 'T', 'G', 'G', 'A', 'G',\n 'C', 'C', 'C', 'A', 'C', 'T', 'G', 'G', 'T', 'C', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'C', 'A', 'G', 'A', 'C', 'T', 'C', 'T', 'A',\n 'T', 'G', 'T', 'A', 'C'],\n ['C', 'C', 'A', 'G', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'C',\n 'T', 'T', 'A', 'G', 'A', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'A',\n 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G',\n 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'C', 'C', 'T', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'T'],\n ['A', 'C', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'T',\n 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G',\n 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'T'],\n ['C', 'C', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'T',\n 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G',\n 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'T'],\n ['C', 'C', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'T',\n 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G',\n 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'T'],\n ['C', 'T', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'C',\n 'T', 'C', 'A', 'A', 'A', 'T', 'T', 'T', 'C', 'A', 'T', 'A', 'A',\n 'T', 'T', 'G', 'C', 'T', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'A',\n 'G', 'C', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'T', 'T', 'C', 'T',\n 'T', 'C', 'C', 'C', 'T', 'A', 'C', 'A', 'C', 'C', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'T'],\n ['C', 'T', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'C',\n 'T', 'T', 'G', 'A', 'A', 'T', 'T', 'T', 'C', 'A', 'T', 'A', 'A',\n 'T', 'T', 'G', 'C', 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'G',\n 'C', 'C', 'T', 'G', 'C', 'T', 'G', 'T', 'T', 'T', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'A', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A',\n 'T', 'G', 'C', 'A', 'T'],\n ['C', 'T', 'A', 'A', 'T', 'T', 'G', 'G', 'G', 'G', 'G', 'A', 'C',\n 'T', 'C', 'A', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'A', 'A', 'A',\n 'T', 'T', 'G', 'C', 'T', 'A', 'A', 'C', 'C', 'G', 'A', 'A', 'G',\n 'C', 'C', 'T', 'G', 'C', 'T', 'G', 'T', 'T', 'T', 'T', 'C', 'T',\n 'T', 'C', 'T', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A',\n 'A', 'G', 'T', 'A', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 44222)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021104 : 3021104 + 32],\n \"CTGTTAGTGCTGTTTTAATGTACCTCGCAGTA\",\n )\n self.assertEqual(alignment[0], \"CTGTTAGTGCTGTTTT---AATGTACCTCGCAGTA\")\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[431 : 431 + 27], \"TATAAAAATTTACATTAAGAAAGTAAT\"\n )\n self.assertEqual(alignment[1], \"-----ATTACTTTCTT---AATGTAAATTTTTATA\")\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"], \"554558687467957999989884575\"\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[4022 : 4022 + 30],\n \"TATAAAATATTACATTGAGAATACTAGCAA\",\n )\n self.assertEqual(alignment[2], \"TTGCTAGTA--TTCTC---AATGTAATATTTTATA\")\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"999979999966656999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[3].seq), 359464)\n self.assertEqual(\n alignment.sequences[3].seq[171187 : 171187 + 32],\n \"TATAAAACATTATATTAAGGGAACACCAGCAA\",\n )\n self.assertEqual(alignment[3], \"TTGCTGGTGTTCCCTT---AATATAATGTTTTATA\")\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"99999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[4].seq), 133105)\n self.assertEqual(\n alignment.sequences[4].seq[10692 : 10692 + 30],\n \"TTACTCGTGCCCTTAATATAGCATTTTATA\",\n )\n self.assertEqual(alignment[4], \"TTACTCGTG--CCCTT---AATATAGCATTTTATA\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155025103 : 155025103 + 30],\n \"TATAAAATGTGATATTAAGAGTACCAGCAA\",\n )\n self.assertEqual(alignment[5], \"TTGCTGGTA--CTCTT---AATATCACATTTTATA\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[6].seq), 173908612)\n self.assertEqual(\n alignment.sequences[6].seq[157515157 : 157515157 + 30],\n \"TATAAAATGTGATATTAAGAGTACCAGCAA\",\n )\n self.assertEqual(alignment[6], \"TTGCTGGTA--CTCTT---AATATCACATTTTATA\")\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[7].seq), 174210431)\n self.assertEqual(\n alignment.sequences[7].seq[158037324 : 158037324 + 30],\n \"TATAAAATGTTATATTAAGAGCACCAGCAA\",\n )\n self.assertEqual(alignment[7], \"TTGCTGGTG--CTCTT---AATATAACATTTTATA\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[8].seq), 125616256)\n self.assertEqual(\n alignment.sequences[8].seq[47544573 : 47544573 + 25],\n \"TGCTACATTTTGAGAGCACCAGCAA\",\n )\n self.assertEqual(alignment[8], \"TTGCTGGTGCTCTCAA---AATGTAGCA-------\")\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 196)\n self.assertEqual(alignment.sequences[9].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[9].seq), 119354)\n self.assertEqual(\n alignment.sequences[9].seq[45961 : 45961 + 25], \"TGTTATATTTTGAGAGCACCAGCAA\"\n )\n self.assertEqual(alignment[9], \"TTGCTGGTGCTCTCAA---AATATAACA-------\")\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"], \"8677668566555658876555655\"\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 6)\n self.assertEqual(alignment.sequences[10].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[10].seq), 10470)\n self.assertEqual(\n alignment.sequences[10].seq[7211 : 7211 + 33],\n \"CATAAAATGTTACATTAATCAGATCACCAGCAA\",\n )\n self.assertEqual(alignment[10], \"TTGCTGGTG--ATCTGATTAATGTAACATTTTATG\")\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"],\n \"856647736775356546747663745776545\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[11].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[11].seq), 100002)\n self.assertEqual(\n alignment.sequences[11].seq[95225 : 95225 + 21], \"CTGTTAATGCTCTGTTTTATG\"\n )\n self.assertEqual(alignment[11], \"CTGTTAATG--CTCTG------------TTTTATG\")\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"], \"999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 7564)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 12)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 2)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021104, 3021109, 3021113, 3021115, 3021120, 3021120,\n 3021129, 3021136],\n [ 458, 458, 454, 452, 447, 447,\n 438, 431],\n [ 4052, 4047, 4043, 4043, 4038, 4038,\n 4029, 4022],\n [ 171219, 171214, 171210, 171208, 171203, 171203,\n 171194, 171187],\n [ 10692, 10697, 10701, 10701, 10706, 10706,\n 10715, 10722],\n [155025133, 155025128, 155025124, 155025124, 155025119, 155025119,\n 155025110, 155025103],\n [157515187, 157515182, 157515178, 157515178, 157515173, 157515173,\n 157515164, 157515157],\n [158037354, 158037349, 158037345, 158037345, 158037340, 158037340,\n 158037331, 158037324],\n [ 47544598, 47544593, 47544589, 47544587, 47544582, 47544582,\n 47544573, 47544573],\n [ 45986, 45981, 45977, 45975, 45970, 45970,\n 45961, 45961],\n [ 7244, 7239, 7235, 7235, 7230, 7227,\n 7218, 7211],\n [ 95225, 95230, 95234, 95234, 95239, 95239,\n 95239, 95246],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021104 CTGTTAGTGCTGTTTT---AATGTACCTCGCAGTA 3021136\ncavPor2.s 458 -----ATTACTTTCTT---AATGTAAATTTTTATA 431\noryCun1.s 4052 TTGCTAGTA--TTCTC---AATGTAATATTTTATA 4022\notoGar1.s 171219 TTGCTGGTGTTCCCTT---AATATAATGTTTTATA 171187\ncalJac1.C 10692 TTACTCGTG--CCCTT---AATATAGCATTTTATA 10722\nhg18.chr6 155025133 TTGCTGGTA--CTCTT---AATATCACATTTTATA 155025103\npanTro2.c 157515187 TTGCTGGTA--CTCTT---AATATCACATTTTATA 157515157\nponAbe2.c 158037354 TTGCTGGTG--CTCTT---AATATAACATTTTATA 158037324\ncanFam2.c 47544598 TTGCTGGTGCTCTCAA---AATGTAGCA------- 47544573\nfelCat3.s 45986 TTGCTGGTGCTCTCAA---AATATAACA------- 45961\ndasNov1.s 7244 TTGCTGGTG--ATCTGATTAATGTAACATTTTATG 7211\nechTel1.s 95225 CTGTTAATG--CTCTG------------TTTTATG 95246\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=44222.000000\ns mm9.chr10 3021104 32 + 129993255 CTGTTAGTGCTGTTTT---AATGTACCTCGCAGTA\ns cavPor2.scaffold_216473 9568 27 - 10026 -----ATTACTTTCTT---AATGTAAATTTTTATA\nq cavPor2.scaffold_216473 -----55455868746---7957999989884575\ni cavPor2.scaffold_216473 C 0 C 0\ns oryCun1.scaffold_156751 674 30 - 4726 TTGCTAGTA--TTCTC---AATGTAATATTTTATA\nq oryCun1.scaffold_156751 999979999--96665---6999999999999999\ni oryCun1.scaffold_156751 C 0 C 0\ns otoGar1.scaffold_334.1-359464 188245 32 - 359464 TTGCTGGTGTTCCCTT---AATATAATGTTTTATA\nq otoGar1.scaffold_334.1-359464 9999999999999999---9999999999999999\ni otoGar1.scaffold_334.1-359464 C 0 C 0\ns calJac1.Contig6394 10692 30 + 133105 TTACTCGTG--CCCTT---AATATAGCATTTTATA\ni calJac1.Contig6394 C 0 C 0\ns hg18.chr6 15874859 30 - 170899992 TTGCTGGTA--CTCTT---AATATCACATTTTATA\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16393425 30 - 173908612 TTGCTGGTA--CTCTT---AATATCACATTTTATA\nq panTro2.chr6 999999999--99999---9999999999999999\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16173077 30 - 174210431 TTGCTGGTG--CTCTT---AATATAACATTTTATA\ni ponAbe2.chr6 C 0 C 0\ns canFam2.chr1 78071658 25 - 125616256 TTGCTGGTGCTCTCAA---AATGTAGCA-------\nq canFam2.chr1 9999999999999999---999999999-------\ni canFam2.chr1 C 0 I 196\ns felCat3.scaffold_205680 73368 25 - 119354 TTGCTGGTGCTCTCAA---AATATAACA-------\nq felCat3.scaffold_205680 8677668566555658---876555655-------\ni felCat3.scaffold_205680 C 0 I 6\ns dasNov1.scaffold_56749 3226 33 - 10470 TTGCTGGTG--ATCTGATTAATGTAACATTTTATG\nq dasNov1.scaffold_56749 856647736--775356546747663745776545\ni dasNov1.scaffold_56749 C 0 C 0\ns echTel1.scaffold_288249 95225 21 + 100002 CTGTTAATG--CTCTG------------TTTTATG\nq echTel1.scaffold_288249 999999999--99999------------9999999\ni echTel1.scaffold_288249 I 7564 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'T', 'G', 'T', 'T', 'A', 'G', 'T', 'G', 'C', 'T', 'G', 'T',\n 'T', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'C',\n 'C', 'T', 'C', 'G', 'C', 'A', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', 'A', 'T', 'T', 'A', 'C', 'T', 'T', 'T',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'A',\n 'A', 'T', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'A', 'G', 'T', 'A', '-', '-', 'T', 'T',\n 'C', 'T', 'C', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'A',\n 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', 'T', 'T', 'C', 'C',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'A',\n 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'A', 'C', 'T', 'C', 'G', 'T', 'G', '-', '-', 'C', 'C',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'G',\n 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'A', '-', '-', 'C', 'T',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'C', 'A',\n 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'A', '-', '-', 'C', 'T',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'C', 'A',\n 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', '-', '-', 'C', 'T',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'A',\n 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', 'C', 'T', 'C', 'T',\n 'C', 'A', 'A', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'G',\n 'C', 'A', '-', '-', '-', '-', '-', '-', '-'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', 'C', 'T', 'C', 'T',\n 'C', 'A', 'A', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'A',\n 'C', 'A', '-', '-', '-', '-', '-', '-', '-'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', '-', '-', 'A', 'T',\n 'C', 'T', 'G', 'A', 'T', 'T', 'A', 'A', 'T', 'G', 'T', 'A', 'A',\n 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'G'],\n ['C', 'T', 'G', 'T', 'T', 'A', 'A', 'T', 'G', '-', '-', 'C', 'T',\n 'C', 'T', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'T', 'T', 'T', 'T', 'A', 'T', 'G']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 43757)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021136 : 3021136 + 44],\n \"AGGCAAATGAGGTGATAAGATTGTGTTTACTCCCTCTGTGCTTG\",\n )\n self.assertEqual(\n alignment[0],\n \"AGGCAAATGAGGTGATAAGA-------TTGTGTT-----TAC----TCCCTCTGTGC----------TTG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[388 : 388 + 43],\n \"catacacacagagaatgAATATATCACTGTTATCTCATCTGCT\",\n )\n self.assertEqual(\n alignment[1],\n \"AG-CAGATGAGATAACAGTG-------ATATATT-----cat----tctctgtgtgt----------atg\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"4996766988786798889867956675666896967579888\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[3980 : 3980 + 42],\n \"CACACAAATAAGAAATAGATGCCCTCATCACCTCATTTGCTT\",\n )\n self.assertEqual(\n alignment[2],\n \"AAGCAAATGAGGTGATGAGG---------GCATC-----TAT----TTCTTATTTGT----------GTG\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"999989999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[3].seq), 359464)\n self.assertEqual(\n alignment.sequences[3].seq[171142 : 171142 + 45],\n \"CACACGTGGGGGACAAGTACATATGTCCTGTGATCTCATTTGTTT\",\n )\n self.assertEqual(\n alignment[3],\n \"AAACAAATGAGATCACA-GG-------ACATATG-----TA--CTTGTCCCCCACGT----------GTG\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"999999999999999999999999999999939999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 15)\n self.assertEqual(alignment.sequences[4].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[4].seq), 133105)\n self.assertEqual(\n alignment.sequences[4].seq[10722 : 10722 + 45],\n \"AAGCAAATGAGATCACAGCACATGTATATTTTTTCTCCGTGTGTG\",\n )\n self.assertEqual(\n alignment[4],\n \"AAGCAAATGAGATCACA----------GCACATG-----TATATTTTTTCTCCGTGT----------GTG\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 15)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155025056 : 155025056 + 47],\n \"CACACACAGAGAAAAAAACATATATGCCCTTGTGATCTCATTTGTTT\",\n )\n self.assertEqual(\n alignment[5],\n \"AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 15)\n self.assertEqual(alignment.sequences[6].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[6].seq), 173908612)\n self.assertEqual(\n alignment.sequences[6].seq[157515110 : 157515110 + 47],\n \"CACACACAGAGAAAAAAACATATATGCCCTTGTGATCTCATTTGTTT\",\n )\n self.assertEqual(\n alignment[6],\n \"AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 15)\n self.assertEqual(alignment.sequences[7].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[7].seq), 174210431)\n self.assertEqual(\n alignment.sequences[7].seq[158037277 : 158037277 + 47],\n \"CACACACAGAGAAAAAAATACATATGCCCTTGTGATCTCATTTGTTT\",\n )\n self.assertEqual(\n alignment[7],\n \"AAACAAATGAGATCACAAGG-------GCATATG-----TAT-TTTTTTCTCTGTGT----------GTG\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 15)\n self.assertEqual(alignment.sequences[8].id, \"eriEur1.scaffold_266115\")\n self.assertEqual(len(alignment.sequences[8].seq), 4589)\n self.assertEqual(\n alignment.sequences[8].seq[358 : 358 + 65],\n \"taaataataagataagatgaaagCATAGCATGTATTTTCTtgccctctccttctctgtctctgtc\",\n )\n self.assertEqual(\n alignment[8],\n \"taaataataagataagatgaaagCATAGCATGTA-----TTTTCTtgccctctccttctctgtctctgtc\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[9].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[9].seq), 125616256)\n self.assertEqual(\n alignment.sequences[9].seq[47544326 : 47544326 + 51],\n \"CACAGACCCCACACAGAGAGAAAGCATATACACACGGTATCTCATTTTCTa\",\n )\n self.assertEqual(\n alignment[9],\n \"tAGAAAATGAGATACC-----------GTGTGTA-----TATGCTTTCTCTCTGTGT---GGGGTCTGTG\",\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 196)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[10].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[10].seq), 119354)\n self.assertEqual(\n alignment.sequences[10].seq[45904 : 45904 + 51],\n \"CACAGACACCACACAGAGAGGAAGAATACACGTGTCTTATCTCATTTGCTT\",\n )\n self.assertEqual(\n alignment[10],\n \"AAGCAAATGAGATAAG-----------ACACGTG-----TATTCTTCCTCTCTGTGT---GGTGTCTGTG\",\n )\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"],\n \"975559665645435353463242434515353544222333635339999\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 6)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[11].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[11].seq), 10470)\n self.assertEqual(\n alignment.sequences[11].seq[7165 : 7165 + 46],\n \"TACACAGAGAAAGAATATTTATTTGCCCTGGTCCTCTCACTTTCCT\",\n )\n self.assertEqual(\n alignment[11],\n \"AGGAAAGTGAGAGGACCAGG-------GCAAATA-----AATATTCTTTCTCTGTGT----------A--\",\n )\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"],\n \"5556976455665765856867685558586864578595356565\",\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[12].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[12].seq), 100002)\n self.assertEqual(\n alignment.sequences[12].seq[95246 : 95246 + 51],\n \"AAGAAGGTGAGATGACAAGGGTGTATAGATAGGATATTCTTGCTTTGGGTG\",\n )\n self.assertEqual(\n alignment[12],\n \"AAGAAGGTGAGATGACAAGG-------GTGTATAGATAGGATATTCTTGCTTTGGGT----------G--\",\n )\n self.assertEqual(\n alignment.sequences[12].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[12].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[12].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 13)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 2)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021136, 3021138, 3021139, 3021152, 3021153, 3021154,\n 3021156, 3021156, 3021158, 3021163, 3021163, 3021165,\n 3021166, 3021166, 3021166, 3021177, 3021177, 3021177,\n 3021178, 3021180],\n [ 431, 429, 429, 416, 415, 414,\n 412, 412, 410, 405, 405, 403,\n 402, 402, 402, 391, 391, 391,\n 390, 388],\n [ 4022, 4020, 4019, 4006, 4005, 4004,\n 4002, 4002, 4002, 3997, 3997, 3995,\n 3994, 3994, 3994, 3983, 3983, 3983,\n 3982, 3980],\n [ 171187, 171185, 171184, 171171, 171170, 171170,\n 171168, 171168, 171166, 171161, 171161, 171159,\n 171159, 171159, 171156, 171145, 171145, 171145,\n 171144, 171142],\n [ 10722, 10724, 10725, 10738, 10739, 10739,\n 10739, 10739, 10741, 10746, 10746, 10748,\n 10749, 10750, 10753, 10764, 10764, 10764,\n 10765, 10767],\n [155025103, 155025101, 155025100, 155025087, 155025086, 155025085,\n 155025083, 155025083, 155025081, 155025076, 155025076, 155025074,\n 155025073, 155025073, 155025070, 155025059, 155025059, 155025059,\n 155025058, 155025056],\n [157515157, 157515155, 157515154, 157515141, 157515140, 157515139,\n 157515137, 157515137, 157515135, 157515130, 157515130, 157515128,\n 157515127, 157515127, 157515124, 157515113, 157515113, 157515113,\n 157515112, 157515110],\n [158037324, 158037322, 158037321, 158037308, 158037307, 158037306,\n 158037304, 158037304, 158037302, 158037297, 158037297, 158037295,\n 158037294, 158037294, 158037291, 158037280, 158037280, 158037280,\n 158037279, 158037277],\n [ 358, 360, 361, 374, 375, 376,\n 378, 385, 387, 392, 392, 394,\n 395, 396, 399, 410, 413, 420,\n 421, 423],\n [ 47544377, 47544375, 47544374, 47544361, 47544361, 47544361,\n 47544361, 47544361, 47544359, 47544354, 47544354, 47544352,\n 47544351, 47544350, 47544347, 47544336, 47544336, 47544329,\n 47544328, 47544326],\n [ 45955, 45953, 45952, 45939, 45939, 45939,\n 45939, 45939, 45937, 45932, 45932, 45930,\n 45929, 45928, 45925, 45914, 45914, 45907,\n 45906, 45904],\n [ 7211, 7209, 7208, 7195, 7194, 7193,\n 7191, 7191, 7189, 7184, 7184, 7182,\n 7181, 7180, 7177, 7166, 7166, 7166,\n 7165, 7165],\n [ 95246, 95248, 95249, 95262, 95263, 95264,\n 95266, 95266, 95268, 95273, 95278, 95280,\n 95281, 95282, 95285, 95296, 95296, 95296,\n 95297, 95297],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021136 AGGCAAATGAGGTGATAAGA-------TTGTGTT-----TAC----TCCCTCTGTGC---\ncavPor2.s 431 AG-CAGATGAGATAACAGTG-------ATATATT-----cat----tctctgtgtgt---\noryCun1.s 4022 AAGCAAATGAGGTGATGAGG---------GCATC-----TAT----TTCTTATTTGT---\notoGar1.s 171187 AAACAAATGAGATCACA-GG-------ACATATG-----TA--CTTGTCCCCCACGT---\ncalJac1.C 10722 AAGCAAATGAGATCACA----------GCACATG-----TATATTTTTTCTCCGTGT---\nhg18.chr6 155025103 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT---\npanTro2.c 157515157 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT---\nponAbe2.c 158037324 AAACAAATGAGATCACAAGG-------GCATATG-----TAT-TTTTTTCTCTGTGT---\neriEur1.s 358 taaataataagataagatgaaagCATAGCATGTA-----TTTTCTtgccctctccttctc\ncanFam2.c 47544377 tAGAAAATGAGATACC-----------GTGTGTA-----TATGCTTTCTCTCTGTGT---\nfelCat3.s 45955 AAGCAAATGAGATAAG-----------ACACGTG-----TATTCTTCCTCTCTGTGT---\ndasNov1.s 7211 AGGAAAGTGAGAGGACCAGG-------GCAAATA-----AATATTCTTTCTCTGTGT---\nechTel1.s 95246 AAGAAGGTGAGATGACAAGG-------GTGTATAGATAGGATATTCTTGCTTTGGGT---\n\nmm9.chr10 3021177 -------TTG 3021180\ncavPor2.s 391 -------atg 388\noryCun1.s 3983 -------GTG 3980\notoGar1.s 171145 -------GTG 171142\ncalJac1.C 10764 -------GTG 10767\nhg18.chr6 155025059 -------GTG 155025056\npanTro2.c 157515113 -------GTG 157515110\nponAbe2.c 158037280 -------GTG 158037277\neriEur1.s 413 tgtctctgtc 423\ncanFam2.c 47544336 GGGGTCTGTG 47544326\nfelCat3.s 45914 GGTGTCTGTG 45904\ndasNov1.s 7166 -------A-- 7165\nechTel1.s 95296 -------G-- 95297\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=43757.000000\ns mm9.chr10 3021136 44 + 129993255 AGGCAAATGAGGTGATAAGA-------TTGTGTT-----TAC----TCCCTCTGTGC----------TTG\ns cavPor2.scaffold_216473 9595 43 - 10026 AG-CAGATGAGATAACAGTG-------ATATATT-----cat----tctctgtgtgt----------atg\nq cavPor2.scaffold_216473 49-96766988786798889-------8679566-----756----66896967579----------888\ni cavPor2.scaffold_216473 C 0 C 0\ns oryCun1.scaffold_156751 704 42 - 4726 AAGCAAATGAGGTGATGAGG---------GCATC-----TAT----TTCTTATTTGT----------GTG\nq oryCun1.scaffold_156751 99998999999999999999---------99999-----999----99999999999----------999\ni oryCun1.scaffold_156751 C 0 C 0\ns otoGar1.scaffold_334.1-359464 188277 45 - 359464 AAACAAATGAGATCACA-GG-------ACATATG-----TA--CTTGTCCCCCACGT----------GTG\nq otoGar1.scaffold_334.1-359464 99999999999999999-99-------9999999-----99--99939999999999----------999\ni otoGar1.scaffold_334.1-359464 C 0 I 15\ns calJac1.Contig6394 10722 45 + 133105 AAGCAAATGAGATCACA----------GCACATG-----TATATTTTTTCTCCGTGT----------GTG\ni calJac1.Contig6394 C 0 I 15\ns hg18.chr6 15874889 47 - 170899992 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG\ni hg18.chr6 C 0 I 15\ns panTro2.chr6 16393455 47 - 173908612 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG\nq panTro2.chr6 99999999999999999999-------9999999-----999-99999999999999----------999\ni panTro2.chr6 C 0 I 15\ns ponAbe2.chr6 16173107 47 - 174210431 AAACAAATGAGATCACAAGG-------GCATATG-----TAT-TTTTTTCTCTGTGT----------GTG\ni ponAbe2.chr6 C 0 I 15\ns eriEur1.scaffold_266115 358 65 + 4589 taaataataagataagatgaaagCATAGCATGTA-----TTTTCTtgccctctccttctctgtctctgtc\nq eriEur1.scaffold_266115 9999999999999999999999999999999999-----9999999999999999999999999999999\ni eriEur1.scaffold_266115 N 0 I 9\ns canFam2.chr1 78071879 51 - 125616256 tAGAAAATGAGATACC-----------GTGTGTA-----TATGCTTTCTCTCTGTGT---GGGGTCTGTG\nq canFam2.chr1 9999999999999999-----------9999999-----999999999999999999---9999999999\ni canFam2.chr1 I 196 I 9\ns felCat3.scaffold_205680 73399 51 - 119354 AAGCAAATGAGATAAG-----------ACACGTG-----TATTCTTCCTCTCTGTGT---GGTGTCTGTG\nq felCat3.scaffold_205680 9755596656454353-----------5346324-----243451535354422233---3635339999\ni felCat3.scaffold_205680 I 6 I 9\ns dasNov1.scaffold_56749 3259 46 - 10470 AGGAAAGTGAGAGGACCAGG-------GCAAATA-----AATATTCTTTCTCTGTGT----------A--\nq dasNov1.scaffold_56749 55569764556657658568-------6768555-----858686457859535656----------5--\ni dasNov1.scaffold_56749 C 0 C 0\ns echTel1.scaffold_288249 95246 51 + 100002 AAGAAGGTGAGATGACAAGG-------GTGTATAGATAGGATATTCTTGCTTTGGGT----------G--\nq echTel1.scaffold_288249 99999999999999999999-------999999999999999999999999999999----------9--\ni echTel1.scaffold_288249 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'G', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'G', 'T',\n 'G', 'A', 'T', 'A', 'A', 'G', 'A', '-', '-', '-', '-', '-', '-',\n '-', 'T', 'T', 'G', 'T', 'G', 'T', 'T', '-', '-', '-', '-', '-',\n 'T', 'A', 'C', '-', '-', '-', '-', 'T', 'C', 'C', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'C', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'T', 'T', 'G'],\n ['A', 'G', '-', 'C', 'A', 'G', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'A', 'A', 'C', 'A', 'G', 'T', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'A', 'T', 'A', 'T', 'A', 'T', 'T', '-', '-', '-', '-', '-',\n 'c', 'a', 't', '-', '-', '-', '-', 't', 'c', 't', 'c', 't', 'g',\n 't', 'g', 't', 'g', 't', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'a', 't', 'g'],\n ['A', 'A', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'G', 'T',\n 'G', 'A', 'T', 'G', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', 'G', 'C', 'A', 'T', 'C', '-', '-', '-', '-', '-',\n 'T', 'A', 'T', '-', '-', '-', '-', 'T', 'T', 'C', 'T', 'T', 'A',\n 'T', 'T', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'C', 'A', 'C', 'A', '-', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'A', 'C', 'A', 'T', 'A', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'A', '-', '-', 'C', 'T', 'T', 'G', 'T', 'C', 'C', 'C', 'C',\n 'C', 'A', 'C', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['A', 'A', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'C', 'A', 'C', 'A', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'C', 'A', 'C', 'A', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C',\n 'C', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'C', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'C', 'A', 'T', 'A', 'T', 'A', '-', '-', '-', '-', '-',\n 'T', 'G', 'T', '-', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'C', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'C', 'A', 'T', 'A', 'T', 'A', '-', '-', '-', '-', '-',\n 'T', 'G', 'T', '-', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'C', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'C', 'A', 'T', 'A', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'A', 'T', '-', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['t', 'a', 'a', 'a', 't', 'a', 'a', 't', 'a', 'a', 'g', 'a', 't',\n 'a', 'a', 'g', 'a', 't', 'g', 'a', 'a', 'a', 'g', 'C', 'A', 'T',\n 'A', 'G', 'C', 'A', 'T', 'G', 'T', 'A', '-', '-', '-', '-', '-',\n 'T', 'T', 'T', 'T', 'C', 'T', 't', 'g', 'c', 'c', 'c', 't', 'c',\n 't', 'c', 'c', 't', 't', 'c', 't', 'c', 't', 'g', 't', 'c', 't',\n 'c', 't', 'g', 't', 'c'],\n ['t', 'A', 'G', 'A', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'A', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'T', 'G', 'T', 'G', 'T', 'A', '-', '-', '-', '-', '-',\n 'T', 'A', 'T', 'G', 'C', 'T', 'T', 'T', 'C', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', 'G', 'G', 'G', 'G', 'T',\n 'C', 'T', 'G', 'T', 'G'],\n ['A', 'A', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'A', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', 'A', 'C', 'A', 'C', 'G', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', 'G', 'G', 'T', 'G', 'T',\n 'C', 'T', 'G', 'T', 'G'],\n ['A', 'G', 'G', 'A', 'A', 'A', 'G', 'T', 'G', 'A', 'G', 'A', 'G',\n 'G', 'A', 'C', 'C', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'C', 'A', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-',\n 'A', 'A', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'A', '-', '-'],\n ['A', 'A', 'G', 'A', 'A', 'G', 'G', 'T', 'G', 'A', 'G', 'A', 'T',\n 'G', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'T', 'G', 'T', 'A', 'T', 'A', 'G', 'A', 'T', 'A', 'G',\n 'G', 'A', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'G', 'C', 'T', 'T',\n 'T', 'G', 'G', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', '-', '-']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 32886)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021180 : 3021180 + 24],\n \"TCCCAGAGAGTCTGATAGGAGGAG\",\n )\n self.assertEqual(\n alignment[0], \"-------------------TCCC-------AGAGAGTCTGA-TAGGAGGAG\"\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[356 : 356 + 32],\n \"TACTTTATACTCAGAGCCACTATACAAaggca\",\n )\n self.assertEqual(\n alignment[1], \"-------------------tgcctTTGTATAGTGGCTCTGAGTATAAAGTA\"\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"67576649966655666885655548785776\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[3953 : 3953 + 27], \"TATATTCAGAAATGCTATACACAGGCA\"\n )\n self.assertEqual(\n alignment[2], \"-------------------TGCCTGTGTATAGCATTTCTGAATATA-----\"\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"], \"999999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158037237 : 158037237 + 25],\n \"TACTTCATATTCATACACACTCAGA\",\n )\n self.assertEqual(\n alignment[3], \"-----------------------TCTG---AGTGTGTATGAATATGAAGTA\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 15)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 173908612)\n self.assertEqual(\n alignment.sequences[4].seq[157515070 : 157515070 + 25],\n \"TACTTCATATTCATACATACTCAGA\",\n )\n self.assertEqual(\n alignment[4], \"-----------------------TCTG---AGTATGTATGAATATGAAGTA\"\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 15)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155025016 : 155025016 + 25],\n \"TACTTCATATTCATACATACTCAGA\",\n )\n self.assertEqual(\n alignment[5], \"-----------------------TCTG---AGTATGTATGAATATGAAGTA\"\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 15)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[6].seq), 133105)\n self.assertEqual(\n alignment.sequences[6].seq[10782 : 10782 + 25], \"TCTGAGTATGTCTGAATATGAAGTG\"\n )\n self.assertEqual(\n alignment[6], \"-----------------------TCTG---AGTATGTCTGAATATGAAGTG\"\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 15)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[7].seq), 359464)\n self.assertEqual(\n alignment.sequences[7].seq[171102 : 171102 + 25],\n \"CACATCATGTTCAGACACACTTAGA\",\n )\n self.assertEqual(\n alignment[7], \"-----------------------TCTA---AGTGTGTCTGAACATGATGTG\"\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 15)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[8].seq), 498454)\n self.assertEqual(\n alignment.sequences[8].seq[323468 : 323468 + 25],\n \"TACCTCAAGTTCAGACACTCAGAGA\",\n )\n self.assertEqual(\n alignment[8], \"-----------------------TCTC---TGAGTGTCTGAACTTGAGGTA\"\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 623)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"eriEur1.scaffold_266115\")\n self.assertEqual(len(alignment.sequences[9].seq), 4589)\n self.assertEqual(\n alignment.sequences[9].seq[432 : 432 + 19], \"TCTCAGTGTGTCTGACCAG\"\n )\n self.assertEqual(\n alignment[9], \"-----------------------TCTC---AGTGTGTCTGACCAG------\"\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"], \"9999999999999999999\"\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[10].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[10].seq), 125616256)\n self.assertEqual(\n alignment.sequences[10].seq[47544292 : 47544292 + 25],\n \"TACCTCACATTCAGACACACTCAGA\",\n )\n self.assertEqual(\n alignment[10], \"-----------------------TCTG---AGTGTGTCTGAATGTGAGGTA\"\n )\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[11].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[11].seq), 119354)\n self.assertEqual(\n alignment.sequences[11].seq[45870 : 45870 + 25], \"CACCTCACATTCAGGAACACTCAGA\"\n )\n self.assertEqual(\n alignment[11], \"-----------------------TCTG---AGTGTTCCTGAATGTGAGGTG\"\n )\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[12].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[12].seq), 10470)\n self.assertEqual(\n alignment.sequences[12].seq[7118 : 7118 + 47],\n \"TACCTCAAGTTCAGACACGCTCAGAAATGCTCCGCAAAGGCACACAA\",\n )\n self.assertEqual(\n alignment[12], \"T-TGTGTGCCTTTGCGGAGCATTTCTG---AGCGTGTCTGAACTTGAGGTA\"\n )\n self.assertEqual(\n alignment.sequences[12].annotations[\"quality\"],\n \"73659557766555777595699547965955937797755656587\",\n )\n self.assertEqual(alignment.sequences[12].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[12].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[13].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[13].seq), 100002)\n self.assertEqual(\n alignment.sequences[13].seq[95297 : 95297 + 48],\n \"TGCCCAGGACTGCGCATGGTATTTCTTGGTGTGTCTGAAGGTGAGATA\",\n )\n self.assertEqual(\n alignment[13], \"TGCCCAGGACTGCGCATGGTATTTCTT---GGTGTGTCTGAAGGTGAGATA\"\n )\n self.assertEqual(\n alignment.sequences[13].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[13].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[13].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 14)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021180, 3021180, 3021180, 3021180, 3021184, 3021184,\n 3021184, 3021195, 3021195, 3021198, 3021199, 3021204],\n [ 388, 388, 388, 388, 384, 380,\n 377, 366, 365, 362, 361, 356],\n [ 3980, 3980, 3980, 3980, 3976, 3972,\n 3969, 3958, 3957, 3954, 3953, 3953],\n [158037262, 158037262, 158037262, 158037262, 158037262, 158037258,\n 158037258, 158037247, 158037246, 158037243, 158037242, 158037237],\n [157515095, 157515095, 157515095, 157515095, 157515095, 157515091,\n 157515091, 157515080, 157515079, 157515076, 157515075, 157515070],\n [155025041, 155025041, 155025041, 155025041, 155025041, 155025037,\n 155025037, 155025026, 155025025, 155025022, 155025021, 155025016],\n [ 10782, 10782, 10782, 10782, 10782, 10786,\n 10786, 10797, 10798, 10801, 10802, 10807],\n [ 171127, 171127, 171127, 171127, 171127, 171123,\n 171123, 171112, 171111, 171108, 171107, 171102],\n [ 323493, 323493, 323493, 323493, 323493, 323489,\n 323489, 323478, 323477, 323474, 323473, 323468],\n [ 432, 432, 432, 432, 432, 436,\n 436, 447, 448, 451, 451, 451],\n [ 47544317, 47544317, 47544317, 47544317, 47544317, 47544313,\n 47544313, 47544302, 47544301, 47544298, 47544297, 47544292],\n [ 45895, 45895, 45895, 45895, 45895, 45891,\n 45891, 45880, 45879, 45876, 45875, 45870],\n [ 7165, 7164, 7164, 7147, 7143, 7139,\n 7139, 7128, 7127, 7124, 7123, 7118],\n [ 95297, 95298, 95299, 95316, 95320, 95324,\n 95324, 95335, 95336, 95339, 95340, 95345],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021180 -------------------TCCC-------AGAGAGTCTGA-TAGGAGGAG\ncavPor2.s 388 -------------------tgcctTTGTATAGTGGCTCTGAGTATAAAGTA\noryCun1.s 3980 -------------------TGCCTGTGTATAGCATTTCTGAATATA-----\nponAbe2.c 158037262 -----------------------TCTG---AGTGTGTATGAATATGAAGTA\npanTro2.c 157515095 -----------------------TCTG---AGTATGTATGAATATGAAGTA\nhg18.chr6 155025041 -----------------------TCTG---AGTATGTATGAATATGAAGTA\ncalJac1.C 10782 -----------------------TCTG---AGTATGTCTGAATATGAAGTG\notoGar1.s 171127 -----------------------TCTA---AGTGTGTCTGAACATGATGTG\ntupBel1.s 323493 -----------------------TCTC---TGAGTGTCTGAACTTGAGGTA\neriEur1.s 432 -----------------------TCTC---AGTGTGTCTGACCAG------\ncanFam2.c 47544317 -----------------------TCTG---AGTGTGTCTGAATGTGAGGTA\nfelCat3.s 45895 -----------------------TCTG---AGTGTTCCTGAATGTGAGGTG\ndasNov1.s 7165 T-TGTGTGCCTTTGCGGAGCATTTCTG---AGCGTGTCTGAACTTGAGGTA\nechTel1.s 95297 TGCCCAGGACTGCGCATGGTATTTCTT---GGTGTGTCTGAAGGTGAGATA\n\nmm9.chr10 3021204\ncavPor2.s 356\noryCun1.s 3953\nponAbe2.c 158037237\npanTro2.c 157515070\nhg18.chr6 155025016\ncalJac1.C 10807\notoGar1.s 171102\ntupBel1.s 323468\neriEur1.s 451\ncanFam2.c 47544292\nfelCat3.s 45870\ndasNov1.s 7118\nechTel1.s 95345\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=32886.000000\ns mm9.chr10 3021180 24 + 129993255 -------------------TCCC-------AGAGAGTCTGA-TAGGAGGAG\ns cavPor2.scaffold_216473 9638 32 - 10026 -------------------tgcctTTGTATAGTGGCTCTGAGTATAAAGTA\nq cavPor2.scaffold_216473 -------------------67576649966655666885655548785776\ni cavPor2.scaffold_216473 C 0 C 0\ns oryCun1.scaffold_156751 746 27 - 4726 -------------------TGCCTGTGTATAGCATTTCTGAATATA-----\nq oryCun1.scaffold_156751 -------------------999999999999999999999999999-----\ni oryCun1.scaffold_156751 C 0 C 0\ns ponAbe2.chr6 16173169 25 - 174210431 -----------------------TCTG---AGTGTGTATGAATATGAAGTA\ni ponAbe2.chr6 I 15 C 0\ns panTro2.chr6 16393517 25 - 173908612 -----------------------TCTG---AGTATGTATGAATATGAAGTA\nq panTro2.chr6 -----------------------9999---999999999999999999999\ni panTro2.chr6 I 15 C 0\ns hg18.chr6 15874951 25 - 170899992 -----------------------TCTG---AGTATGTATGAATATGAAGTA\ni hg18.chr6 I 15 C 0\ns calJac1.Contig6394 10782 25 + 133105 -----------------------TCTG---AGTATGTCTGAATATGAAGTG\ni calJac1.Contig6394 I 15 C 0\ns otoGar1.scaffold_334.1-359464 188337 25 - 359464 -----------------------TCTA---AGTGTGTCTGAACATGATGTG\nq otoGar1.scaffold_334.1-359464 -----------------------9999---999999999999999999999\ni otoGar1.scaffold_334.1-359464 I 15 C 0\ns tupBel1.scaffold_114895.1-498454 174961 25 - 498454 -----------------------TCTC---TGAGTGTCTGAACTTGAGGTA\nq tupBel1.scaffold_114895.1-498454 -----------------------9999---999999999999999999999\ni tupBel1.scaffold_114895.1-498454 I 623 C 0\ns eriEur1.scaffold_266115 432 19 + 4589 -----------------------TCTC---AGTGTGTCTGACCAG------\nq eriEur1.scaffold_266115 -----------------------9999---999999999999999------\ni eriEur1.scaffold_266115 I 9 C 0\ns canFam2.chr1 78071939 25 - 125616256 -----------------------TCTG---AGTGTGTCTGAATGTGAGGTA\nq canFam2.chr1 -----------------------9999---999999999999999999999\ni canFam2.chr1 I 9 C 0\ns felCat3.scaffold_205680 73459 25 - 119354 -----------------------TCTG---AGTGTTCCTGAATGTGAGGTG\nq felCat3.scaffold_205680 -----------------------9999---999999999999999999999\ni felCat3.scaffold_205680 I 9 C 0\ns dasNov1.scaffold_56749 3305 47 - 10470 T-TGTGTGCCTTTGCGGAGCATTTCTG---AGCGTGTCTGAACTTGAGGTA\nq dasNov1.scaffold_56749 7-3659557766555777595699547---965955937797755656587\ni dasNov1.scaffold_56749 C 0 C 0\ns echTel1.scaffold_288249 95297 48 + 100002 TGCCCAGGACTGCGCATGGTATTTCTT---GGTGTGTCTGAAGGTGAGATA\nq echTel1.scaffold_288249 999999999999999999999999999---999999999999999999999\ni echTel1.scaffold_288249 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', 'T', 'C', 'C', 'C', '-', '-', '-',\n '-', '-', '-', '-', 'A', 'G', 'A', 'G', 'A', 'G', 'T', 'C', 'T',\n 'G', 'A', '-', 'T', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'G'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', 't', 'g', 'c', 'c', 't', 'T', 'T',\n 'G', 'T', 'A', 'T', 'A', 'G', 'T', 'G', 'G', 'C', 'T', 'C', 'T',\n 'G', 'A', 'G', 'T', 'A', 'T', 'A', 'A', 'A', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', 'T', 'G', 'C', 'C', 'T', 'G', 'T',\n 'G', 'T', 'A', 'T', 'A', 'G', 'C', 'A', 'T', 'T', 'T', 'C', 'T',\n 'G', 'A', 'A', 'T', 'A', 'T', 'A', '-', '-', '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'A', 'T',\n 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'A', 'T', 'G', 'T', 'A', 'T',\n 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'A', 'T', 'G', 'T', 'A', 'T',\n 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'A', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'G'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'A', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'C', 'A', 'T', 'G', 'A', 'T', 'G', 'T', 'G'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'C', '-', '-', '-', 'T', 'G', 'A', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'C', 'T', 'T', 'G', 'A', 'G', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'C', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'C', 'C', 'A', 'G', '-', '-', '-', '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'T', 'G', 'T', 'G', 'A', 'G', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'T', 'C', 'C', 'T',\n 'G', 'A', 'A', 'T', 'G', 'T', 'G', 'A', 'G', 'G', 'T', 'G'],\n ['T', '-', 'T', 'G', 'T', 'G', 'T', 'G', 'C', 'C', 'T', 'T', 'T',\n 'G', 'C', 'G', 'G', 'A', 'G', 'C', 'A', 'T', 'T', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'C', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'C', 'T', 'T', 'G', 'A', 'G', 'G', 'T', 'A'],\n ['T', 'G', 'C', 'C', 'C', 'A', 'G', 'G', 'A', 'C', 'T', 'G', 'C',\n 'G', 'C', 'A', 'T', 'G', 'G', 'T', 'A', 'T', 'T', 'T', 'C', 'T',\n 'T', '-', '-', '-', 'G', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'G', 'G', 'T', 'G', 'A', 'G', 'A', 'T', 'A']],\n dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 309116)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021204 : 3021204 + 71],\n \"TGCACTGGTTTTCCTGCAGTGGTTCTCAGTAATAGGAAGACAACAGAATTTGAAGTATCCGGCTTTGGCCA\",\n )\n self.assertEqual(\n alignment[0],\n \"TGCACTGGTTTTCC-TGCAGTGGTTCTCAGTAATAGGAAGACA-ACAGAATTTGAAGTATCCGGCTTTGGCCA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[1].seq), 100002)\n self.assertEqual(\n alignment.sequences[1].seq[95345 : 95345 + 73],\n \"GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAAATATTCTTGGCTA\",\n )\n self.assertEqual(\n alignment[1],\n \"GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAAATATTCTTGGCTA\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[2].seq), 10470)\n self.assertEqual(\n alignment.sequences[2].seq[7048 : 7048 + 70],\n \"TAGCCAAGAGCATTTATTATAAATTCAAAATGCTCTCTTAGTGTGATTTCCCTCACTGAAAATCAATGCA\",\n )\n self.assertEqual(\n alignment[2],\n \"TGCATTGATTTTCAGTGAGGGAAATCACAC---TAAGAGAGCATTTTGAATTTATAATAAATGCTCTTGGCTA\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"5796635799979575966667835948658458696597898258979678997999677999997699\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[3].seq), 119354)\n self.assertEqual(\n alignment.sequences[3].seq[45798 : 45798 + 72],\n \"CAGCCAAAAACATTTGCTATAATTTCAAAATGCATTCCTATTCATGTGAATCAATGCATGAAAATCAATGCA\",\n )\n self.assertEqual(\n alignment[3],\n \"TGCATTGATTTTCA-TGCATTGATTCACATGAATAGGAATGCATTTTGAAATTATAGCAAATGTTTTTGGCTG\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[4].seq), 125616256)\n self.assertEqual(\n alignment.sequences[4].seq[47544221 : 47544221 + 71],\n \"CAGCCAAAAGCATTTCCTATAAATTCAAATGTATTCCTATTCATGTGAATCAACGCATGAAAATTAATGCA\",\n )\n self.assertEqual(\n alignment[4],\n \"TGCATTAATTTTCA-TGCGTTGATTCACATGAATAGGAATACA-TTTGAATTTATAGGAAATGCTTTTGGCTG\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"eriEur1.scaffold_266115\")\n self.assertEqual(len(alignment.sequences[5].seq), 4589)\n self.assertEqual(\n alignment.sequences[5].seq[451 : 451 + 70],\n \"GCACTGATTCTCGAGGGTTGATTCCCAGTAAGAGGAAACTGCGTGAGTTTACAGTACATGGGCTTGGCTG\",\n )\n self.assertEqual(\n alignment[5],\n \"-GCACTGATTCTCG-AGGGTTGATTCCCAGTAAGAGGAAACTG-CGTGAGTTTACAGTACATGGGCTTGGCTG\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999799\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"sorAra1.scaffold_2476\")\n self.assertEqual(len(alignment.sequences[6].seq), 4997)\n self.assertEqual(\n alignment.sequences[6].seq[1615 : 1615 + 70],\n \"TGGCCAAATCATTTATCATAAATTGAAGTGCTTTCCTTTTCATGTGAATCAATACTTAAAAATCAATGCA\",\n )\n self.assertEqual(\n alignment[6],\n \"TGCATTGATTTTTA-AGTATTGATTCACATGAAAAGGAAAGCA-CTTCAATTTATGATAAAT-GATTTGGCCA\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"8999999999998999999999999999999999999999999999999997999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[7].seq), 498454)\n self.assertEqual(\n alignment.sequences[7].seq[323397 : 323397 + 71],\n \"TGGTCAGAAGCATTTCCTATCAATTAGAATCGTTTCCTATTAATGTGACATAACACATGGAATTCAATGCA\",\n )\n self.assertEqual(\n alignment[7],\n \"TGCATTGAATTCCA-TGTGTTATGTCACATTAATAGGAAACGA-TTCTAATTGATAGGAAATGCTTCTGACCA\",\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"],\n \"99999899899999999999999999999999999999999999999999999999999999999999997\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[8].seq), 359464)\n self.assertEqual(\n alignment.sequences[8].seq[171035 : 171035 + 67],\n \"TGGCCAAATGCCTTTCCTACAAATTCACATGTTTTCCCGTTAAGGTGAATCAATGTGTAAAAATCCA\",\n )\n self.assertEqual(\n alignment[8],\n \"TG----GATTTTTA-CACATTGATTCACCTTAACGGGAAAACA-TGTGAATTTGTAGGAAAGGCATTTGGCCA\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"8899999999989999989994384888899999999966359999569699999923799351281\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 6280)\n self.assertEqual(alignment.sequences[9].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[9].seq), 133105)\n self.assertEqual(\n alignment.sequences[9].seq[10807 : 10807 + 71],\n \"TGCATTGGTTTTTATGCCTTGATTCACATGAATAGGAAAACGTTTGAATTTATAGGAAATGGTTTTGGCCA\",\n )\n self.assertEqual(\n alignment[9],\n \"TGCATTGGTTTTTA-TGCCTTGATTCACATGAATAGGAAAACG-TTTGAATTTATAGGAAATGGTTTTGGCCA\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[10].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[10].seq), 170899992)\n self.assertEqual(\n alignment.sequences[10].seq[155024945 : 155024945 + 71],\n \"TGGCCAAAACCATTTACTATAAATTCAAACATTTTCCTATTCATGTAAATCAATGCATAAAAATCAAAGCA\",\n )\n self.assertEqual(\n alignment[10],\n \"TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAATG-TTTGAATTTATAGTAAATGGTTTTGGCCA\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[11].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[11].seq), 173908612)\n self.assertEqual(\n alignment.sequences[11].seq[157514999 : 157514999 + 71],\n \"TGGCCAAAACCATTTACTATAAATTCAAATGTTTTCCTATTCATGTAAATCAATGCATAAAAATCAAAGCA\",\n )\n self.assertEqual(\n alignment[11],\n \"TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAACA-TTTGAATTTATAGTAAATGGTTTTGGCCA\",\n )\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[12].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[12].seq), 174210431)\n self.assertEqual(\n alignment.sequences[12].seq[158037166 : 158037166 + 71],\n \"TGGCCAAAACCATTTACTATAAATTCAAACGTTTTCCTATCCATGTAAATCAATGCATAAAAATCAAAGCA\",\n )\n self.assertEqual(\n alignment[12],\n \"TGCTTTGATTTTTA-TGCATTGATTTACATGGATAGGAAAACG-TTTGAATTTATAGTAAATGGTTTTGGCCA\",\n )\n self.assertEqual(alignment.sequences[12].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[12].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[13].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[13].seq), 4726)\n self.assertEqual(\n alignment.sequences[13].seq[3888 : 3888 + 65],\n \"TGACCAAAAGCCATTGCTATAAATGCAAATGTTTTCCCGTCGATGTAAATCAAAGTATGTAAAGA\",\n )\n self.assertEqual(\n alignment[13],\n \"------TCTTTACA-TACTTTGATTTACATCGACGGGAAAACA-TTTGCATTTATAGCAATGGCTTTTGGTCA\",\n )\n self.assertEqual(\n alignment.sequences[13].annotations[\"quality\"],\n \"99999994999999999999989999999999999999999999999999899999999999999\",\n )\n self.assertEqual(alignment.sequences[13].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[13].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[14].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[14].seq), 10026)\n self.assertEqual(\n alignment.sequences[14].seq[285 : 285 + 71],\n \"TGGCCAAAACCATTTACTATAAATTGGACTGTTTTCCTATTAATGTGAATTAATGCATGGAAATCAATGCC\",\n )\n self.assertEqual(\n alignment[14],\n \"GGCATTGATTTCCA-TGCATTAATTCACATTAATAGGAAAACA-GTCCAATTTATAGTAAATGGTTTTGGCCA\",\n )\n self.assertEqual(\n alignment.sequences[14].annotations[\"quality\"],\n \"77888768786695388675879644655668865666547868687676669688688666687574686\",\n )\n self.assertEqual(alignment.sequences[14].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[14].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[14].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[14].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 15)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021204, 3021205, 3021206, 3021210, 3021218, 3021218,\n 3021233, 3021236, 3021246, 3021246, 3021264, 3021265,\n 3021275],\n [ 95345, 95346, 95347, 95351, 95359, 95360,\n 95375, 95378, 95388, 95389, 95407, 95408,\n 95418],\n [ 7118, 7117, 7116, 7112, 7104, 7103,\n 7088, 7088, 7078, 7077, 7059, 7058,\n 7048],\n [ 45870, 45869, 45868, 45864, 45856, 45856,\n 45841, 45838, 45828, 45827, 45809, 45808,\n 45798],\n [ 47544292, 47544291, 47544290, 47544286, 47544278, 47544278,\n 47544263, 47544260, 47544250, 47544250, 47544232, 47544231,\n 47544221],\n [ 451, 451, 452, 456, 464, 464,\n 479, 482, 492, 492, 510, 511,\n 521],\n [ 1685, 1684, 1683, 1679, 1671, 1671,\n 1656, 1653, 1643, 1643, 1625, 1625,\n 1615],\n [ 323468, 323467, 323466, 323462, 323454, 323454,\n 323439, 323436, 323426, 323426, 323408, 323407,\n 323397],\n [ 171102, 171101, 171100, 171100, 171092, 171092,\n 171077, 171074, 171064, 171064, 171046, 171045,\n 171035],\n [ 10807, 10808, 10809, 10813, 10821, 10821,\n 10836, 10839, 10849, 10849, 10867, 10868,\n 10878],\n [155025016, 155025015, 155025014, 155025010, 155025002, 155025002,\n 155024987, 155024984, 155024974, 155024974, 155024956, 155024955,\n 155024945],\n [157515070, 157515069, 157515068, 157515064, 157515056, 157515056,\n 157515041, 157515038, 157515028, 157515028, 157515010, 157515009,\n 157514999],\n [158037237, 158037236, 158037235, 158037231, 158037223, 158037223,\n 158037208, 158037205, 158037195, 158037195, 158037177, 158037176,\n 158037166],\n [ 3953, 3953, 3953, 3953, 3945, 3945,\n 3930, 3927, 3917, 3917, 3899, 3898,\n 3888],\n [ 356, 355, 354, 350, 342, 342,\n 327, 324, 314, 314, 296, 295,\n 285],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021204 TGCACTGGTTTTCC-TGCAGTGGTTCTCAGTAATAGGAAGACA-ACAGAATTTGAAGTAT\nechTel1.s 95345 GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAA\ndasNov1.s 7118 TGCATTGATTTTCAGTGAGGGAAATCACAC---TAAGAGAGCATTTTGAATTTATAATAA\nfelCat3.s 45870 TGCATTGATTTTCA-TGCATTGATTCACATGAATAGGAATGCATTTTGAAATTATAGCAA\ncanFam2.c 47544292 TGCATTAATTTTCA-TGCGTTGATTCACATGAATAGGAATACA-TTTGAATTTATAGGAA\neriEur1.s 451 -GCACTGATTCTCG-AGGGTTGATTCCCAGTAAGAGGAAACTG-CGTGAGTTTACAGTAC\nsorAra1.s 1685 TGCATTGATTTTTA-AGTATTGATTCACATGAAAAGGAAAGCA-CTTCAATTTATGATAA\ntupBel1.s 323468 TGCATTGAATTCCA-TGTGTTATGTCACATTAATAGGAAACGA-TTCTAATTGATAGGAA\notoGar1.s 171102 TG----GATTTTTA-CACATTGATTCACCTTAACGGGAAAACA-TGTGAATTTGTAGGAA\ncalJac1.C 10807 TGCATTGGTTTTTA-TGCCTTGATTCACATGAATAGGAAAACG-TTTGAATTTATAGGAA\nhg18.chr6 155025016 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAATG-TTTGAATTTATAGTAA\npanTro2.c 157515070 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAACA-TTTGAATTTATAGTAA\nponAbe2.c 158037237 TGCTTTGATTTTTA-TGCATTGATTTACATGGATAGGAAAACG-TTTGAATTTATAGTAA\noryCun1.s 3953 ------TCTTTACA-TACTTTGATTTACATCGACGGGAAAACA-TTTGCATTTATAGCAA\ncavPor2.s 356 GGCATTGATTTCCA-TGCATTAATTCACATTAATAGGAAAACA-GTCCAATTTATAGTAA\n\nmm9.chr10 3021262 CCGGCTTTGGCCA 3021275\nechTel1.s 95405 ATATTCTTGGCTA 95418\ndasNov1.s 7061 ATGCTCTTGGCTA 7048\nfelCat3.s 45811 ATGTTTTTGGCTG 45798\ncanFam2.c 47544234 ATGCTTTTGGCTG 47544221\neriEur1.s 508 ATGGGCTTGGCTG 521\nsorAra1.s 1627 AT-GATTTGGCCA 1615\ntupBel1.s 323410 ATGCTTCTGACCA 323397\notoGar1.s 171048 AGGCATTTGGCCA 171035\ncalJac1.C 10865 ATGGTTTTGGCCA 10878\nhg18.chr6 155024958 ATGGTTTTGGCCA 155024945\npanTro2.c 157515012 ATGGTTTTGGCCA 157514999\nponAbe2.c 158037179 ATGGTTTTGGCCA 158037166\noryCun1.s 3901 TGGCTTTTGGTCA 3888\ncavPor2.s 298 ATGGTTTTGGCCA 285\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=309116.000000\ns mm9.chr10 3021204 71 + 129993255 TGCACTGGTTTTCC-TGCAGTGGTTCTCAGTAATAGGAAGACA-ACAGAATTTGAAGTATCCGGCTTTGGCCA\ns echTel1.scaffold_288249 95345 73 + 100002 GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAAATATTCTTGGCTA\nq echTel1.scaffold_288249 9999999999999999999999999999999999999999999999999999999999999999999999999\ni echTel1.scaffold_288249 C 0 C 0\ns dasNov1.scaffold_56749 3352 70 - 10470 TGCATTGATTTTCAGTGAGGGAAATCACAC---TAAGAGAGCATTTTGAATTTATAATAAATGCTCTTGGCTA\nq dasNov1.scaffold_56749 579663579997957596666783594865---8458696597898258979678997999677999997699\ni dasNov1.scaffold_56749 C 0 C 0\ns felCat3.scaffold_205680 73484 72 - 119354 TGCATTGATTTTCA-TGCATTGATTCACATGAATAGGAATGCATTTTGAAATTATAGCAAATGTTTTTGGCTG\nq felCat3.scaffold_205680 99999999999999-9999999999999999999999999999999999999999999999999999999999\ni felCat3.scaffold_205680 C 0 C 0\ns canFam2.chr1 78071964 71 - 125616256 TGCATTAATTTTCA-TGCGTTGATTCACATGAATAGGAATACA-TTTGAATTTATAGGAAATGCTTTTGGCTG\nq canFam2.chr1 99999999999999-9999999999999999999999999999-99999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ns eriEur1.scaffold_266115 451 70 + 4589 -GCACTGATTCTCG-AGGGTTGATTCCCAGTAAGAGGAAACTG-CGTGAGTTTACAGTACATGGGCTTGGCTG\nq eriEur1.scaffold_266115 -9999999999999-9999999999999999999999999999-99999999999999999999999999799\ni eriEur1.scaffold_266115 C 0 C 0\ns sorAra1.scaffold_2476 3312 70 - 4997 TGCATTGATTTTTA-AGTATTGATTCACATGAAAAGGAAAGCA-CTTCAATTTATGATAAAT-GATTTGGCCA\nq sorAra1.scaffold_2476 89999999999989-9999999999999999999999999999-999999999799999999-9999999999\ni sorAra1.scaffold_2476 N 0 C 0\ns tupBel1.scaffold_114895.1-498454 174986 71 - 498454 TGCATTGAATTCCA-TGTGTTATGTCACATTAATAGGAAACGA-TTCTAATTGATAGGAAATGCTTCTGACCA\nq tupBel1.scaffold_114895.1-498454 99999899899999-9999999999999999999999999999-99999999999999999999999999997\ni tupBel1.scaffold_114895.1-498454 C 0 C 0\ns otoGar1.scaffold_334.1-359464 188362 67 - 359464 TG----GATTTTTA-CACATTGATTCACCTTAACGGGAAAACA-TGTGAATTTGTAGGAAAGGCATTTGGCCA\nq otoGar1.scaffold_334.1-359464 88----99999999-9899999899943848888999999999-66359999569699999923799351281\ni otoGar1.scaffold_334.1-359464 C 0 I 6280\ns calJac1.Contig6394 10807 71 + 133105 TGCATTGGTTTTTA-TGCCTTGATTCACATGAATAGGAAAACG-TTTGAATTTATAGGAAATGGTTTTGGCCA\ni calJac1.Contig6394 C 0 C 0\ns hg18.chr6 15874976 71 - 170899992 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAATG-TTTGAATTTATAGTAAATGGTTTTGGCCA\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16393542 71 - 173908612 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAACA-TTTGAATTTATAGTAAATGGTTTTGGCCA\nq panTro2.chr6 99999999999999-9999999999999999999999999999-99999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16173194 71 - 174210431 TGCTTTGATTTTTA-TGCATTGATTTACATGGATAGGAAAACG-TTTGAATTTATAGTAAATGGTTTTGGCCA\ni ponAbe2.chr6 C 0 C 0\ns oryCun1.scaffold_156751 773 65 - 4726 ------TCTTTACA-TACTTTGATTTACATCGACGGGAAAACA-TTTGCATTTATAGCAATGGCTTTTGGTCA\nq oryCun1.scaffold_156751 ------99999994-9999999999999899999999999999-99999999999999899999999999999\ni oryCun1.scaffold_156751 C 0 C 0\ns cavPor2.scaffold_216473 9670 71 - 10026 GGCATTGATTTCCA-TGCATTAATTCACATTAATAGGAAAACA-GTCCAATTTATAGTAAATGGTTTTGGCCA\nq cavPor2.scaffold_216473 77888768786695-3886758796446556688656665478-68687676669688688666687574686\ni cavPor2.scaffold_216473 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 891219)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021275 : 3021275 + 146],\n \"CTTTCTCTGACATTACTGTAACTGAAGTAGCTCAGAAGCACAAAAGGTCACATCATGCATCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGCCACGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG\",\n )\n self.assertEqual(\n alignment[0],\n \"CTTTCTCTGACATTACTGTAACTGAAGTAGCTC-AGAAGCACAAAAGGTCACATCATGCATCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGC-----------------------CACGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[116 : 116 + 169],\n \"TTGAAATATGGAAGGAAATGATGGCGTGACTGGATTTCCTGCGAGACACATGAACTAAGTAATAAAATGCGAGGTGCCTTTATGAACGGAACTAGTAAATTTTGCATAAATGCCTGACATGACCTTTTGTGCTTTTCAGCTAGTTCGCTTACAGTAACATCAGCAAAGG\",\n )\n self.assertEqual(\n alignment[1],\n \"CCTTTGCTGATGTTACTGTAAGCGAACTAGCTG-AAAAGCACAAAAGGTCATGTCAGGCATTTATGCAAAATTTACTAGTTCCGTTCATAAAGGCACCTCGCATTTTATTACTTAGTTCATGTGTCTCGCAGGAAATCCAGTCACGCCATCATTTCCTTCCATATTTCAA\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"6685365455476645398666666666666688787886799997788875886655536666688786768476688854689668876558688874778656675665668746666788474786888875667457786687996867886548798845555\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[3730 : 3730 + 158],\n \"TTGAAATGTGGAAGGAAATCGCGGCGTGACTGGATTTCCTGAACAAAGTAATACAACACAAGGTGCTGTTATAAACAGTGCTAGTACATTTGACATAAATGCCTGCCATGGCCTTTTGTGCTTTGGAGCGCTTTCAGCTAGAGTAACATCAGAGACGA\",\n )\n self.assertEqual(\n alignment[2],\n \"TCGTCTCTGATGTTACTCTAGCTGAAAGCGCTC-CAAAGCACAAAAGGCCATGGCAGGCATTTATGTCAAATGTACTAGCACTGTTTATAACAGCACCTTGTGTTGTATTACTTTGTTCA-----------GGAAATCCAGTCACGCCGCGATTTCCTTCCACATTTCAA\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999987999999999999999999999799999999799999999898999999988999999988999999989996999999999988897996999999999999979999987899998987999799998998999999999777999899\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158036997 : 158036997 + 169],\n \"ATGAAATATGGAAGGAAATGATGGCGTGACTGAATTTCCTGAAAGATACATTAACAAAGTAATAAAACACAAGGTACCCTTATAAACAGCACTAGTAAGTTTTACATGAATGCCTCCCATGACCTTTTGTGCTTTTGAGCTATTTCAGTTACAGTAACATCAGAGAAGG\",\n )\n self.assertEqual(\n alignment[3],\n \"CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTCATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTATCTTTCAGGAAATTCAGTCACGCCATCATTTCCTTCCATATTTCAT\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 173908612)\n self.assertEqual(\n alignment.sequences[4].seq[157514830 : 157514830 + 169],\n \"ATGAAATATGGAAGGAAATGATGGCATGACTGGATTTCCTGAAAGGTACATTAACAAAGTAATAAAACACAAGGTACCCTTATAAACAGCACTAGTAAGTTTTACATAAATGCCTCCCATGACCTTTTGTGCTTTTGAGCTATTTCAGTTACAGTAACATCAGAGAAGG\",\n )\n self.assertEqual(\n alignment[4],\n \"CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155024776 : 155024776 + 169],\n \"ATGAAATATGGAAGGAAATGATGGCATGACTGGATTTCCTGAAAGGTACATTAACAAAGTAATAAAACACAAGATACCCTTATAAACAGCACTAGTAAGTTTTACATAAATGCCTCCCATGACCTTTTGTGCTTTTGAGCTATTTCAGTTACAGTAACATCAGAGAAGG\",\n )\n self.assertEqual(\n alignment[5],\n \"CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTATCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[6].seq), 133105)\n self.assertEqual(\n alignment.sequences[6].seq[10878 : 10878 + 169],\n \"CCTTCTCTGATATTACTGTAACTGAAATAGCTCAAAAGCACAAAAGGTCATGGCAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\",\n )\n self.assertEqual(\n alignment[6],\n \"CCTTCTCTGATATTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGCAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[7].seq), 498454)\n self.assertEqual(\n alignment.sequences[7].seq[323241 : 323241 + 156],\n \"CTGAGATATGGAAGGAAATGATGGCCCGACTGGATTTCCTGTAAGGCACATGAACAAAGTAATAAAACACGAGATGCCTTCAGAAACTTTACATCAATGCCTGGCATGACCTTTTGTGCTTCTGAGCTACTTTGGTTACAGGAACATCTGAGAGGA\",\n )\n self.assertEqual(\n alignment[7],\n \"TCCTCTCAGATGTTCCTGTAACCAAAGTAGCTC-AGAAGCACAAAAGGTCATGCCAGGCATTGATGTAAA-------------GTTTCTGAAGGCATCTCGTGTTTTATTACTTTGTTCATGTGCCTTACAGGAAATCCAGTCGGGCCATCATTTCCTTCCATATCTCAG\",\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"sorAra1.scaffold_2476\")\n self.assertEqual(len(alignment.sequences[8].seq), 4997)\n self.assertEqual(\n alignment.sequences[8].seq[1445 : 1445 + 170],\n \"CTGGAATATGGGAGGAAATGATGAGATTACAGGATTTCCGGAAAAGTTCATGATCAACAACATTATATGCAAGGGGTCTTTATAAACAGCACTGGTATATTTTACATCAATGCCTGACATGACCTTTTGTGCTTTTTGAGCTACCTCAGTTACAGTAACATCAGAGAAGG\",\n )\n self.assertEqual(\n alignment[8],\n \"CCTTCTCTGATGTTACTGTAACTGAGGTAGCTCAAAAAGCACAAAAGGTCATGTCAGGCATTGATGTAAAATATACCAGTGCTGTTTATAAAGACCCCTTGCATATAATGTTGTTGATCATGAACTTTTCCGGAAATCCTGTAATCTCATCATTTCCTCCCATATTCCAG\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"99999999999999997999999999999999999999999999999999999999999999999999999999999979999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"eriEur1.scaffold_266115\")\n self.assertEqual(len(alignment.sequences[9].seq), 4589)\n self.assertEqual(\n alignment.sequences[9].seq[521 : 521 + 156],\n \"CCTTCTCTGATCTGACTGTAACCGAAGTCTCTCGAAAGCACAAAAGCTCACGGCAGGCCTTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgcagatgtctctcacgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCCTTCCTG\",\n )\n self.assertEqual(\n alignment[9],\n \"CCTTCTCTGATCTGACTGTAACCGAAGTCTCTC-GAAAGCACAAAAGCTCACGGCAGGCCTTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgca------gatgtctctcacgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCC-------TTCCTG\",\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999799999999999999999999998987999899999999999999999999999999999999999999999999999999999999999998999989\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[10].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[10].seq), 125616256)\n self.assertEqual(\n alignment.sequences[10].seq[47544053 : 47544053 + 168],\n \"TTGAAATATGGAAGGAAGTAACAGGATGACAGGATTTCCTGTAAAGTACATGAACAAAGCAATATTACACGAGGTGCCTTTATAAACAGCTCTAGTAAATTTTACATAAAGCCTGACATGACCTTTTGTGCTTTTGAGCTACTTCAGTTACAGTAACATCAGAGACAG\",\n )\n self.assertEqual(\n alignment[10],\n \"CTGTCTCTGATGTTACTGTAACTGAAGTAGCTC-AAAAGCACAAAAGGTCATGTCAGGC-TTTATGTAAAATTTACTAGAGCTGTTTATAAAGGCACCTCGTGTAATATTGCTTTGTTCATGTACTTTACAGGAAATCCTGTCATCCTGTTACTTCCTTCCATATTTCAA\",\n )\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[11].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[11].seq), 119354)\n self.assertEqual(\n alignment.sequences[11].seq[45629 : 45629 + 169],\n \"CTGAACTATGGAAGGAAATGACAGGATGACAGGATTTCCTATAAAGTGCATGAACAAAGCAATAATACACAAGGTACCTTTATAAACAGCACTAGTAAATTTTACATAAATGCCTGACATCACCTTTTGTGCTTTTGAACTATTTCAGTTACAGTAACATCAGAGACAG\",\n )\n self.assertEqual(\n alignment[11],\n \"CTGTCTCTGATGTTACTGTAACTGAAATAGTTC-AAAAGCACAAAAGGTGATGTCAGGCATTTATGTAAAATTTACTAGTGCTGTTTATAAAGGTACCTTGTGTATTATTGCTTTGTTCATGCACTTTATAGGAAATCCTGTCATCCTGTCATTTCCTTCCATAGTTCAG\",\n )\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 34165)\n self.assertEqual(alignment.sequences[12].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[12].seq), 10470)\n self.assertEqual(\n alignment.sequences[12].seq[6880 : 6880 + 168],\n \"GTGACTTATGGAAGGAAATGATGGTATGACAGGATTTCCTGTAAGGGGGATAGAAAAAGTAATAGAACACAAGGTCCTTTATAAACAGCACTAGTAAATTTTACATCAATGCCCGACATGACCTTTTGTGCTTTTGAGCCTCTTCAGTTACAGTAACATCAGAGAAGG\",\n )\n self.assertEqual(\n alignment[12],\n \"CCTTCTCTGATGTTACTGTAACTGAAGAGGCTC-AAAAGCACAAAAGGTCATGTCGGGCATTGATGTAAAATTTACTAGTGCTG-TTTATAAAGGACCTTGTGTTCTATTACTTTTTCTATCCCCCTTACAGGAAATCCTGTCATACCATCATTTCCTTCCATAAGTCAC\",\n )\n self.assertEqual(\n alignment.sequences[12].annotations[\"quality\"],\n \"989999999999999937699999999999999799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[12].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[12].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[13].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[13].seq), 100002)\n self.assertEqual(\n alignment.sequences[13].seq[95418 : 95418 + 169],\n \"CCATCTCTGATATTACTGTAATGGAATTACTTTGAAAGCACAAAAGGTCAGGACAAGCGTGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCATTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG\",\n )\n self.assertEqual(\n alignment[13],\n \"CCATCTCTGATATTACTGTAATGGAATTACTTT-GAAAGCACAAAAGGTCAGGACAAGCGTGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCATTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG\",\n )\n self.assertEqual(\n alignment.sequences[13].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[13].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[13].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[14].id, \"ornAna1.chr2\")\n self.assertEqual(len(alignment.sequences[14].seq), 54797317)\n self.assertEqual(\n alignment.sequences[14].seq[40040263 : 40040263 + 169],\n \"TGAAGATATGGAAGGAAATGATGGCTTGACAGGATTTCCCCTAAGGTGAATGAATAGCCTCATAAAACACAAAGCAGCTTTATGAACAGGGCTATTAAGTTGCACATGATTGGCTGATATGACCTTTCCTATCTTCTGGGTAGCTGAGTTACAGTGATATCAGAGGTGG\",\n )\n self.assertEqual(\n alignment[14],\n \"CCACCTCTGATATCACTGTAACTCAGCTACCCA-GAAGATAGGAAAGGTCATATCAGCCAATCATGTGCAACTTAATAGCCCTGTTCATAAAGCTGCTTTGTGTTTTATGAGGCTATTCATTCACCTTAGGGGAAATCCTGTCAAGCCATCATTTCCTTCCATATCTTCA\",\n )\n self.assertEqual(alignment.sequences[14].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[14].annotations[\"leftCount\"], 5690)\n self.assertEqual(alignment.sequences[14].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[14].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171035, 164755))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 15)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021275, 3021308, 3021308, 3021333, 3021334, 3021344,\n 3021357, 3021358, 3021359, 3021369, 3021369, 3021369,\n 3021369, 3021371, 3021382, 3021408, 3021415, 3021421],\n [ 285, 252, 252, 227, 226, 216,\n 203, 202, 201, 191, 183, 177,\n 168, 166, 155, 129, 122, 116],\n [ 3888, 3855, 3855, 3830, 3829, 3819,\n 3806, 3805, 3804, 3794, 3786, 3780,\n 3771, 3769, 3769, 3743, 3736, 3730],\n [158037166, 158037133, 158037133, 158037108, 158037107, 158037097,\n 158037084, 158037083, 158037082, 158037072, 158037064, 158037058,\n 158037049, 158037047, 158037036, 158037010, 158037003, 158036997],\n [157514999, 157514966, 157514966, 157514941, 157514940, 157514930,\n 157514917, 157514916, 157514915, 157514905, 157514897, 157514891,\n 157514882, 157514880, 157514869, 157514843, 157514836, 157514830],\n [155024945, 155024912, 155024912, 155024887, 155024886, 155024876,\n 155024863, 155024862, 155024861, 155024851, 155024843, 155024837,\n 155024828, 155024826, 155024815, 155024789, 155024782, 155024776],\n [ 10878, 10911, 10911, 10936, 10937, 10947,\n 10960, 10961, 10962, 10972, 10980, 10986,\n 10995, 10997, 11008, 11034, 11041, 11047],\n [ 323397, 323364, 323364, 323339, 323338, 323328,\n 323328, 323327, 323326, 323316, 323308, 323302,\n 323293, 323291, 323280, 323254, 323247, 323241],\n [ 1615, 1582, 1581, 1556, 1555, 1545,\n 1532, 1531, 1530, 1520, 1512, 1506,\n 1497, 1495, 1484, 1458, 1451, 1445],\n [ 521, 554, 554, 579, 580, 590,\n 603, 604, 605, 615, 623, 623,\n 632, 634, 645, 671, 671, 677],\n [ 47544221, 47544188, 47544188, 47544163, 47544163, 47544153,\n 47544140, 47544139, 47544138, 47544128, 47544120, 47544114,\n 47544105, 47544103, 47544092, 47544066, 47544059, 47544053],\n [ 45798, 45765, 45765, 45740, 45739, 45729,\n 45716, 45715, 45714, 45704, 45696, 45690,\n 45681, 45679, 45668, 45642, 45635, 45629],\n [ 7048, 7015, 7015, 6990, 6989, 6979,\n 6966, 6965, 6965, 6955, 6947, 6941,\n 6932, 6930, 6919, 6893, 6886, 6880],\n [ 95418, 95451, 95451, 95476, 95477, 95487,\n 95500, 95501, 95502, 95512, 95520, 95526,\n 95535, 95537, 95548, 95574, 95581, 95587],\n [ 40040432, 40040399, 40040399, 40040374, 40040373, 40040363,\n 40040350, 40040349, 40040348, 40040338, 40040330, 40040324,\n 40040315, 40040313, 40040302, 40040276, 40040269, 40040263],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021275 CTTTCTCTGACATTACTGTAACTGAAGTAGCTC-AGAAGCACAAAAGGTCACATCATGCA\ncavPor2.s 285 CCTTTGCTGATGTTACTGTAAGCGAACTAGCTG-AAAAGCACAAAAGGTCATGTCAGGCA\noryCun1.s 3888 TCGTCTCTGATGTTACTCTAGCTGAAAGCGCTC-CAAAGCACAAAAGGCCATGGCAGGCA\nponAbe2.c 158037166 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCA\npanTro2.c 157514999 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCA\nhg18.chr6 155024945 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCA\ncalJac1.C 10878 CCTTCTCTGATATTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGCAGGCA\ntupBel1.s 323397 TCCTCTCAGATGTTCCTGTAACCAAAGTAGCTC-AGAAGCACAAAAGGTCATGCCAGGCA\nsorAra1.s 1615 CCTTCTCTGATGTTACTGTAACTGAGGTAGCTCAAAAAGCACAAAAGGTCATGTCAGGCA\neriEur1.s 521 CCTTCTCTGATCTGACTGTAACCGAAGTCTCTC-GAAAGCACAAAAGCTCACGGCAGGCC\ncanFam2.c 47544221 CTGTCTCTGATGTTACTGTAACTGAAGTAGCTC-AAAAGCACAAAAGGTCATGTCAGGC-\nfelCat3.s 45798 CTGTCTCTGATGTTACTGTAACTGAAATAGTTC-AAAAGCACAAAAGGTGATGTCAGGCA\ndasNov1.s 7048 CCTTCTCTGATGTTACTGTAACTGAAGAGGCTC-AAAAGCACAAAAGGTCATGTCGGGCA\nechTel1.s 95418 CCATCTCTGATATTACTGTAATGGAATTACTTT-GAAAGCACAAAAGGTCAGGACAAGCG\nornAna1.c 40040432 CCACCTCTGATATCACTGTAACTCAGCTACCCA-GAAGATAGGAAAGGTCATATCAGCCA\n\nmm9.chr10 3021334 TCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGC-----------------------CA\ncavPor2.s 226 TTTATGCAAAATTTACTAGTTCCGTTCATAAAGGCACCTCGCATTTTATTACTTAGTTCA\noryCun1.s 3829 TTTATGTCAAATGTACTAGCACTGTTTATAACAGCACCTTGTGTTGTATTACTTTGTTCA\nponAbe2.c 158037107 TTCATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAA\npanTro2.c 157514940 TTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAA\nhg18.chr6 155024886 TTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTATCTTGTGTTTTATTACTTTGTTAA\ncalJac1.C 10937 TTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAA\ntupBel1.s 323338 TTGATGTAAA-------------GTTTCTGAAGGCATCTCGTGTTTTATTACTTTGTTCA\nsorAra1.s 1555 TTGATGTAAAATATACCAGTGCTGTTTATAAAGACCCCTTGCATATAATGTTGTTGATCA\neriEur1.s 580 TTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgca------gatgtctctca\ncanFam2.c 47544163 TTTATGTAAAATTTACTAGAGCTGTTTATAAAGGCACCTCGTGTAATATTGCTTTGTTCA\nfelCat3.s 45739 TTTATGTAAAATTTACTAGTGCTGTTTATAAAGGTACCTTGTGTATTATTGCTTTGTTCA\ndasNov1.s 6989 TTGATGTAAAATTTACTAGTGCTG-TTTATAAAGGACCTTGTGTTCTATTACTTTTTCTA\nechTel1.s 95477 TGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCA\nornAna1.c 40040373 ATCATGTGCAACTTAATAGCCCTGTTCATAAAGCTGCTTTGTGTTTTATGAGGCTATTCA\n\nmm9.chr10 3021371 CGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG 3021421\ncavPor2.s 166 TGTGTCTCGCAGGAAATCCAGTCACGCCATCATTTCCTTCCATATTTCAA 116\noryCun1.s 3769 -----------GGAAATCCAGTCACGCCGCGATTTCCTTCCACATTTCAA 3730\nponAbe2.c 158037047 TGTATCTTTCAGGAAATTCAGTCACGCCATCATTTCCTTCCATATTTCAT 158036997\npanTro2.c 157514880 TGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT 157514830\nhg18.chr6 155024826 TGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT 155024776\ncalJac1.C 10997 TGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT 11047\ntupBel1.s 323291 TGTGCCTTACAGGAAATCCAGTCGGGCCATCATTTCCTTCCATATCTCAG 323241\nsorAra1.s 1495 TGAACTTTTCCGGAAATCCTGTAATCTCATCATTTCCTCCCATATTCCAG 1445\neriEur1.s 634 cgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCC-------TTCCTG 677\ncanFam2.c 47544103 TGTACTTTACAGGAAATCCTGTCATCCTGTTACTTCCTTCCATATTTCAA 47544053\nfelCat3.s 45679 TGCACTTTATAGGAAATCCTGTCATCCTGTCATTTCCTTCCATAGTTCAG 45629\ndasNov1.s 6930 TCCCCCTTACAGGAAATCCTGTCATACCATCATTTCCTTCCATAAGTCAC 6880\nechTel1.s 95537 TTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG 95587\nornAna1.c 40040313 TTCACCTTAGGGGAAATCCTGTCAAGCCATCATTTCCTTCCATATCTTCA 40040263\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=891219.000000\ns mm9.chr10 3021275 146 + 129993255 CTTTCTCTGACATTACTGTAACTGAAGTAGCTC-AGAAGCACAAAAGGTCACATCATGCATCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGC-----------------------CACGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG\ns cavPor2.scaffold_216473 9741 169 - 10026 CCTTTGCTGATGTTACTGTAAGCGAACTAGCTG-AAAAGCACAAAAGGTCATGTCAGGCATTTATGCAAAATTTACTAGTTCCGTTCATAAAGGCACCTCGCATTTTATTACTTAGTTCATGTGTCTCGCAGGAAATCCAGTCACGCCATCATTTCCTTCCATATTTCAA\nq cavPor2.scaffold_216473 668536545547664539866666666666668-8787886799997788875886655536666688786768476688854689668876558688874778656675665668746666788474786888875667457786687996867886548798845555\ni cavPor2.scaffold_216473 C 0 C 0\ns oryCun1.scaffold_156751 838 158 - 4726 TCGTCTCTGATGTTACTCTAGCTGAAAGCGCTC-CAAAGCACAAAAGGCCATGGCAGGCATTTATGTCAAATGTACTAGCACTGTTTATAACAGCACCTTGTGTTGTATTACTTTGTTCA-----------GGAAATCCAGTCACGCCGCGATTTCCTTCCACATTTCAA\nq oryCun1.scaffold_156751 999999879999999999999999999997999-99999799999999898999999988999999988999999989996999999999988897996999999999999979999987-----------899998987999799998998999999999777999899\ni oryCun1.scaffold_156751 C 0 C 0\ns ponAbe2.chr6 16173265 169 - 174210431 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTCATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTATCTTTCAGGAAATTCAGTCACGCCATCATTTCCTTCCATATTTCAT\ni ponAbe2.chr6 C 0 C 0\ns panTro2.chr6 16393613 169 - 173908612 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\nq panTro2.chr6 999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns hg18.chr6 15875047 169 - 170899992 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTATCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\ni hg18.chr6 C 0 C 0\ns calJac1.Contig6394 10878 169 + 133105 CCTTCTCTGATATTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGCAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\ni calJac1.Contig6394 C 0 C 0\ns tupBel1.scaffold_114895.1-498454 175057 156 - 498454 TCCTCTCAGATGTTCCTGTAACCAAAGTAGCTC-AGAAGCACAAAAGGTCATGCCAGGCATTGATGTAAA-------------GTTTCTGAAGGCATCTCGTGTTTTATTACTTTGTTCATGTGCCTTACAGGAAATCCAGTCGGGCCATCATTTCCTTCCATATCTCAG\nq tupBel1.scaffold_114895.1-498454 999999999999999999999999999999999-999999999999999999999999999999999999-------------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni tupBel1.scaffold_114895.1-498454 C 0 C 0\ns sorAra1.scaffold_2476 3382 170 - 4997 CCTTCTCTGATGTTACTGTAACTGAGGTAGCTCAAAAAGCACAAAAGGTCATGTCAGGCATTGATGTAAAATATACCAGTGCTGTTTATAAAGACCCCTTGCATATAATGTTGTTGATCATGAACTTTTCCGGAAATCCTGTAATCTCATCATTTCCTCCCATATTCCAG\nq sorAra1.scaffold_2476 99999999999999997999999999999999999999999999999999999999999999999999999999999979999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni sorAra1.scaffold_2476 C 0 C 0\ns eriEur1.scaffold_266115 521 156 + 4589 CCTTCTCTGATCTGACTGTAACCGAAGTCTCTC-GAAAGCACAAAAGCTCACGGCAGGCCTTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgca------gatgtctctcacgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCC-------TTCCTG\nq eriEur1.scaffold_266115 999999999999999999999999999999999-999999999999999999999999799999999999999999999998987999899999999999999------999999999999999999999999999999999999999999999998-------999989\ni eriEur1.scaffold_266115 C 0 C 0\ns canFam2.chr1 78072035 168 - 125616256 CTGTCTCTGATGTTACTGTAACTGAAGTAGCTC-AAAAGCACAAAAGGTCATGTCAGGC-TTTATGTAAAATTTACTAGAGCTGTTTATAAAGGCACCTCGTGTAATATTGCTTTGTTCATGTACTTTACAGGAAATCCTGTCATCCTGTTACTTCCTTCCATATTTCAA\nq canFam2.chr1 999999999999999999999999999999999-9999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ns felCat3.scaffold_205680 73556 169 - 119354 CTGTCTCTGATGTTACTGTAACTGAAATAGTTC-AAAAGCACAAAAGGTGATGTCAGGCATTTATGTAAAATTTACTAGTGCTGTTTATAAAGGTACCTTGTGTATTATTGCTTTGTTCATGCACTTTATAGGAAATCCTGTCATCCTGTCATTTCCTTCCATAGTTCAG\nq felCat3.scaffold_205680 999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni felCat3.scaffold_205680 C 0 I 34165\ns dasNov1.scaffold_56749 3422 168 - 10470 CCTTCTCTGATGTTACTGTAACTGAAGAGGCTC-AAAAGCACAAAAGGTCATGTCGGGCATTGATGTAAAATTTACTAGTGCTG-TTTATAAAGGACCTTGTGTTCTATTACTTTTTCTATCCCCCTTACAGGAAATCCTGTCATACCATCATTTCCTTCCATAAGTCAC\nq dasNov1.scaffold_56749 989999999999999937699999999999999-79999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni dasNov1.scaffold_56749 C 0 C 0\ns echTel1.scaffold_288249 95418 169 + 100002 CCATCTCTGATATTACTGTAATGGAATTACTTT-GAAAGCACAAAAGGTCAGGACAAGCGTGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCATTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG\nq echTel1.scaffold_288249 999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni echTel1.scaffold_288249 C 0 C 0\ns ornAna1.chr2 14756885 169 - 54797317 CCACCTCTGATATCACTGTAACTCAGCTACCCA-GAAGATAGGAAAGGTCATATCAGCCAATCATGTGCAACTTAATAGCCCTGTTCATAAAGCTGCTTTGTGTTTTATGAGGCTATTCATTCACCTTAGGGGAAATCCTGTCAAGCCATCATTTCCTTCCATATCTTCA\ni ornAna1.chr2 I 5690 C 0\ne otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 30254)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021421 : 3021421 + 44],\n \"ACGTTGCTCATTGTAATTGAAGCATTTATTACCAATGCCTTCCC\",\n )\n self.assertEqual(\n alignment[0],\n \"-ACGTTGCTCATTGT-----AATTGAAGCATTTATTACCAA--------TG--------------CCTTCCC\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[69 : 69 + 47],\n \"CAGAGGGGCCGTCAGCAAAACATACTTTTATTTGTAACAAGGAACAG\",\n )\n self.assertEqual(\n alignment[1],\n \"-CTGTTCCTTGTTACA----AATAAAAGTATGTTTTGCTGA--------CG-------G-----CCCCTCTG\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"47675464566778886867867744466523545576436669356\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[3693 : 3693 + 37],\n \"ATTAGCAGTGAATGCTTTAATCCATAATGAGGAACCA\",\n )\n self.assertEqual(\n alignment[2],\n \"-TGGTTCCTCATTATG----GATTAAAGCATTCACTGCTAA--------T----------------------\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999998999998879999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 2345)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158036952 : 158036952 + 45],\n \"GAGAAAGCATTAGCAATAAACACTTTTATTTATAATGAGCAACAG\",\n )\n self.assertEqual(\n alignment[3],\n \"-CTGTTGCTCATTATA----AATAAAAGTGTTTATTGCTAA--------T--------------GCTTTCTC\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 4)\n self.assertEqual(alignment.sequences[4].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 173908612)\n self.assertEqual(\n alignment.sequences[4].seq[157514785 : 157514785 + 45],\n \"GAGAAAGCGTTAGCAATAAACACTTTTATTTATAATGAGGAACAG\",\n )\n self.assertEqual(\n alignment[4],\n \"-CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 4)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155024731 : 155024731 + 45],\n \"GAGAAAGCGTTAGCAATAAACACTTTTATTTATAATGAGGAACAG\",\n )\n self.assertEqual(\n alignment[5],\n \"-CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 4)\n self.assertEqual(alignment.sequences[6].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[6].seq), 133105)\n self.assertEqual(\n alignment.sequences[6].seq[11047 : 11047 + 43],\n \"CTGTTTCTCATTATAAATAAGTGTTTATTGCTAACGCTTTCTC\",\n )\n self.assertEqual(\n alignment[6],\n \"-CTGTTTCTCATTATA----AAT--AAGTGTTTATTGCTAA--------C--------------GCTTTCTC\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 701)\n self.assertEqual(alignment.sequences[7].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[7].seq), 498454)\n self.assertEqual(\n alignment.sequences[7].seq[323206 : 323206 + 35],\n \"TTAGCAACAAACGCTATATTTATCATGAGGAGCAG\",\n )\n self.assertEqual(\n alignment[7],\n \"-CTGCTCCTCATGATA----AAT-ATAGCGTTTGTTGCTAA-------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"],\n \"99999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 10695)\n self.assertEqual(alignment.sequences[8].id, \"sorAra1.scaffold_2476\")\n self.assertEqual(len(alignment.sequences[8].seq), 4997)\n self.assertEqual(\n alignment.sequences[8].seq[1397 : 1397 + 48],\n \"GGAACCTGCTGGTCATAAACGCTCtttttttAATCTAAGAAGGAACAG\",\n )\n self.assertEqual(\n alignment[8],\n \"-CTGTTCCTTCTTAGATTaaaaaaaGAGCGTTTATGACCAG--------CA-------GGTTCC--------\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"999999999999999999999999999999999766975599999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"eriEur1.scaffold_266115\")\n self.assertEqual(len(alignment.sequences[9].seq), 4589)\n self.assertEqual(\n alignment.sequences[9].seq[677 : 677 + 35],\n \"CTCCTTGTTCTTGAAGCCGTTTTTTATTGTCAGTG\",\n )\n self.assertEqual(\n alignment[9],\n \"-CTCCTTGTTCTTGAAGC----------CGTTTTTTATTGT--------CA-------GTG-----------\",\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"98959997997999999999999999999989999\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[10].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[10].seq), 125616256)\n self.assertEqual(\n alignment.sequences[10].seq[47544013 : 47544013 + 40],\n \"GACATTAGCAATAAATGCTTTTATTTATAATGAGAAACAG\",\n )\n self.assertEqual(\n alignment[10],\n \"-CTGTTTCTCATTATA----AATAAAAGCATTTATTGCTAA--------TG-------T------------C\",\n )\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[11].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[11].seq), 10470)\n self.assertEqual(\n alignment.sequences[11].seq[6836 : 6836 + 44],\n \"GAGGAGCCGTTAGCAGTAAATGCTTTTATTATAAAGAGGAACAG\",\n )\n self.assertEqual(\n alignment[11],\n \"-CTGTTCCTCTTTAT-----AATAAAAGCATTTACTGCTAA--------CGGCTCCTC--------------\",\n )\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 904)\n self.assertEqual(alignment.sequences[12].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[12].seq), 100002)\n self.assertEqual(\n alignment.sequences[12].seq[95587 : 95587 + 38],\n \"CTGATCCTCATTATAAATAAAAGTGTTTGTTACTAATG\",\n )\n self.assertEqual(\n alignment[12],\n \"-CTGATCCTCATTATA----AATAAAAGTGTTTGTTACTAA--------TG---------------------\",\n )\n self.assertEqual(\n alignment.sequences[12].annotations[\"quality\"],\n \"99999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[12].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[12].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[12].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[13].id, \"ornAna1.chr2\")\n self.assertEqual(len(alignment.sequences[13].seq), 54797317)\n self.assertEqual(\n alignment.sequences[13].seq[40040218 : 40040218 + 45],\n \"GGGGGATCTTTAGTAATAAAAGAGTCCCTGTACAATGAGGACAGT\",\n )\n self.assertEqual(\n alignment[13],\n \"ACTG-TCCTCATTGTA----CAGGGACTCTTTTATTACTAAAGATCCCCC----------------------\",\n )\n self.assertEqual(alignment.sequences[13].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[13].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (45629, 11464))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171035, 164755))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 14)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 2)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021421, 3021421, 3021424, 3021425, 3021435, 3021435,\n 3021435, 3021435, 3021438, 3021439, 3021440, 3021443,\n 3021456, 3021456, 3021457, 3021458, 3021458, 3021458,\n 3021458, 3021458, 3021458, 3021464, 3021465],\n [ 116, 116, 113, 112, 102, 101,\n 101, 101, 98, 97, 96, 93,\n 80, 80, 79, 78, 78, 77,\n 77, 77, 76, 70, 69],\n [ 3730, 3730, 3727, 3726, 3716, 3715,\n 3715, 3715, 3712, 3711, 3710, 3707,\n 3694, 3694, 3693, 3693, 3693, 3693,\n 3693, 3693, 3693, 3693, 3693],\n [158036997, 158036997, 158036994, 158036993, 158036983, 158036982,\n 158036982, 158036982, 158036979, 158036978, 158036977, 158036974,\n 158036961, 158036961, 158036960, 158036960, 158036960, 158036960,\n 158036960, 158036960, 158036959, 158036953, 158036952],\n [157514830, 157514830, 157514827, 157514826, 157514816, 157514815,\n 157514815, 157514815, 157514812, 157514811, 157514810, 157514807,\n 157514794, 157514794, 157514793, 157514793, 157514793, 157514793,\n 157514793, 157514793, 157514792, 157514786, 157514785],\n [155024776, 155024776, 155024773, 155024772, 155024762, 155024761,\n 155024761, 155024761, 155024758, 155024757, 155024756, 155024753,\n 155024740, 155024740, 155024739, 155024739, 155024739, 155024739,\n 155024739, 155024739, 155024738, 155024732, 155024731],\n [ 11047, 11047, 11050, 11051, 11061, 11062,\n 11062, 11062, 11065, 11065, 11065, 11068,\n 11081, 11081, 11082, 11082, 11082, 11082,\n 11082, 11082, 11083, 11089, 11090],\n [ 323241, 323241, 323238, 323237, 323227, 323226,\n 323226, 323226, 323223, 323223, 323222, 323219,\n 323206, 323206, 323206, 323206, 323206, 323206,\n 323206, 323206, 323206, 323206, 323206],\n [ 1445, 1445, 1442, 1441, 1431, 1430,\n 1428, 1426, 1423, 1422, 1421, 1418,\n 1405, 1405, 1404, 1403, 1403, 1402,\n 1400, 1397, 1397, 1397, 1397],\n [ 677, 677, 680, 681, 691, 692,\n 694, 694, 694, 694, 694, 694,\n 707, 707, 708, 709, 709, 710,\n 712, 712, 712, 712, 712],\n [ 47544053, 47544053, 47544050, 47544049, 47544039, 47544038,\n 47544038, 47544038, 47544035, 47544034, 47544033, 47544030,\n 47544017, 47544017, 47544016, 47544015, 47544015, 47544014,\n 47544014, 47544014, 47544014, 47544014, 47544013],\n [ 6880, 6880, 6877, 6876, 6866, 6866,\n 6866, 6866, 6863, 6862, 6861, 6858,\n 6845, 6845, 6844, 6843, 6836, 6836,\n 6836, 6836, 6836, 6836, 6836],\n [ 95587, 95587, 95590, 95591, 95601, 95602,\n 95602, 95602, 95605, 95606, 95607, 95610,\n 95623, 95623, 95624, 95625, 95625, 95625,\n 95625, 95625, 95625, 95625, 95625],\n [ 40040263, 40040262, 40040259, 40040259, 40040249, 40040248,\n 40040248, 40040248, 40040245, 40040244, 40040243, 40040240,\n 40040227, 40040219, 40040218, 40040218, 40040218, 40040218,\n 40040218, 40040218, 40040218, 40040218, 40040218],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021421 -ACGTTGCTCATTGT-----AATTGAAGCATTTATTACCAA--------TG---------\ncavPor2.s 116 -CTGTTCCTTGTTACA----AATAAAAGTATGTTTTGCTGA--------CG-------G-\noryCun1.s 3730 -TGGTTCCTCATTATG----GATTAAAGCATTCACTGCTAA--------T----------\nponAbe2.c 158036997 -CTGTTGCTCATTATA----AATAAAAGTGTTTATTGCTAA--------T----------\npanTro2.c 157514830 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C----------\nhg18.chr6 155024776 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C----------\ncalJac1.C 11047 -CTGTTTCTCATTATA----AAT--AAGTGTTTATTGCTAA--------C----------\ntupBel1.s 323241 -CTGCTCCTCATGATA----AAT-ATAGCGTTTGTTGCTAA-------------------\nsorAra1.s 1445 -CTGTTCCTTCTTAGATTaaaaaaaGAGCGTTTATGACCAG--------CA-------GG\neriEur1.s 677 -CTCCTTGTTCTTGAAGC----------CGTTTTTTATTGT--------CA-------GT\ncanFam2.c 47544053 -CTGTTTCTCATTATA----AATAAAAGCATTTATTGCTAA--------TG-------T-\ndasNov1.s 6880 -CTGTTCCTCTTTAT-----AATAAAAGCATTTACTGCTAA--------CGGCTCCTC--\nechTel1.s 95587 -CTGATCCTCATTATA----AATAAAAGTGTTTGTTACTAA--------TG---------\nornAna1.c 40040263 ACTG-TCCTCATTGTA----CAGGGACTCTTTTATTACTAAAGATCCCCC----------\n\nmm9.chr10 3021458 -----CCTTCCC 3021465\ncavPor2.s 77 ----CCCCTCTG 69\noryCun1.s 3693 ------------ 3693\nponAbe2.c 158036960 ----GCTTTCTC 158036952\npanTro2.c 157514793 ----GCTTTCTC 157514785\nhg18.chr6 155024739 ----GCTTTCTC 155024731\ncalJac1.C 11082 ----GCTTTCTC 11090\ntupBel1.s 323206 ------------ 323206\nsorAra1.s 1401 TTCC-------- 1397\neriEur1.s 711 G----------- 712\ncanFam2.c 47544014 -----------C 47544013\ndasNov1.s 6836 ------------ 6836\nechTel1.s 95625 ------------ 95625\nornAna1.c 40040218 ------------ 40040218\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=30254.000000\ns mm9.chr10 3021421 44 + 129993255 -ACGTTGCTCATTGT-----AATTGAAGCATTTATTACCAA--------TG--------------CCTTCCC\ns cavPor2.scaffold_216473 9910 47 - 10026 -CTGTTCCTTGTTACA----AATAAAAGTATGTTTTGCTGA--------CG-------G-----CCCCTCTG\nq cavPor2.scaffold_216473 -476754645667788----868678677444665235455--------76-------4-----36669356\ni cavPor2.scaffold_216473 C 0 C 0\ns oryCun1.scaffold_156751 996 37 - 4726 -TGGTTCCTCATTATG----GATTAAAGCATTCACTGCTAA--------T----------------------\nq oryCun1.scaffold_156751 -999999999899999----887999999999999999999--------9----------------------\ni oryCun1.scaffold_156751 C 0 I 2345\ns ponAbe2.chr6 16173434 45 - 174210431 -CTGTTGCTCATTATA----AATAAAAGTGTTTATTGCTAA--------T--------------GCTTTCTC\ni ponAbe2.chr6 C 0 I 4\ns panTro2.chr6 16393782 45 - 173908612 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC\nq panTro2.chr6 -999999999999999----999999999999999999999--------9--------------99999999\ni panTro2.chr6 C 0 I 4\ns hg18.chr6 15875216 45 - 170899992 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC\ni hg18.chr6 C 0 I 4\ns calJac1.Contig6394 11047 43 + 133105 -CTGTTTCTCATTATA----AAT--AAGTGTTTATTGCTAA--------C--------------GCTTTCTC\ni calJac1.Contig6394 C 0 I 701\ns tupBel1.scaffold_114895.1-498454 175213 35 - 498454 -CTGCTCCTCATGATA----AAT-ATAGCGTTTGTTGCTAA-------------------------------\nq tupBel1.scaffold_114895.1-498454 -999999999999999----999-99999999999999999-------------------------------\ni tupBel1.scaffold_114895.1-498454 C 0 I 10695\ns sorAra1.scaffold_2476 3552 48 - 4997 -CTGTTCCTTCTTAGATTaaaaaaaGAGCGTTTATGACCAG--------CA-------GGTTCC--------\nq sorAra1.scaffold_2476 -9999999999999999999999999999999997669755--------99-------999999--------\ni sorAra1.scaffold_2476 C 0 N 0\ns eriEur1.scaffold_266115 677 35 + 4589 -CTCCTTGTTCTTGAAGC----------CGTTTTTTATTGT--------CA-------GTG-----------\nq eriEur1.scaffold_266115 -98959997997999999----------9999999999999--------89-------999-----------\ni eriEur1.scaffold_266115 C 0 N 0\ns canFam2.chr1 78072203 40 - 125616256 -CTGTTTCTCATTATA----AATAAAAGCATTTATTGCTAA--------TG-------T------------C\nq canFam2.chr1 -999999999999999----999999999999999999999--------99-------9------------9\ni canFam2.chr1 C 0 C 0\ns dasNov1.scaffold_56749 3590 44 - 10470 -CTGTTCCTCTTTAT-----AATAAAAGCATTTACTGCTAA--------CGGCTCCTC--------------\nq dasNov1.scaffold_56749 -99999999999999-----999999999999999999999--------999999999--------------\ni dasNov1.scaffold_56749 C 0 I 904\ns echTel1.scaffold_288249 95587 38 + 100002 -CTGATCCTCATTATA----AATAAAAGTGTTTGTTACTAA--------TG---------------------\nq echTel1.scaffold_288249 -999999999999999----999999999999999999999--------99---------------------\ni echTel1.scaffold_288249 C 0 N 0\ns ornAna1.chr2 14757054 45 - 54797317 ACTG-TCCTCATTGTA----CAGGGACTCTTTTATTACTAAAGATCCCCC----------------------\ni ornAna1.chr2 C 0 C 0\ne felCat3.scaffold_205680 73725 34165 - 119354 I\ne otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, -9167)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021465 : 3021465 + 29],\n \"CCCTACACTGTCAAGTGGGAGGAGACAGT\",\n )\n self.assertEqual(\n alignment[0], \"CCCT--ACACTGTC----AAGTGGGAGGAGACAGT--------------------\"\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[41 : 41 + 28], \"accatcccaccccacccccagtgtGGCT\"\n )\n self.assertEqual(\n alignment[1], \"AGCC--acactgg-----gggtggggtgggatggt--------------------\"\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"7667687856666544895554554677\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 174210431)\n self.assertEqual(\n alignment.sequences[2].seq[158036924 : 158036924 + 24],\n \"GCTGCTCCTATCGCCCCCACAGGG\",\n )\n self.assertEqual(\n alignment[2], \"-------CCCTGTG----GGGGCGATAGGAGCAGC--------------------\"\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 4)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[3].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 173908612)\n self.assertEqual(\n alignment.sequences[3].seq[157514757 : 157514757 + 24],\n \"GCTGCCCCTATCGCCCCCACATGG\",\n )\n self.assertEqual(\n alignment[3], \"-------CCATGTG----GGGGCGATAGGGGCAGC--------------------\"\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"], \"999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 4)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[4].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 170899992)\n self.assertEqual(\n alignment.sequences[4].seq[155024703 : 155024703 + 24],\n \"GCTGCCCCTATCGCCCCCACATGG\",\n )\n self.assertEqual(\n alignment[4], \"-------CCATGTG----GGGGCGATAGGGGCAGC--------------------\"\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 4)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[5].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[5].seq), 125616256)\n self.assertEqual(\n alignment.sequences[5].seq[47543982 : 47543982 + 31],\n \"CACACACACACACCCCCCATGTGGTTCAGGG\",\n )\n self.assertEqual(\n alignment[5], \"CCCTGAACCACATG----GGGGGTGTGTGTGTGTG--------------------\"\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 13)\n self.assertEqual(alignment.sequences[6].id, \"ornAna1.chr2\")\n self.assertEqual(len(alignment.sequences[6].seq), 54797317)\n self.assertEqual(\n alignment.sequences[6].seq[40040173 : 40040173 + 45],\n \"GCCAGCAAAGATGAAAGAGGGCTACATCCAAACTCCTATGACACA\",\n )\n self.assertEqual(\n alignment[6], \"----------TGTGTCATAGGAGTTTGGATGTAGCCCTCTTTCATCTTTGCTGGC\"\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(record.seq), 10470)\n self.assertEqual(segment, (6836, 5932))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (45629, 11464))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (11090, 11791))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (323206, 312511))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171035, 164755))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(record.seq), 4726)\n self.assertEqual(segment, (3693, 1348))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 7)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021465, 3021469, 3021469, 3021470, 3021473, 3021476,\n 3021477, 3021477, 3021494, 3021494],\n [ 69, 65, 65, 64, 61, 58,\n 58, 58, 41, 41],\n [158036948, 158036948, 158036948, 158036948, 158036945, 158036942,\n 158036941, 158036941, 158036924, 158036924],\n [157514781, 157514781, 157514781, 157514781, 157514778, 157514775,\n 157514774, 157514774, 157514757, 157514757],\n [155024727, 155024727, 155024727, 155024727, 155024724, 155024721,\n 155024720, 155024720, 155024703, 155024703],\n [ 47544013, 47544009, 47544007, 47544006, 47544003, 47544000,\n 47543999, 47543999, 47543982, 47543982],\n [ 40040218, 40040218, 40040218, 40040218, 40040218, 40040215,\n 40040214, 40040210, 40040193, 40040173],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021465 CCCT--ACACTGTC----AAGTGGGAGGAGACAGT--------------------\ncavPor2.s 69 AGCC--acactgg-----gggtggggtgggatggt--------------------\nponAbe2.c 158036948 -------CCCTGTG----GGGGCGATAGGAGCAGC--------------------\npanTro2.c 157514781 -------CCATGTG----GGGGCGATAGGGGCAGC--------------------\nhg18.chr6 155024727 -------CCATGTG----GGGGCGATAGGGGCAGC--------------------\ncanFam2.c 47544013 CCCTGAACCACATG----GGGGGTGTGTGTGTGTG--------------------\nornAna1.c 40040218 ----------TGTGTCATAGGAGTTTGGATGTAGCCCTCTTTCATCTTTGCTGGC\n\nmm9.chr10 3021494\ncavPor2.s 41\nponAbe2.c 158036924\npanTro2.c 157514757\nhg18.chr6 155024703\ncanFam2.c 47543982\nornAna1.c 40040173\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=-9167.000000\ns mm9.chr10 3021465 29 + 129993255 CCCT--ACACTGTC----AAGTGGGAGGAGACAGT--------------------\ns cavPor2.scaffold_216473 9957 28 - 10026 AGCC--acactgg-----gggtggggtgggatggt--------------------\nq cavPor2.scaffold_216473 7667--6878566-----66544895554554677--------------------\ni cavPor2.scaffold_216473 C 0 N 0\ns ponAbe2.chr6 16173483 24 - 174210431 -------CCCTGTG----GGGGCGATAGGAGCAGC--------------------\ni ponAbe2.chr6 I 4 I 9\ns panTro2.chr6 16393831 24 - 173908612 -------CCATGTG----GGGGCGATAGGGGCAGC--------------------\nq panTro2.chr6 -------9999999----99999999999999999--------------------\ni panTro2.chr6 I 4 I 9\ns hg18.chr6 15875265 24 - 170899992 -------CCATGTG----GGGGCGATAGGGGCAGC--------------------\ni hg18.chr6 I 4 I 9\ns canFam2.chr1 78072243 31 - 125616256 CCCTGAACCACATG----GGGGGTGTGTGTGTGTG--------------------\nq canFam2.chr1 99999999999999----99999999999999999--------------------\ni canFam2.chr1 C 0 I 13\ns ornAna1.chr2 14757099 45 - 54797317 ----------TGTGTCATAGGAGTTTGGATGTAGCCCTCTTTCATCTTTGCTGGC\ni ornAna1.chr2 C 0 C 0\ne dasNov1.scaffold_56749 3634 904 - 10470 I\ne felCat3.scaffold_205680 73725 34165 - 119354 I\ne calJac1.Contig6394 11090 701 + 133105 I\ne tupBel1.scaffold_114895.1-498454 175248 10695 - 498454 I\ne otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I\ne oryCun1.scaffold_156751 1033 2345 - 4726 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'C', 'C', 'T', '-', '-', 'A', 'C', 'A', 'C', 'T', 'G', 'T',\n 'C', '-', '-', '-', '-', 'A', 'A', 'G', 'T', 'G', 'G', 'G', 'A',\n 'G', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'T', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['A', 'G', 'C', 'C', '-', '-', 'a', 'c', 'a', 'c', 't', 'g', 'g',\n '-', '-', '-', '-', '-', 'g', 'g', 'g', 't', 'g', 'g', 'g', 'g',\n 't', 'g', 'g', 'g', 'a', 't', 'g', 'g', 't', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'C', 'T', 'G', 'T',\n 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'C', 'G', 'A', 'T',\n 'A', 'G', 'G', 'A', 'G', 'C', 'A', 'G', 'C', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'A', 'T', 'G', 'T',\n 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'C', 'G', 'A', 'T',\n 'A', 'G', 'G', 'G', 'G', 'C', 'A', 'G', 'C', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'A', 'T', 'G', 'T',\n 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'C', 'G', 'A', 'T',\n 'A', 'G', 'G', 'G', 'G', 'C', 'A', 'G', 'C', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['C', 'C', 'C', 'T', 'G', 'A', 'A', 'C', 'C', 'A', 'C', 'A', 'T',\n 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'G', 'T', 'G', 'T',\n 'G', 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'G', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'G', 'T',\n 'G', 'T', 'C', 'A', 'T', 'A', 'G', 'G', 'A', 'G', 'T', 'T', 'T',\n 'G', 'G', 'A', 'T', 'G', 'T', 'A', 'G', 'C', 'C', 'C', 'T', 'C',\n 'T', 'T', 'T', 'C', 'A', 'T', 'C', 'T', 'T', 'T', 'G', 'C', 'T',\n 'G', 'G', 'C']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 15763)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021494 : 3021494 + 42],\n \"TGTTTAGTACCATGCTTAGGAATGATAAACTCACTTAGTGtt\",\n )\n self.assertEqual(alignment[0], \"TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt\")\n self.assertEqual(alignment.sequences[1].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 174210431)\n self.assertEqual(\n alignment.sequences[1].seq[158036869 : 158036869 + 46],\n \"AAGATTGGGTGAGCCTATCACGCCAAAGAATAAAGGACATGCAACA\",\n )\n self.assertEqual(alignment[1], \"TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 943)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157514702 : 157514702 + 46],\n \"AAGATTGGGTGAGCCTATCACGCCAAAGAATAAAGGATATGCAACA\",\n )\n self.assertEqual(alignment[2], \"TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\")\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 10)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155024648 : 155024648 + 46],\n \"AAGATTGGGTGAGCCTATCACGCCAAAGAATAAACGACATGCAACA\",\n )\n self.assertEqual(alignment[3], \"TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 931)\n self.assertEqual(alignment.sequences[4].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[4].seq), 125616256)\n self.assertEqual(\n alignment.sequences[4].seq[47543923 : 47543923 + 46],\n \"ATGATGGAGTGAAGCTATCACTTTGAACAGCAAGTGAGACTTAACA\",\n )\n self.assertEqual(alignment[4], \"TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT\")\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 13)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 1)\n self.assertEqual(alignment.sequences[5].id, \"ornAna1.chr2\")\n self.assertEqual(len(alignment.sequences[5].seq), 54797317)\n self.assertEqual(\n alignment.sequences[5].seq[40040137 : 40040137 + 36],\n \"TCCAGTGAGTAGAAGTTCTAGCAATCATTTTAAACA\",\n )\n self.assertEqual(alignment[5], \"TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(record.seq), 10470)\n self.assertEqual(segment, (6836, 5932))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (45629, 11464))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (11090, 11791))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (323206, 312511))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171035, 164755))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(record.seq), 4726)\n self.assertEqual(segment, (3693, 1348))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 6)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021494, 3021505, 3021505, 3021521, 3021523, 3021532,\n 3021536],\n [158036915, 158036904, 158036900, 158036884, 158036882, 158036873,\n 158036869],\n [157514748, 157514737, 157514733, 157514717, 157514715, 157514706,\n 157514702],\n [155024694, 155024683, 155024679, 155024663, 155024661, 155024652,\n 155024648],\n [ 47543969, 47543958, 47543954, 47543938, 47543936, 47543927,\n 47543923],\n [ 40040173, 40040162, 40040162, 40040146, 40040146, 40040137,\n 40040137],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021494 TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt 3021536\nponAbe2.c 158036915 TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT 158036869\npanTro2.c 157514748 TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT 157514702\nhg18.chr6 155024694 TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT 155024648\ncanFam2.c 47543969 TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT 47543923\nornAna1.c 40040173 TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA---- 40040137\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=15763.000000\ns mm9.chr10 3021494 42 + 129993255 TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt\ns ponAbe2.chr6 16173516 46 - 174210431 TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\ni ponAbe2.chr6 I 9 I 943\ns panTro2.chr6 16393864 46 - 173908612 TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\nq panTro2.chr6 9999999999999999999999999999999999999999999999\ni panTro2.chr6 I 9 I 10\ns hg18.chr6 15875298 46 - 170899992 TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\ni hg18.chr6 I 9 I 931\ns canFam2.chr1 78072287 46 - 125616256 TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT\nq canFam2.chr1 9999999999999999999999999999999999999999999999\ni canFam2.chr1 I 13 I 1\ns ornAna1.chr2 14757144 36 - 54797317 TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----\ni ornAna1.chr2 C 0 C 0\ne dasNov1.scaffold_56749 3634 904 - 10470 I\ne felCat3.scaffold_205680 73725 34165 - 119354 I\ne calJac1.Contig6394 11090 701 + 133105 I\ne tupBel1.scaffold_114895.1-498454 175248 10695 - 498454 I\ne otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I\ne oryCun1.scaffold_156751 1033 2345 - 4726 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'G', 'T', 'T', 'T', 'A', 'G', 'T', 'A', 'C', 'C', '-', '-',\n '-', '-', 'A', 'T', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A',\n 'T', 'G', 'A', 'T', 'A', 'A', 'A', 'C', 'T', 'C', 'A', 'C', 'T',\n 'T', 'A', 'G', 'T', 'G', 't', 't'],\n ['T', 'G', 'T', 'T', 'G', 'C', 'A', 'T', 'G', 'T', 'C', 'C', 'T',\n 'T', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'G', 'G', 'C', 'G',\n 'T', 'G', 'A', 'T', 'A', 'G', 'G', 'C', 'T', 'C', 'A', 'C', 'C',\n 'C', 'A', 'A', 'T', 'C', 'T', 'T'],\n ['T', 'G', 'T', 'T', 'G', 'C', 'A', 'T', 'A', 'T', 'C', 'C', 'T',\n 'T', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'G', 'G', 'C', 'G',\n 'T', 'G', 'A', 'T', 'A', 'G', 'G', 'C', 'T', 'C', 'A', 'C', 'C',\n 'C', 'A', 'A', 'T', 'C', 'T', 'T'],\n ['T', 'G', 'T', 'T', 'G', 'C', 'A', 'T', 'G', 'T', 'C', 'G', 'T',\n 'T', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'G', 'G', 'C', 'G',\n 'T', 'G', 'A', 'T', 'A', 'G', 'G', 'C', 'T', 'C', 'A', 'C', 'C',\n 'C', 'A', 'A', 'T', 'C', 'T', 'T'],\n ['T', 'G', 'T', 'T', 'A', 'A', 'G', 'T', 'C', 'T', 'C', 'A', 'C',\n 'T', 'T', 'G', 'C', 'T', 'G', 'T', 'T', 'C', 'A', 'A', 'A', 'G',\n 'T', 'G', 'A', 'T', 'A', 'G', 'C', 'T', 'T', 'C', 'A', 'C', 'T',\n 'C', 'C', 'A', 'T', 'C', 'A', 'T'],\n ['T', 'G', 'T', 'T', 'T', 'A', 'A', 'A', 'A', 'T', 'G', '-', '-',\n '-', '-', 'A', 'T', 'T', 'G', 'C', 'T', 'A', 'G', 'A', 'A', 'C',\n 'T', 'T', 'C', 'T', 'A', '-', '-', 'C', 'T', 'C', 'A', 'C', 'T',\n 'G', 'G', 'A', '-', '-', '-', '-']], dtype='U')\n # fmt: on\n )\n )\n self.assertRaises(StopIteration, next, alignments)",
"def test_reading_ucsc_mm9_chr10_bad(self):\n path = \"MAF/ucsc_mm9_chr10_bad.maf\"\n alignments = Align.parse(path, \"maf\")\n self.assertEqual(alignments.metadata[\"MAF Version\"], \"1\")\n self.assertEqual(alignments.metadata[\"Scoring\"], \"autoMZ.v1\")\n next(alignments)\n next(alignments)\n next(alignments)\n next(alignments)\n next(alignments)\n next(alignments)\n with self.assertRaises(ValueError) as cm:\n next(alignments)\n self.assertEqual(\n str(cm.exception), \"sequence size is incorrect (found 219, expected 319)\"\n )",
"def test_parse_map_invalid_sample_name(self):",
"def testMapFile(self):\n test_path = self._GetTestFilePath(['SYSTEM'])\n self._SkipIfPathNotExists(test_path)\n\n win_registry = registry.WinRegistry(\n registry_file_reader=TestWinRegistryFileReader())\n\n registry_file = win_registry._OpenFile(test_path)\n\n win_registry = registry.WinRegistry()\n key_path_prefix = win_registry.GetRegistryFileMapping(registry_file)\n win_registry.MapFile(key_path_prefix, registry_file)",
"def _read_maps(self):\n try:\n f = open(self._procpath('%d/maps' % self.pid))\n except IOError as e:\n # ignore killed process\n if e.errno != errno.ENOENT:\n raise\n return\n for line in f:\n try:\n so = line.split()[5].strip()\n self.mapped.append(so)\n except IndexError:\n pass",
"def test_read_movie_memmap():\n fname = public_file('tifffile/movie.tif')\n with TiffFile(fname) as tif:\n # assert data\n data = tif.asarray(out='memmap')\n assert isinstance(data, numpy.core.memmap)\n assert data.flags['C_CONTIGUOUS']\n assert data.shape == (30000, 64, 64)\n assert data.dtype.name == 'uint16'\n assert data[29999, 32, 32] == 460\n del data\n assert not tif.filehandle.closed\n assert__str__(tif, 0)",
"def test_10_read_mgf(self):\n res = read_mgf(os.path.join(\".\", \"plymgf\", \"data\", \"test.mgf\"))\n self.assertEqual(res[\"meta\"], {'charges': [3, 2, 1]})\n self.assertEqual(res[\"ions\"][2][\"rtinseconds\"], 603)\n self.assertEqual(res[\"ions\"][3][\"charges\"], [3])",
"def test_create_map():\n S = stormstats.Storm()\n filename = 'map_2016-11-03.html'\n if os.path.isfile(filename):\n os.remove(filename)\n mx = S.get_map()\n assert os.path.isfile(filename), \"Error, no html mapfile found\"\n os.remove(filename)",
"def load_map(maps):\n with open(maps,\"r\") as read_file:\n map_data = json.load(read_file)\n if map_data != '': # You should probably raise an exception here. Not return ''\n return map_data, True\n else:\n return '', False",
"def test_writing_ucsc_mm9_chr10(self):\n path = \"MAF/ucsc_mm9_chr10.maf\"\n alignments = Align.parse(path, \"maf\")\n output = StringIO()\n n = Align.write(alignments, output, \"maf\")\n self.assertEqual(n, 48)\n output.seek(0)\n with open(path) as stream:\n for line1, line2 in zip(output, stream):\n words1 = line1.split()\n words2 = line2.split()\n if line1.startswith(\"e \"):\n (\n prefix1,\n name1,\n start1,\n size1,\n strand1,\n length1,\n status1,\n ) = line1.split()\n (\n prefix2,\n name2,\n start2,\n size2,\n strand2,\n length2,\n status2,\n ) = line2.split()\n size1 = int(size1)\n size2 = int(size2)\n if size1 == 0 and strand1 != strand2:\n start1 = int(start1)\n start2 = int(start2)\n size1 = int(size1)\n size2 = int(size2)\n length1 = int(length1)\n length2 = int(length2)\n self.assertEqual(prefix1, \"e\")\n self.assertEqual(prefix2, \"e\")\n self.assertEqual(name1, name2)\n self.assertEqual(status1, status2)\n self.assertEqual(size1, size2)\n self.assertEqual(length1, length2)\n self.assertEqual(start1, length2 - start2 - size2)\n self.assertEqual(start2, length1 - start1 - size1)\n continue\n self.assertEqual(words1, words2)",
"def test_get_wordmap():\n SMILES = np.array(['CC'])\n # test output file type\n result = DataUtils.get_wordmap(SMILES)\n assert isinstance(result, dict)\n\n return"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Tests reading materials from an R6 MAP file
|
def test_R6_MAP_Materials(self):
settings = load_settings(TEST_SETTINGS_FILE)
map_filepath = path.join(settings["gamePath_R6_EW"], "data", "map", "m02", "mansion.map")
loadedFile = MAPLevelReader.MAPLevelFile()
loadedFile.read_file(map_filepath)
#TODO: This is currently disabled as this file has an unread part at the end, but the rest of this test is meaninful
#self.assertTrue(readSucessfullyToEOF, "Failed to read whole file")
#self.check_section_strings(loadedFile)
self.assertEqual(loadedFile.materialListHeader.numMaterials, 137, "Unexpected number of materials")
firstMaterial = loadedFile.materials[0]
self.assertEqual(firstMaterial.get_material_game_version(), RSEGameVersions.RAINBOW_SIX, "Wrong material format detected")
self.assertEqual(firstMaterial.versionNumber, 1, "Wrong material version number")
self.assertEqual(firstMaterial.material_name.string, "WI_plain5", "Wrong material name")
self.assertEqual(firstMaterial.texture_name.string, "Wl_paper_congo_tan_leaves1.BMP", "Wrong texture name")
self.assertAlmostEqual(firstMaterial.opacity, 1.0, 3, "Wrong opacity value")
self.assertAlmostEqual(firstMaterial.emissiveStrength, 0.0, 3, "Wrong emissive strength value")
self.assertEqual(firstMaterial.textureAddressMode, 3, "Wrong texture address mode value")
self.assertEqual(firstMaterial.ambientColorUInt, [25, 25, 25], "Wrong ambient color")
self.assertEqual(firstMaterial.diffuseColorUInt, [255, 255, 255], "Wrong diffuse color")
self.assertEqual(firstMaterial.specularColorUInt, [229, 229, 229], "Wrong specular color")
self.assertEqual(firstMaterial.normalizedColors, False, "Incorrectly determined whether colors are normalized in the file")
self.assertAlmostEqual(firstMaterial.specularLevel, 0.0, 3, "Wrong specular value")
self.assertEqual(firstMaterial.twoSided, False, "Wrong two sided material flag value")
|
[
"def test_R6_MAP_Structure(self):\n settings = load_settings(TEST_SETTINGS_FILE)\n\n map_filepath = path.join(settings[\"gamePath_R6_EW\"], \"data\", \"map\", \"m01\", \"M01.map\")\n\n loadedFile = MAPLevelReader.MAPLevelFile()\n readSucessfullyToEOF = loadedFile.read_file(map_filepath)\n\n self.assertTrue(readSucessfullyToEOF, \"Failed to read whole file\")\n\n self.check_section_strings(loadedFile)\n\n self.assertEqual(loadedFile.materialListHeader.numMaterials, 263, \"Unexpected number of materials\")\n\n self.assertEqual(loadedFile.geometryListHeader.count, 57, \"Unexpected number of geometry objects\")\n\n self.assertEqual(loadedFile.portalList.portalCount, 65, \"Unexpected number of portals\")\n\n self.assertEqual(loadedFile.lightList.lightCount, 162, \"Unexpected number of lights\")\n\n self.assertEqual(loadedFile.objectList.objectCount, 38, \"Unexpected number of objects\")\n\n self.assertEqual(loadedFile.roomList.roomCount, 47, \"Unexpected number of rooms\")\n\n self.assertEqual(loadedFile.planningLevelList.planningLevelCount, 4, \"Unexpected number of planning levels\")",
"def test_load_all_R6_maps(self):\n settings = load_settings(TEST_SETTINGS_FILE)\n\n discovered_files = gather_files_in_path(\".MAP\", settings[\"gamePath_R6_EW\"])\n\n for map_filepath in discovered_files:\n if map_filepath.endswith(\"obstacletest.map\") or map_filepath.endswith(\"mansion.map\") or map_filepath.endswith(\"m8.map\") or map_filepath.endswith(\"m14.map\"):\n #TODO: remove all of these maps, except obstacletest.map from this skip, once the last data structure is deciphered\n #I believe this is an early test map that was shipped by accident.\n # It's data structures are not consistent with the rest of the map files\n # and it is not used anywhere so it is safe to skip\n continue\n\n loadedFile = MAPLevelReader.MAPLevelFile()\n readSucessfullyToEOF = loadedFile.read_file(map_filepath)\n\n self.assertTrue(readSucessfullyToEOF, f'Failed to read whole file: {map_filepath}')\n\n self.check_section_strings(loadedFile)",
"def test_mip_map_generation(self):\n settings = load_settings(TEST_SETTINGS_FILE)\n\n RSB_filepath = path.join(settings[\"gamePath_R6_EW\"], \"data\", \"texture\", \"08_engine.RSB\")\n\n loadedFile = RSBImageReader.RSBImageFile()\n readSucessfullyToEOF = loadedFile.read_file(RSB_filepath)\n\n self.assertTrue(readSucessfullyToEOF, \"Failed to read whole file\")\n\n fullColorImage = loadedFile.convert_full_color_image()\n\n mips = generate_mip_maps(fullColorImage)\n\n self.assertEqual(len(mips), 8, \"Failed to generate correct number of mipmaps\")",
"def test_load_map(self):\r\n test = Maps()\r\n test.load_map(path_to_map)\r\n self.assertIn(\"facile\", test.names)\r\n self.assertNotIn(\"empty\", test.names)\r\n self.assertEqual(len(test.drawings), 1)",
"def test_get_ifc_materials(self):\n pass",
"def test_get_ifc_material(self):\n pass",
"def test_parse_map_file(self):\n\n correct_map = [0,1.,1.]\n parsed_map = fizzy.parse_map_file(self.map_file_handle, \"Class\", [u'ID0',u'ID1',u'ID2'])\n self.assertEqual(parsed_map, correct_map)",
"def readMaterials(self, filename):\n \n currentMat = None\n commentre = re.compile(\"^#\")\n newmatre = re.compile(\"^newmtl ([^\\s]+)\")\n mapre = re.compile(\"^map_Kd ([^\\s]+)\")\n illumre = re.compile(\"^illum ([0-9]+)\")\n floatrx = '(-?([0-9]+(\\.[0-9]+)?e(\\+|-)[0-9]+)|-?([0-9]+(\\.[0-9]+)?))'\n kre = re.compile(\"^(K[dase])\\s+\" + floatrx + \"\\s+\" + floatrx + \"\\s+\" + floatrx)\n nre = re.compile(\"^(N[s])\\s+\" + floatrx)\n for line in open(filename).readlines():\n if commentre.match(line):\n continue\n newmatmatch = newmatre.match(line)\n if newmatmatch:\n if currentMat != None:\n self.materials.append(currentMat)\n currentMat = Material(newmatmatch.groups()[0])\n continue\n mapmatch = mapre.match(line)\n if mapmatch:\n currentMat.map_Kd = os.path.join(os.path.dirname(filename), mapmatch.groups()[0])\n continue\n illummatch = illumre.match(line)\n if illummatch:\n currentMat.illum = int(illummatch.groups()[0])\n continue\n kmatch = kre.match(line)\n if kmatch:\n t = kmatch.groups()[0]\n val = (kmatch.groups()[1], kmatch.groups()[7], kmatch.groups()[11])\n if t == \"Kd\":\n currentMat.Kd = val\n elif t == \"Ka\":\n currentMat.Ka = val\n elif t == \"Ks\":\n currentMat.Ks = val\n elif t == \"Ke\":\n currentMat.Ke = val\n nmatch = nre.match(line)\n if nmatch:\n t = nmatch.groups()[0]\n if t == \"Ns\":\n currentMat.Ns = nmatch.groups()[1]\n \n if currentMat != None:\n self.materials.append(currentMat)",
"def readMaterial(fh):\n\n mat = Material()\n while True:\n words = fh.readline().split()\n if len(words) == 1: break\n name = words[1]\n if name == \"Am242g\":\n name = \"Am242\"\n original_mass = float(words[3])\n if name[0:3] == \"sfp\":\n mat.isotopes[name] = FissionProduct(name,original_mass)\n else:\n mat.isotopes[name] = Isotope(name, original_mass)\n return mat",
"def test_impossible_mip_map_generation(self):\n settings = load_settings(TEST_SETTINGS_FILE)\n\n RSB_filepath = path.join(settings[\"gamePath_R6_EW\"], \"data\", \"shell\", \"briefing\", \"Ac_a13.RSB\")\n\n loadedFile = RSBImageReader.RSBImageFile()\n readSucessfullyToEOF = loadedFile.read_file(RSB_filepath)\n\n self.assertTrue(readSucessfullyToEOF, \"Failed to read whole file\")\n\n fullColorImage = loadedFile.convert_full_color_image()\n\n mips = generate_mip_maps(fullColorImage)\n\n self.assertIsNone(mips, \"Did not return None, instead generated mip-maps\")",
"def read_mf6(tape, mat, mt):\n mf = 6\n df = tape._get_section_df(mat, mf, mt)\n out = {\"MAT\": mat, \"MF\": mf, \"MT\": mt}\n i = 0\n C, i = sandy.read_cont(df, i)\n out.update({\n \"ZA\": C.C1,\n \"AWR\": C.C2,\n \"LCT\": C.L2, # Reference system for secondary energy and angle\n })\n subsections = {}\n # Each subsection describes one reaction product. There can be more than\n # one subsection for a given particle, but the combination of the product\n # identifier with its final isomeric state create a unique identifier for\n # each reaction.\n for a in range(C.N1):\n T, i = sandy.read_tab1(df, i)\n LAW = T.L2 # Distintion between different distribution function\n ZAP = T.C1 # Product identifier\n LIP = T.L1 # Product isomeric state identifier\n ZAM = zam.za2zam(ZAP, meta=LIP, method=False)\n add = {\n \"AWP\": T.C2, # Product mass in neutron units\n \"LAW\": T.L2,\n \"NR\": T.NBT,\n \"NP\": T.INT,\n \"E\": T.x, # Neutron incident energy\n \"Y\": T.y, # The product multiplicity\n }\n # LAW dependent structures:\n if LAW == 1: # Continuum Energy-Angle Distributions\n L, i = sandy.read_tab2(df, i)\n NE = L.NBT[0] # How many NE incident energies\n add.update({\n \"LANG\": L.L1, # Angular representation identificator\n \"LEP\": L.L2, # Interpolation for secondary energy\n \"ENR\": L.NR, # I put here ENR insted of NR to do not overwrite NR of the tab1 section.\n \"ENE\": L.NBT, # Number of different product energy\n \"EINT\": L.INT, # product energy diferent values\n })\n add_e = {}\n # To repeat for all the NE incident energies\n for j in range(NE):\n T, i = sandy.read_list(df, i)\n E = T.C2 # Incident energy\n if int(T.L2) == 0:\n Ep = T.B[::2]\n b = T.B[1::2]\n else:\n Ep = T.B[::T.L2+2]\n b = T.B[::1]\n del b[::T.L2+2] # To delete from b the energy values\n add_2 = {\n \"ND\": T.L1, # Number of discrete energies\n \"NA\": T.L2, # Number of angular parameters\n \"NW\": T.NPL, # Total number of words\n \"NEP\": T.N2, # Secondary energy points in distribution\n \"Ep\": Ep, # The energy of the product emitted\n \"b\": b, # Coefficients for the angular representation\n # the contents of the b depend on LANG\n }\n add_e[E] = add_2\n add[\"EGROUPS\"] = add_e\n\n elif LAW == 2: # Discrete Two-Body Scattering\n L, i = sandy.read_tab2(df, i)\n NE = L.NBT[0]\n add.update({\n \"ENR\": L.NZ,\n \"ENE\": L.NBT, # Number of different product energy\n \"EINT\": L.INT, # Product energy values\n })\n add_e = {}\n # To repeat list records for all the incident energies\n for j in range(NE):\n T, i = sandy.read_list(df, i)\n E = T.C2 # Incident energy\n add_2 = {\n \"LANG\": T.L1, # Angular representation identificator\n \"NW\": T.NPL, # Number of parameters\n \"NL\": T.N2, # Highest coefficient identificator\n \"Al\": T.B, # Coeficcient of angular representation\n }\n add_e[E] = add_2\n add[\"EGROUPS\"] = add_e\n\n elif LAW == 5: # Charged-Particle Elastic Scattering\n logging.warning(f\"\"\"'(LAW) = ({LAW})' is not validated.\n Please report any posible error/bug.\"\"\")\n L, i = sandy.read_tab2(df, i)\n NE = L.NBT[0] # How many NE incident energies\n LIDP = L.L1\n add.update({\n \"SPI\": L.C1,\n \"LIDP\": LIDP,\n \"ENR\": L.NR,\n \"ENE\": L.NBT,\n \"EINT\": L.INT,\n })\n add_e = {}\n for j in range(NE): # To repeat the LIST records for all the NE\n T, i = sandy.read_list(df, i)\n E = T.C2\n LTP = T.L1\n add_2 = {\n \"LTP\": T.L1,\n \"NW\": T.NPL,\n \"NL\": T.N2,\n }\n # We have to do the distintion between the different Ai organizations.\n if LTP == 1 and LIDP == 0 or LIDP == 1:\n mark = T.N2+1\n b = T.B[0:mark]\n Ra = T.B[mark::2]\n Ia = T.B[mark+1::2]\n add_2[\"A\"] = {\n \"B\": b,\n \"Ra\": Ra,\n \"Ia\": Ia,\n }\n elif LTP == 2:\n add_2[\"A\"] = {\n \"C\": T.B,\n }\n elif LTP > 2:\n nu = T.B[::2]\n p = T.B[1::2]\n add_2[\"A\"] = {\n \"nu\": nu,\n \"p\": p,\n }\n add_e[E] = add_2\n add[\"EGROUPS\"] = add_e\n\n elif LAW == 6: # N-Body Phase-Space Distributions\n T, i = sandy.read_cont(df, i)\n add.update({\n \"APSX\": T.C1, # Total mass(neutron uni) of N particles\n \"NPSX\": T.N2, # Number of particles distributed\n })\n elif LAW == 7: # Laboratory Angle-Energy Law\n L, i = sandy.read_tab2(df, i)\n NE = L.NBT[0] # How many interpolation range we have\n # Interpolation parameters for incident energy E\n add.update({\n \"ENR\": L.NZ,\n \"ENE\": L.NBT, # The incident energies number\n \"EINT\": L.INT, # Incident energy values\n })\n add_e = {}\n # To repeat for all NE incident energies\n for j in range(NE):\n T, i = sandy.read_tab2(df, i)\n # Interpolation parameters for emission cosine\n E = T.C2 # Incident energy\n NMU = T.NBT[0] # Number of possible emission cosines\n add_2 = {\n \"NRM\": T.NZ,\n \"NMU\": T.NBT, # Number of different cosines\n \"NU_INT\": T.INT, # Value of emission cosines\n }\n add_e[E] = add_2\n # To repeat for all the NMU emission cosines\n add_nu = {}\n for hz in range(NMU):\n Z, i = sandy.read_tab1(df, i)\n # Interpolation parameters for secondary energy E′\n nu = Z.C2 # Value for emission cosine\n E_p = Z.y[::2]\n E_distr = Z.y[1::2]\n add_3 = {\n \"NRP\": Z.NBT,\n \"NEP\": Z.INT,\n \"EP_INT\": Z.x, # Energies for E'\n \"E_p\": E_p, # Secondary energy value\n \"E_distr\": E_distr, # Distribution according to nu, E and E'\n }\n add_nu[nu] = add_3\n add_e[E][\"COSGROUPS\"] = add_nu\n add[\"EGROUPS\"] = add_e\n subsections[ZAM] = add\n out[\"NK\"] = subsections\n return out",
"def test_reduction_6(mgame_file):\n with stdout() as out, stderr() as err:\n assert run(\"red\", \"-tidr\", \"-i\", mgame_file), err.getvalue()\n gamereader.loads(out.getvalue())",
"def test_10_read_mgf(self):\n res = read_mgf(os.path.join(\".\", \"plymgf\", \"data\", \"test.mgf\"))\n self.assertEqual(res[\"meta\"], {'charges': [3, 2, 1]})\n self.assertEqual(res[\"ions\"][2][\"rtinseconds\"], 603)\n self.assertEqual(res[\"ions\"][3][\"charges\"], [3])",
"def test_reading_ucsc_mm9_chr10(self):\n path = \"MAF/ucsc_mm9_chr10.maf\"\n alignments = Align.parse(path, \"maf\")\n self.assertEqual(alignments.metadata[\"MAF Version\"], \"1\")\n self.assertEqual(alignments.metadata[\"Scoring\"], \"autoMZ.v1\")\n alignment = next(alignments)\n self.assertEqual(alignment.score, 6441)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3009319 : 3009319 + 162],\n \"TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACCCCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT\",\n )\n self.assertEqual(\n alignment[0],\n \"TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT\",\n )\n self.assertEqual(alignment.sequences[1].id, \"oryCun1.scaffold_133159\")\n self.assertEqual(len(alignment.sequences[1].seq), 13221)\n self.assertEqual(\n alignment.sequences[1].seq[11087 : 11087 + 164],\n \"TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT\",\n )\n self.assertEqual(\n alignment[1],\n \"TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99569899999998999999999999999999999999999999999999999999999999999999999757878999975999999999999999979999999999997899999999999997997999999869999996999988997997999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(len(alignment.sequences), 2)\n self.assertNotIn(\"empty\", alignment.annotations)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n # fmt: off\n np.array([[3009319, 3009392, 3009392, 3009481],\n [ 11087, 11160, 11162, 11251],\n ])\n # fmt: on\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3009319 TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAA\n 0 |||.||.||||||.|.||||||||||||||.|.|||||.||.....||..|.||||||..\noryCun1.s 11087 TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGG\n\nmm9.chr10 3009379 AATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCT\n 60 |||.|||||||||--|..||.||.|..|.||.||.|||.||....||..||....|.|||\noryCun1.s 11147 AATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCT\n\nmm9.chr10 3009437 CACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT 3009481\n 120 ....||||.|||.|||..|||..|.|..||.|||||.||||||| 164\noryCun1.s 11207 TGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT 11251\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=6441.000000\ns mm9.chr10 3009319 162 + 129993255 TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT\ns oryCun1.scaffold_133159 11087 164 + 13221 TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT\nq oryCun1.scaffold_133159 99569899999998999999999999999999999999999999999999999999999999999999999757878999975999999999999999979999999999997899999999999997997999999869999996999988997997999999\ni oryCun1.scaffold_133159 N 0 N 0\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'C', 'A', 'T', 'A', 'G', 'G', 'T', 'A', 'T', 'T', 'T', 'A',\n 'T', 'T', 'T', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'G', 'G',\n 'T', 'T', 'T', 'G', 'C', 'T', 'T', 'T', 'A', 'T', 'G', 'G', 'C',\n 'T', 'A', 'G', 'A', 'A', 'C', 'A', 'C', 'A', 'C', 'C', 'G', 'A',\n 'T', 'T', 'A', 'C', 'T', 'T', 'A', 'A', 'A', 'A', 'T', 'A', 'G',\n 'G', 'A', 'T', 'T', 'A', 'A', 'C', 'C', '-', '-', 'C', 'C', 'C',\n 'A', 'T', 'A', 'C', 'A', 'C', 'T', 'T', 'T', 'A', 'A', 'A', 'A',\n 'A', 'T', 'G', 'A', 'T', 'T', 'A', 'A', 'A', 'C', 'A', 'A', 'C',\n 'A', 'T', 'T', 'T', 'C', 'T', 'G', 'C', 'T', 'G', 'C', 'T', 'C',\n 'G', 'C', 'T', 'C', 'A', 'C', 'A', 'T', 'T', 'C', 'T', 'T', 'C',\n 'A', 'T', 'A', 'G', 'A', 'A', 'G', 'A', 'T', 'G', 'A', 'C', 'A',\n 'T', 'A', 'A', 'T', 'G', 'T', 'A', 'T', 'T', 'T', 'T', 'C', 'C',\n 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'T'],\n ['T', 'C', 'A', 'C', 'A', 'G', 'A', 'T', 'A', 'T', 'T', 'T', 'A',\n 'C', 'T', 'A', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'G', 'G',\n 'T', 'T', 'T', 'G', 'T', 'T', 'A', 'T', 'A', 'T', 'G', 'G', 'T',\n 'T', 'A', 'C', 'G', 'G', 'T', 'T', 'C', 'A', 'T', 'A', 'G', 'G',\n 'T', 'T', 'A', 'C', 'T', 'T', 'G', 'G', 'A', 'A', 'T', 'T', 'G',\n 'G', 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'T', 'T', 'C', 'T', 'T',\n 'A', 'T', 'T', 'C', 'A', 'T', 'T', 'G', 'C', 'A', 'G', 'A', 'A',\n 'T', 'T', 'G', 'G', 'T', 'T', 'A', 'C', 'A', 'C', 'T', 'G', 'T',\n 'G', 'T', 'T', 'C', 'T', 'T', 'G', 'A', 'C', 'C', 'T', 'T', 'T',\n 'G', 'C', 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'C', 'T', 'C', 'C',\n 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'C', 'T', 'G', 'A', 'T', 'G',\n 'T', 'C', 'A', 'A', 'A', 'T', 'A', 'C', 'T', 'T', 'T', 'C', 'C',\n 'C', 'T', 'T', 'T', 'G', 'G', 'T', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 103072)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3012076 : 3012076 + 365],\n \"AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGCACTCCCAACAGCAAGACACTAAGTTCACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCACCAAATTAAATAACCAGTGAGCAGAGTTGTGACGAGCATCAGGCTCTGGATTTAGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGATGAGTCAAGTGAAGGTCCTGAGACAACAAGTCCTCGGCTATGTGGGGGTGAGGGATGCAGCTGGAACCTCAGGGATCTCTGTAAGCAGTGGCATAAATGCTTGGCGGGAGAGAGCATGTTAGAGCTCACACGACATAGGAAGCCACTGAGACACTG\",\n )\n self.assertEqual(\n alignment[0],\n \"AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGC-----ACTCCCAACAGCAAGACACTAAGTT---------CACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCAC-----CAAATTAAATAACCAGTGAGCAGAGTTG--TGACGAGCATCAGGCTCTGGATTTAGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGAT--------------------------GAGTCAAGTGAAGGTCCTGAGACAA-------------------CAAGTCCTC----GGCTATGTGGGGGTGAGGG-------------ATGC----AG--------CTGGAACCTCAGGGA-TCTCTGT-AAGCAGTGGCATAAATGCTTGGCGG--GAGAGAGCATGTTAGAGCTCACACGACATAGGAAGCCACTGA--GACACTG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 174210431)\n self.assertEqual(\n alignment.sequences[1].seq[158049785 : 158049785 + 443],\n \"GAACACAAGTCCATGGCCTTTTCAACCACGTTAGGCGTTGGAGGCCACGTCAGCCCCCACAGATCCACTCTACAACTTTAGAAAGAATTTGTTAGGCACCAGTGGCTTGCTTCAGAGTTCTAGTTCCTACGCTGTCAGGGAGTCTACAGCAGCCCTATCCACAACTTACCTCCAGGATTTTGCTTAATTTCTGTGGAAAGCGATCTCAACTTCCCAGTTCACACACAGATGCAACCAGCATGAGACATTCCTAGAAATCAACAACCTTTGGTGACTGGTCTATCTCATGCTATTCTAAATACTGCTTGCTCACTTCATAAGTACGACATTCCAAGAGCACAAGGCTATCTGGTAAGGATGAGTATGGAGATAAATATTAACATCTTTTTACTGTGATGATTTGGCTGGAATAATTAAAACTTATATTTCCACTTATGAAGACT\",\n )\n self.assertEqual(\n alignment[1],\n \"AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCCAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTACTTATGAAGTGAGCAAGCAGTATTTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGCTGCTGTAGACTCCCTGACAGCGTAGGAACT--------AGAACTCTGAAGCAAGCCACTGGTGCCTAACAAATTCTTTCTAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACGTGGTTGAAAAGGCCATGGACTTGTGTTC\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157529165 : 157529165 + 443],\n \"GAACACAAGTCCATGGCCTTTTCAACCATGTTAGGCGTTGGAGGCCACGTCAGCCCCCACAGATCCACTCTACAACTTTATAAAGAATTTGTTAGGCACCAGTGGCTTGCTTCAGAGTTCTAGTTCCTATGCTGTCAGGGAGTCTACAGCATCCCTATCCACAACTTACCTCCAGGATTTTGCTTAATTTCTGTGGAAAGCGATCTCAACTTCCCAGTTCACACACAGATGCAACCAGCATGAGACATTCCTAGAAATCAACAACCTTTGGTGACTGGTCTATCTCATGCTATTCTACATACTGCTTGCTCACTTCACAAATACGACATTCCAAGAGCACAAGGCTATCTGGTAAGGATGAGTATGGAGATAAATATTAACATCTTTTTACTGTGATGATTTAGCTGGAATAATTAAAACTTATATTTCCACTTATGAAGACT\",\n )\n self.assertEqual(\n alignment[2],\n \"AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGATGCTGTAGACTCCCTGACAGCATAGGAACTAGAACTCTGAAGC----AAGCCA----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155039093 : 155039093 + 443],\n \"GAACACAAGTCCATGGCCTTTTCAACCATGTTAGGCGTTGGAGGCCACGTCAGCCCCCATGGATCCACTCTACAACTTTATAAAGAATTTGTTAGGCACCAGTGGCTTGCTTCAGAGTTCTAGTTCCTATGCTGTCAGGGAGTCTACAGCATCCCTATCCACAACTTACCTCCAGGATTTTGCTTAATTTCTGTGGAAAGCGATCTCAACTTCCCAGTTCACACACAGATGCAACCAGCATGAGACATTCCTAGAAATCAACAACCTTTGGTGACTGGTCTATCTCATGCTATTCTACATACTGCTTGCTCACTTCACAAATACGACATTCCAAGAGCACAAGGCTATCTGGTAAGGATGAGTATGGAGATAAATATTAACATCTTTTTACTGTGATGATTTAGCTGGAATAATTAAAACTTATATTTCCACTTATGAAGACT\",\n )\n self.assertEqual(\n alignment[3],\n \"AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGATAGGGATGCTGTAGACTCCCT---GACAGCATAGGAAC-TAGAACTCTGAAGC---AAGC----CA--------CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCCATGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(len(alignment.sequences), 4)\n self.assertNotIn(\"empty\", alignment.annotations)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3012076, 3012116, 3012116, 3012141, 3012141, 3012183,\n 3012183, 3012211, 3012211, 3012231, 3012235, 3012286,\n 3012286, 3012311, 3012311, 3012311, 3012320, 3012320,\n 3012320, 3012334, 3012335, 3012339, 3012339, 3012339,\n 3012339, 3012339, 3012343, 3012343, 3012345, 3012345,\n 3012345, 3012360, 3012360, 3012367, 3012367, 3012392,\n 3012392, 3012434, 3012434, 3012441],\n [158050228, 158050188, 158050183, 158050158, 158050149, 158050107,\n 158050102, 158050074, 158050072, 158050052, 158050052, 158050001,\n 158049975, 158049950, 158049942, 158049942, 158049933, 158049932,\n 158049929, 158049915, 158049914, 158049910, 158049906, 158049906,\n 158049906, 158049905, 158049901, 158049897, 158049895, 158049891,\n 158049887, 158049872, 158049871, 158049864, 158049863, 158049838,\n 158049836, 158049794, 158049792, 158049785],\n [157529608, 157529568, 157529563, 157529538, 157529529, 157529487,\n 157529482, 157529454, 157529452, 157529432, 157529432, 157529381,\n 157529355, 157529330, 157529322, 157529322, 157529313, 157529312,\n 157529309, 157529295, 157529294, 157529290, 157529286, 157529280,\n 157529278, 157529277, 157529273, 157529273, 157529271, 157529267,\n 157529267, 157529252, 157529251, 157529244, 157529243, 157529218,\n 157529216, 157529174, 157529172, 157529165],\n [155039536, 155039496, 155039491, 155039466, 155039457, 155039415,\n 155039410, 155039382, 155039380, 155039360, 155039360, 155039309,\n 155039283, 155039258, 155039250, 155039239, 155039230, 155039229,\n 155039229, 155039215, 155039215, 155039211, 155039207, 155039201,\n 155039201, 155039201, 155039197, 155039197, 155039195, 155039195,\n 155039195, 155039180, 155039179, 155039172, 155039171, 155039146,\n 155039144, 155039102, 155039100, 155039093],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3012076 AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGC-----ACTCCCAACAGCAAG\nponAbe2.c 158050228 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCCAAATCATCACAGTAAAAAG\npanTro2.c 157529608 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAG\nhg18.chr6 155039536 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAG\n\nmm9.chr10 3012131 ACACTAAGTT---------CACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCA\nponAbe2.c 158050168 ATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCG\npanTro2.c 157529548 ATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCG\nhg18.chr6 155039476 ATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCG\n\nmm9.chr10 3012182 C-----CAAATTAAATAACCAGTGAGCAGAGTTG--TGACGAGCATCAGGCTCTGGATTT\nponAbe2.c 158050108 TACTTATGAAGTGAGCAAGCAGTATTTAGAATAGCATGAGATAGACCAGTCACCAA----\npanTro2.c 157529488 TATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----\nhg18.chr6 155039416 TATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----\n\nmm9.chr10 3012235 AGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGAT---------\nponAbe2.c 158050052 AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTT\npanTro2.c 157529432 AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTT\nhg18.chr6 155039360 AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTT\n\nmm9.chr10 3012286 -----------------GAGTCAAGTGAAGGTCCTGAGACAA------------------\nponAbe2.c 158049992 GAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA----------\npanTro2.c 157529372 GAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA----------\nhg18.chr6 155039300 GAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGATAGGGATGCT\n\nmm9.chr10 3012311 -CAAGTCCTC----GGCTATGTGGGGGTGAGGG-------------ATGC----AG----\nponAbe2.c 158049942 -TAGGGCTGCTGTAGACTCCCTGACAGCGTAGGAACT--------AGAACTCTGAAGCAA\npanTro2.c 157529322 -TAGGGATGCTGTAGACTCCCTGACAGCATAGGAACTAGAACTCTGAAGC----AAGCCA\nhg18.chr6 155039240 GTAGACTCCCT---GACAGCATAGGAAC-TAGAACTCTGAAGC---AAGC----CA----\n\nmm9.chr10 3012345 ----CTGGAACCTCAGGGA-TCTCTGT-AAGCAGTGGCATAAATGCTTGGCGG--GAGAG\nponAbe2.c 158049891 GCCACTGGTGCCTAACAAATTCTTTCTAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGT\npanTro2.c 157529267 ----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGT\nhg18.chr6 155039195 ----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCCATGGGGGCTGACGT\n\nmm9.chr10 3012397 AGCATGTTAGAGCTCACACGACATAGGAAGCCACTGA--GACACTG 3012441\nponAbe2.c 158049831 GGCCTCCAACGCCTAACGTGGTTGAAAAGGCCATGGACTTGTGTTC 158049785\npanTro2.c 157529211 GGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC 157529165\nhg18.chr6 155039139 GGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC 155039093\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=103072.000000\ns mm9.chr10 3012076 365 + 129993255 AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGC-----ACTCCCAACAGCAAGACACTAAGTT---------CACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCAC-----CAAATTAAATAACCAGTGAGCAGAGTTG--TGACGAGCATCAGGCTCTGGATTTAGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGAT--------------------------GAGTCAAGTGAAGGTCCTGAGACAA-------------------CAAGTCCTC----GGCTATGTGGGGGTGAGGG-------------ATGC----AG--------CTGGAACCTCAGGGA-TCTCTGT-AAGCAGTGGCATAAATGCTTGGCGG--GAGAGAGCATGTTAGAGCTCACACGACATAGGAAGCCACTGA--GACACTG\ns ponAbe2.chr6 16160203 443 - 174210431 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCCAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTACTTATGAAGTGAGCAAGCAGTATTTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGCTGCTGTAGACTCCCTGACAGCGTAGGAACT--------AGAACTCTGAAGCAAGCCACTGGTGCCTAACAAATTCTTTCTAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACGTGGTTGAAAAGGCCATGGACTTGTGTTC\ni ponAbe2.chr6 N 0 C 0\ns panTro2.chr6 16379004 443 - 173908612 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGATGCTGTAGACTCCCTGACAGCATAGGAACTAGAACTCTGAAGC----AAGCCA----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC\nq panTro2.chr6 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----------9999999999999999999999999999999999999999999999999----999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni panTro2.chr6 N 0 C 0\ns hg18.chr6 15860456 443 - 170899992 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGATAGGGATGCTGTAGACTCCCT---GACAGCATAGGAAC-TAGAACTCTGAAGC---AAGC----CA--------CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCCATGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC\ni hg18.chr6 N 0 C 0\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 49128)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3012441 : 3012441 + 125],\n \"TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACCTGAATTGAATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGCTCGACAC\",\n )\n self.assertEqual(\n alignment[0],\n \"TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACCTGAATTG--AATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGCTCGACAC\",\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155038979 : 155038979 + 114],\n \"GCTTCCAGCATTTTCCATTGGCCCTCAGCAAGGTGCTCCCCAAGATCAGCGGTCAAGAGAGGTGGTCAATACACACCAGGTTACGTGAGGACTTGGTTATTCTAGAGGAACCCA\",\n )\n self.assertEqual(\n alignment[1],\n \"TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157529051 : 157529051 + 114],\n \"GCTTCCAGCATTTTCCATTGGCCCTCAGCAAGGTGCTCCCCAAGATCAGCGGTCAAGAGAGGTGGTCAATACACACCAGGTTACGTGAGGACTTGGTTATTCTAGAGGAACCCA\",\n )\n self.assertEqual(\n alignment[2],\n \"TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158049671 : 158049671 + 114],\n \"GCTTCCAGCATTTTCCATTGGCCCTCAGCAAGGTGCTCCCCAAGATCAACAGTCAAGACAGGTGGTCAATATAGACCAGGTTACGTGAGGACTTGGTTATTCTAGAGGAACCCA\",\n )\n self.assertEqual(\n alignment[3],\n \"TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTCTATATTGACCACCTGTCTTGACTGTTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[4].seq), 359464)\n self.assertEqual(\n alignment.sequences[4].seq[178838 : 178838 + 101],\n \"GCTTCCCGTGTTTGCTGTTGCCCCTCAGCAAAGGGCTCCCCAAGTTTGGTGGTCAGTGTAAACCCGGGTGAGTGAGGACTTGGCCAGGTCAGGGGGGCCCA\",\n )\n self.assertEqual(\n alignment[4],\n \"TGGGCCCCCCTGACCTGGCCAAG--TCCTCACTCACCCGGGTTTACACTGACCACC-------------AAACTTGGGGAG----------CCCTTTGCT-GAGGGGCAACAGCAAACACGGGAAGC\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999979999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(len(alignment.sequences), 5)\n self.assertNotIn(\"empty\", alignment.annotations)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3012441, 3012464, 3012466, 3012497, 3012508, 3012508,\n 3012520, 3012530, 3012539, 3012540, 3012566],\n [155039093, 155039070, 155039070, 155039039, 155039028, 155039026,\n 155039014, 155039014, 155039005, 155039005, 155038979],\n [157529165, 157529142, 157529142, 157529111, 157529100, 157529098,\n 157529086, 157529086, 157529077, 157529077, 157529051],\n [158049785, 158049762, 158049762, 158049731, 158049720, 158049718,\n 158049706, 158049706, 158049697, 158049697, 158049671],\n [ 178939, 178916, 178916, 178885, 178885, 178885,\n 178873, 178873, 178864, 178864, 178838],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3012441 TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACC\nhg18.chr6 155039093 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTC\npanTro2.c 157529165 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTC\nponAbe2.c 158049785 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTCTATATTGACCACCTGTC\notoGar1.s 178939 TGGGCCCCCCTGACCTGGCCAAG--TCCTCACTCACCCGGGTTTACACTGACCACC----\n\nmm9.chr10 3012501 TGAATTG--AATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGC\nhg18.chr6 155039035 TTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGC\npanTro2.c 157529107 TTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGC\nponAbe2.c 158049727 TTGACTGTTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGC\notoGar1.s 178885 ---------AAACTTGGGGAG----------CCCTTTGCT-GAGGGGCAACAGCAAACAC\n\nmm9.chr10 3012559 TCGACAC 3012566\nhg18.chr6 155038986 TGGAAGC 155038979\npanTro2.c 157529058 TGGAAGC 157529051\nponAbe2.c 158049678 TGGAAGC 158049671\notoGar1.s 178845 GGGAAGC 178838\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=49128.000000\ns mm9.chr10 3012441 125 + 129993255 TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACCTGAATTG--AATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGCTCGACAC\ns hg18.chr6 15860899 114 - 170899992 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16379447 114 - 173908612 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\nq panTro2.chr6 99999999999999999999999--99999999999999999999999999999999999999999999999999999999----------999999999-99999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16160646 114 - 174210431 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTCTATATTGACCACCTGTCTTGACTGTTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC\ni ponAbe2.chr6 C 0 C 0\ns otoGar1.scaffold_334.1-359464 180525 101 - 359464 TGGGCCCCCCTGACCTGGCCAAG--TCCTCACTCACCCGGGTTTACACTGACCACC-------------AAACTTGGGGAG----------CCCTTTGCT-GAGGGGCAACAGCAAACACGGGAAGC\nq otoGar1.scaffold_334.1-359464 99999999999999999999999--9999999999999999999999999999999-------------999999999999----------999999999-99999979999999999999999999\ni otoGar1.scaffold_334.1-359464 N 0 C 0\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'G', 'G', 'G', 'T', 'C', 'C', 'C', 'C', 'T', 'T', 'G', 'G',\n 'C', 'A', 'C', 'A', 'T', 'C', 'C', 'A', 'G', 'A', 'T', 'C', 'T',\n 'C', 'C', 'C', 'C', 'A', 'G', 'T', 'T', 'A', 'A', 'C', 'C', 'T',\n 'G', 'T', 'C', 'C', 'T', 'G', 'C', 'T', 'T', 'A', 'G', 'A', 'C',\n 'C', 'A', 'C', 'T', 'T', 'A', 'C', 'C', 'T', 'G', 'A', 'A', 'T',\n 'T', 'G', '-', '-', 'A', 'A', 'T', 'T', 'G', 'G', 'G', 'A', 'G',\n 'G', 'A', 'G', 'A', 'G', 'A', 'A', 'A', 'G', 'A', 'A', 'G', 'C',\n 'C', 'A', 'G', 'T', 'T', 'T', 'C', 'C', 'C', 'A', 'G', 'A', 'G',\n 'A', 'G', 'G', 'G', 'A', 'A', 'A', 'A', 'G', 'G', 'A', 'A', 'A',\n 'A', 'G', 'C', 'T', 'C', 'G', 'A', 'C', 'A', 'C'],\n ['T', 'G', 'G', 'G', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'A', 'G',\n 'A', 'A', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T',\n 'C', 'C', 'T', 'C', 'A', 'C', 'G', 'T', 'A', 'A', 'C', 'C', 'T',\n 'G', 'G', 'T', 'G', 'T', 'G', 'T', 'A', 'T', 'T', 'G', 'A', 'C',\n 'C', 'A', 'C', 'C', 'T', 'C', 'T', 'C', 'T', 'T', 'G', 'A', 'C',\n 'C', 'G', 'C', 'T', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'G', 'G',\n 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'C', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G',\n 'G', 'G', 'C', 'C', 'A', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'A',\n 'T', 'G', 'C', 'T', 'G', 'G', 'A', 'A', 'G', 'C'],\n ['T', 'G', 'G', 'G', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'A', 'G',\n 'A', 'A', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T',\n 'C', 'C', 'T', 'C', 'A', 'C', 'G', 'T', 'A', 'A', 'C', 'C', 'T',\n 'G', 'G', 'T', 'G', 'T', 'G', 'T', 'A', 'T', 'T', 'G', 'A', 'C',\n 'C', 'A', 'C', 'C', 'T', 'C', 'T', 'C', 'T', 'T', 'G', 'A', 'C',\n 'C', 'G', 'C', 'T', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'G', 'G',\n 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'C', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G',\n 'G', 'G', 'C', 'C', 'A', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'A',\n 'T', 'G', 'C', 'T', 'G', 'G', 'A', 'A', 'G', 'C'],\n ['T', 'G', 'G', 'G', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'A', 'G',\n 'A', 'A', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T',\n 'C', 'C', 'T', 'C', 'A', 'C', 'G', 'T', 'A', 'A', 'C', 'C', 'T',\n 'G', 'G', 'T', 'C', 'T', 'A', 'T', 'A', 'T', 'T', 'G', 'A', 'C',\n 'C', 'A', 'C', 'C', 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'A', 'C',\n 'T', 'G', 'T', 'T', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'G', 'G',\n 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'C', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G',\n 'G', 'G', 'C', 'C', 'A', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'A',\n 'T', 'G', 'C', 'T', 'G', 'G', 'A', 'A', 'G', 'C'],\n ['T', 'G', 'G', 'G', 'C', 'C', 'C', 'C', 'C', 'C', 'T', 'G', 'A',\n 'C', 'C', 'T', 'G', 'G', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T',\n 'C', 'C', 'T', 'C', 'A', 'C', 'T', 'C', 'A', 'C', 'C', 'C', 'G',\n 'G', 'G', 'T', 'T', 'T', 'A', 'C', 'A', 'C', 'T', 'G', 'A', 'C',\n 'C', 'A', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'A', 'A', 'A', 'C', 'T', 'T', 'G', 'G', 'G',\n 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'C', 'C', 'C', 'T', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G',\n 'G', 'G', 'G', 'C', 'A', 'A', 'C', 'A', 'G', 'C', 'A', 'A', 'A',\n 'C', 'A', 'C', 'G', 'G', 'G', 'A', 'A', 'G', 'C']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 117109)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3012566 : 3012566 + 262],\n \"TGTGGGCTCCTCACTTTCCTGTCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTACAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCTGTCCTCTTTAGCTTATCTCAGGCAACCTATCTTATTTTGTTTGCTTTCAGAAGGCAAGCGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtgCGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG\",\n )\n self.assertEqual(\n alignment[0],\n \"--TGTGGGCTCCTCACTTTCCTG-TCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTACAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCTGTCCTCTTTAGC-------TTATCTCAGGCAACCTATCTTATTTTGTT-TGCTTTC--AGAAGGCAAG---CGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtgCGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155038780 : 155038780 + 199],\n \"CCAAAACTCATACACAACTCATCTTCTGGGAAAACAGAATAAGTAAGATGTGTTGCTAGAAATAAGGTAGTGAAGGAAAAAAATAAGAGGATTGATTGACAGGAATGAAAACTCAGACTGGATTTTGAGGCTGTTTCTGGATGGCTTCCACCAAAAACCATAGACCCATCTAAGATCAGGGATACAAGGAGGGCTCATG\",\n )\n self.assertEqual(\n alignment[1],\n \"CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTCTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157528852 : 157528852 + 199],\n \"CCAAAACTCATACACAACTCATCTTCTGGGAAAACAAAATAAGTAAGATGTGTTGCTAGAAATAAGGTAGTGAAGGAAAAAAATAAGAGGATTGATTGACAGGAATGAAAACTCAGACTGGATTTTGAGGCTGTTTCTGGATGGCTTCCACCAAAAACCATAGACCCATCTAAGATCAGGGATACAAGGAGGGCTCATG\",\n )\n self.assertEqual(\n alignment[2],\n \"CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158049472 : 158049472 + 199],\n \"CCAAAACTCATACACAACTCATCTTCTGGGAAAACAAAATAAGTAAGATATGTTGCTAGAAATAAGGTAATGAAGGAAAAAAACAAGAGGATTGATTGACAGGAATGACAACTCAGACTGGATTTTGAGGCTGTTTCTGGATGGCTTCCACCAAAAACCATAGACCCATCTAAGATCAGGGATACAAGGAGGGCTCATG\",\n )\n self.assertEqual(\n alignment[3],\n \"CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTGTCATTCCTGTCAATCAATCCTCTTGTTTTTTTCCTTCATTACC----TTATTTCTAGCAACATATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[4].seq), 359464)\n self.assertEqual(\n alignment.sequences[4].seq[178634 : 178634 + 204],\n \"TCAAAACTCATACACAAGTCACCACTTGTCTTCTGGGAAAACAAAACAAAGTAAGCTATGTCACCTGAAATAACAAGGCAACCTAAAAATAAGGGACTGATTGCCAGCAATGACCACAGAGACTGGGTTTTCAGGTGGTTTTCTGGACAGCTTTCCCCAGAAACCAGGGCTACGCCTAAGACAGAGACACGATGAGTGCATGTG\",\n )\n self.assertEqual(\n alignment[4],\n \"CACATGCACTCATCGTGTCTCTG-TCTTAGGCGTAGCCCTGGTTTCTGGGGAAAGCTGTCCAGAAAACCACCTGAAAACCCAGTCTCTGTGGTCATTGCTGGCAATCAGTCC-CTTATTTTTAGGTTGCCTTG------TTATTTCAGGTGACATAGCTTACTTTGTTTTGTTTTCCCAGAAGACAAGTGGTGACTTGTGTATGAGTTTTGA------------------------------------------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"cavPor2.scaffold_290371\")\n self.assertEqual(len(alignment.sequences[5].seq), 39932)\n self.assertEqual(\n alignment.sequences[5].seq[39417 : 39417 + 205],\n \"CTCAAACtcacacaaaattcatttatcttccaggaaaacagaacaaaataagatATGTTTTGCAATAACGAGGTCACTATGGGGTAAAAACAAGAGGATTGGCAGGAGGGAATAACAATTTAGACTAGGTTTTGAAGTTCTTTTCTGGATGGCTTTCACCAAAAACCACAGCCACACCTCGGATCAGGATCGCAAGGGATACGCA\",\n )\n self.assertEqual(\n alignment[5],\n \"--TGCGTATCCCTTGCGATCCTGATCCGAGGTGTGGCTGTGGTTTTTGGTGAAAGCCATCCAGAAAAGAACTTCAAAACCTAGTCTAAATTGTTATTCCCTCCTGCCAATCCTCTTGTTTTTACCCCATAGTGACCTCGTTATTGCAA--AACATatcttattttgttctgttttcctggaagataaa---tgaattttgtgtgaGTTTGAG------------------------------------------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(len(alignment.sequences), 6)\n self.assertNotIn(\"empty\", alignment.annotations)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3012566, 3012566, 3012587, 3012587, 3012626, 3012627,\n 3012675, 3012676, 3012695, 3012695, 3012695, 3012695,\n 3012704, 3012706, 3012718, 3012719, 3012724, 3012724,\n 3012731, 3012731, 3012737, 3012741, 3012741, 3012762,\n 3012828],\n [155038979, 155038977, 155038956, 155038955, 155038916, 155038916,\n 155038868, 155038867, 155038848, 155038847, 155038845, 155038845,\n 155038836, 155038834, 155038822, 155038822, 155038817, 155038816,\n 155038809, 155038807, 155038801, 155038801, 155038801, 155038780,\n 155038780],\n [157529051, 157529049, 157529028, 157529027, 157528988, 157528988,\n 157528940, 157528939, 157528920, 157528919, 157528917, 157528917,\n 157528908, 157528906, 157528894, 157528894, 157528889, 157528888,\n 157528881, 157528879, 157528873, 157528873, 157528873, 157528852,\n 157528852],\n [158049671, 158049669, 158049648, 158049647, 158049608, 158049608,\n 158049560, 158049559, 158049540, 158049539, 158049537, 158049537,\n 158049528, 158049526, 158049514, 158049514, 158049509, 158049508,\n 158049501, 158049499, 158049493, 158049493, 158049493, 158049472,\n 158049472],\n [ 178838, 178836, 178815, 178815, 178776, 178775,\n 178727, 178727, 178708, 178707, 178707, 178707,\n 178698, 178696, 178684, 178683, 178678, 178677,\n 178670, 178668, 178662, 178658, 178655, 178634,\n 178634],\n [ 39622, 39622, 39601, 39600, 39561, 39560,\n 39512, 39511, 39492, 39491, 39489, 39485,\n 39476, 39476, 39464, 39463, 39458, 39457,\n 39450, 39448, 39442, 39438, 39438, 39417,\n 39417],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3012566 --TGTGGGCTCCTCACTTTCCTG-TCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTA\nhg18.chr6 155038979 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATC\npanTro2.c 157529051 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATC\nponAbe2.c 158049671 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATC\notoGar1.s 178838 CACATGCACTCATCGTGTCTCTG-TCTTAGGCGTAGCCCTGGTTTCTGGGGAAAGCTGTC\ncavPor2.s 39622 --TGCGTATCCCTTGCGATCCTGATCCGAGGTGTGGCTGTGGTTTTTGGTGAAAGCCATC\n\nmm9.chr10 3012623 CAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCT\nhg18.chr6 155038919 CAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTT\npanTro2.c 157528991 CAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTT\nponAbe2.c 158049611 CAG-AAACAGCCTCAAAATCCAGTCTGAGTTGTCATTCCTGTCAATCAATCCTCTTGTTT\notoGar1.s 178779 CAGAAAACCACCTGAAAACCCAGTCTCTGTGGTCATTGCTGGCAATCAGTCC-CTTATTT\ncavPor2.s 39564 CAGAAAAGAACTTCAAAACCTAGTCTAAATTGTTATTCCCTCCTGCCAATCCTCTTGTTT\n\nmm9.chr10 3012683 GTCCTCTTTAGC-------TTATCTCAGGCAACCTATCTTATTTTGTT-TGCTTTC--AG\nhg18.chr6 155038860 TTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTCTGTTTTCCCAG\npanTro2.c 157528932 TTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTTTGTTTTCCCAG\nponAbe2.c 158049552 TTTTCCTTCATTACC----TTATTTCTAGCAACATATCTTAC-TTATTTTGTTTTCCCAG\notoGar1.s 178720 TTAGGTTGCCTTG------TTATTTCAGGTGACATAGCTTACTTTGTTTTGTTTTCCCAG\ncavPor2.s 39504 TTACCCCATAGTGACCTCGTTATTGCAA--AACATatcttattttgttctgttttcctgg\n\nmm9.chr10 3012733 AAGGCAAG---CGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtg\nhg18.chr6 155038805 AAGA-------TGAGTTGTGTATGAGTTTTGG----------------------------\npanTro2.c 157528877 AAGA-------TGAGTTGTGTATGAGTTTTGG----------------------------\nponAbe2.c 158049497 AAGA-------TGAGTTGTGTATGAGTTTTGG----------------------------\notoGar1.s 178666 AAGACAAGTGGTGACTTGTGTATGAGTTTTGA----------------------------\ncavPor2.s 39446 aagataaa---tgaattttgtgtgaGTTTGAG----------------------------\n\nmm9.chr10 3012790 CGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG 3012828\nhg18.chr6 155038780 -------------------------------------- 155038780\npanTro2.c 157528852 -------------------------------------- 157528852\nponAbe2.c 158049472 -------------------------------------- 158049472\notoGar1.s 178634 -------------------------------------- 178634\ncavPor2.s 39417 -------------------------------------- 39417\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=117109.000000\ns mm9.chr10 3012566 262 + 129993255 --TGTGGGCTCCTCACTTTCCTG-TCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTACAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCTGTCCTCTTTAGC-------TTATCTCAGGCAACCTATCTTATTTTGTT-TGCTTTC--AGAAGGCAAG---CGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtgCGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG\ns hg18.chr6 15861013 199 - 170899992 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTCTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16379561 199 - 173908612 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\nq panTro2.chr6 999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999-999999999999999999999-------999999999999999999999------------------------------------------------------------------\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16160760 199 - 174210431 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTGTCATTCCTGTCAATCAATCCTCTTGTTTTTTTCCTTCATTACC----TTATTTCTAGCAACATATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------\ni ponAbe2.chr6 C 0 C 0\ns otoGar1.scaffold_334.1-359464 180626 204 - 359464 CACATGCACTCATCGTGTCTCTG-TCTTAGGCGTAGCCCTGGTTTCTGGGGAAAGCTGTCCAGAAAACCACCTGAAAACCCAGTCTCTGTGGTCATTGCTGGCAATCAGTCC-CTTATTTTTAGGTTGCCTTG------TTATTTCAGGTGACATAGCTTACTTTGTTTTGTTTTCCCAGAAGACAAGTGGTGACTTGTGTATGAGTTTTGA------------------------------------------------------------------\nq otoGar1.scaffold_334.1-359464 99999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999------9999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------------------------------------\ni otoGar1.scaffold_334.1-359464 C 0 C 0\ns cavPor2.scaffold_290371 310 205 - 39932 --TGCGTATCCCTTGCGATCCTGATCCGAGGTGTGGCTGTGGTTTTTGGTGAAAGCCATCCAGAAAAGAACTTCAAAACCTAGTCTAAATTGTTATTCCCTCCTGCCAATCCTCTTGTTTTTACCCCATAGTGACCTCGTTATTGCAA--AACATatcttattttgttctgttttcctggaagataaa---tgaattttgtgtgaGTTTGAG------------------------------------------------------------------\nq cavPor2.scaffold_290371 --99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999997999999999999999999999999999999999999999--99999999999999999999999999999999999999---999999999999999999999------------------------------------------------------------------\ni cavPor2.scaffold_290371 N 0 C 0\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 128047)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3012828 : 3012828 + 168],\n \"TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATGCACTTAGCACAGCCTGCCCTGAGGGATGAACACTATTGTTAAAGAACTATTCCGCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT\",\n )\n self.assertEqual(\n alignment[0],\n \"TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATGCACTTAGCACAGCCTGCCCTGAGGGAT----GAACACT--ATTGTTAA-AGAACTATTCCGCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_290371\")\n self.assertEqual(len(alignment.sequences[1].seq), 39932)\n self.assertEqual(\n alignment.sequences[1].seq[39251 : 39251 + 166],\n \"ATATGACCAGCAGATGGCACTAGAATCCCACGGAACCTGAAGTTGCCTCCTGCTAAACAGCTTTGCTGACAATAAAGGTCTCAGAGCTACTAGAGCGAACCATGATAACCTCATTATTTTCataaatgcttaaatataagACTATTTAGCTGTCAAGACATCCCAC\",\n )\n self.assertEqual(\n alignment[1],\n \"-----GTGGGATGTCTTGACAGCTAAATAGTcttatatttaagcatttatGAAAATAATGAGGTTATCATGGTTCGCTCTAGTAGCTCTGAGACCTTT--ATTGTCAGCAAAGCTGTTTAGC--AGGAGGCAACTTCAGGTTCCGTGGGATTCTAGTGCCATCTGCTGGTCATAT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[2].seq), 359464)\n self.assertEqual(\n alignment.sequences[2].seq[178473 : 178473 + 161],\n \"CTGTGACCAGCAGATGGCGCTAAAATCCCACAGATCCTGAGGCTGCTGCTCCGCAAAACCGCTTCCCTGACAGTAGCCTCTCACTTCTAAGGGGCTGAGCTAAGTTTATCATTTCAACAAATGTTTAAATAGAACACTATTTGCCTGTCACGAATGTCCAC\",\n )\n self.assertEqual(\n alignment[2],\n \"-----GTGGACATTCGTGACAGGCAAATAGTGTTCTATTTAAACATTTGTTGAAATGATAAACTTAGCTCAGCC--CCTT---AGAAGTG-AGAGGCT--ACTGTCAGGGAAGCGGTTTTGCG-GAGCAGCAGCCTCAGGATCTGTGGGATTTTAGCGCCATCTGCTGGTCACAG\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999989996999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158049311 : 158049311 + 161],\n \"ATGTGACCAGCAGATGGCATTAGAGTCCCACAGATCCTGAGATTGAGCCTTAGCTAAACAACTTCACTAGGCATACCACATCTGTCAAGGCAGGTTATGCTAAGCTTATTATTTTCATAAATGTTTAAATATAACGCTATTTGGTTGTCAGGATAGTCCAC\",\n )\n self.assertEqual(\n alignment[3],\n \"-----GTGGACTATCCTGACAACCAAATAGCGTTATATTTAAACATTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGTTTAGCT-AAGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAT\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 173908612)\n self.assertEqual(\n alignment.sequences[4].seq[157528691 : 157528691 + 161],\n \"GTGTGACCAGCAGATGGCATTAGAGTCCCACAGATCCTGAGATTGAGCCATAGCTAAGCAACTTCACTAGGCATACCACATCTGTCAAGGCAGGTTATGCTAAGCTTATTATTTTCATAAACGTTTAAATATAACGCTATTTGGTTGTCAAGATAGTCCGC\",\n )\n self.assertEqual(\n alignment[4],\n \"-----GCGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155038619 : 155038619 + 161],\n \"GTGTGACCAGCAGATGGCATTAGAGTCCCACAGATCCTGAGATTGAGCCATAGCTAAGCAACTTCACTAGGCATACCACATCTGTCAAGGCAGGTTATGCTAAGCTTATTATTTTCACAAACGTTTAAATATAACGCTATTTGGTTGTCAAGATAGTCCAC\",\n )\n self.assertEqual(\n alignment[5],\n \"-----GTGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTGTGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[6].seq), 100002)\n self.assertEqual(\n alignment.sequences[6].seq[87492 : 87492 + 169],\n \"TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATGAGTTTGTCATAACTGCCTCCTCCCAAGTGGGAAGCTGAAGCACCAAGTACTGACTCAGCAGTCCCTGACCTCACATCCATGGAAATCTAGTGACATCTGCTGGACACAT\",\n )\n self.assertEqual(\n alignment[6],\n \"TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATGAGTTTGTCATAACT-GCCTCCTCCCAAGTG-GGAAGCTGAAGCACCAA-GTACTGACTCAGC--AGTCCCTGACCTCA-CATCCATGGAAATCTAGTGACATCTGCTGGACACAT\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"9998999999897966589999999999967689989799789997987889999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 7564)\n self.assertEqual(len(alignment.sequences), 7)\n self.assertNotIn(\"empty\", alignment.annotations)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3012828, 3012833, 3012902, 3012903, 3012904, 3012908,\n 3012911, 3012915, 3012915, 3012915, 3012921, 3012922,\n 3012922, 3012926, 3012930, 3012930, 3012943, 3012944,\n 3012945, 3012959, 3012960, 3012996],\n [ 39417, 39417, 39348, 39347, 39346, 39342,\n 39339, 39335, 39332, 39331, 39325, 39324,\n 39324, 39320, 39316, 39315, 39302, 39302,\n 39302, 39288, 39287, 39251],\n [ 178634, 178634, 178565, 178565, 178565, 178561,\n 178561, 178557, 178554, 178554, 178548, 178547,\n 178547, 178543, 178539, 178538, 178525, 178524,\n 178524, 178510, 178509, 178473],\n [158049472, 158049472, 158049403, 158049402, 158049401, 158049397,\n 158049394, 158049390, 158049387, 158049387, 158049381, 158049381,\n 158049381, 158049381, 158049377, 158049376, 158049363, 158049362,\n 158049362, 158049348, 158049347, 158049311],\n [157528852, 157528852, 157528783, 157528782, 157528781, 157528777,\n 157528774, 157528770, 157528767, 157528767, 157528761, 157528761,\n 157528761, 157528761, 157528757, 157528756, 157528743, 157528742,\n 157528742, 157528728, 157528727, 157528691],\n [155038780, 155038780, 155038711, 155038710, 155038709, 155038705,\n 155038702, 155038698, 155038695, 155038695, 155038689, 155038689,\n 155038689, 155038689, 155038685, 155038684, 155038671, 155038670,\n 155038670, 155038656, 155038655, 155038619],\n [ 87492, 87497, 87566, 87566, 87567, 87571,\n 87574, 87578, 87581, 87581, 87587, 87588,\n 87590, 87594, 87598, 87598, 87611, 87611,\n 87611, 87625, 87625, 87661],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3012828 TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATG\ncavPor2.s 39417 -----GTGGGATGTCTTGACAGCTAAATAGTcttatatttaagcatttatGAAAATAATG\notoGar1.s 178634 -----GTGGACATTCGTGACAGGCAAATAGTGTTCTATTTAAACATTTGTTGAAATGATA\nponAbe2.c 158049472 -----GTGGACTATCCTGACAACCAAATAGCGTTATATTTAAACATTTATGAAAATAATA\npanTro2.c 157528852 -----GCGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTATGAAAATAATA\nhg18.chr6 155038780 -----GTGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTGTGAAAATAATA\nechTel1.s 87492 TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATG\n\nmm9.chr10 3012888 CACTTAGCACAGCCTGCCCTGAGGGAT----GAACACT--ATTGTTAA-AGAACTATTCC\ncavPor2.s 39362 AGGTTATCATGGTTCGCTCTAGTAGCTCTGAGACCTTT--ATTGTCAGCAAAGCTGTTTA\notoGar1.s 178579 AACTTAGCTCAGCC--CCTT---AGAAGTG-AGAGGCT--ACTGTCAGGGAAGCGGTTTT\nponAbe2.c 158049417 AGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGTTTA\npanTro2.c 157528797 AGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTA\nhg18.chr6 155038725 AGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTA\nechTel1.s 87552 AGTTTGTCATAACT-GCCTCCTCCCAAGTG-GGAAGCTGAAGCACCAA-GTACTGACTCA\n\nmm9.chr10 3012941 GCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT\ncavPor2.s 39304 GC--AGGAGGCAACTTCAGGTTCCGTGGGATTCTAGTGCCATCTGCTGGTCATAT\notoGar1.s 178527 GCG-GAGCAGCAGCCTCAGGATCTGTGGGATTTTAGCGCCATCTGCTGGTCACAG\nponAbe2.c 158049365 GCT-AAGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAT\npanTro2.c 157528745 GCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\nhg18.chr6 155038673 GCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\nechTel1.s 87609 GC--AGTCCCTGACCTCA-CATCCATGGAAATCTAGTGACATCTGCTGGACACAT\n\nmm9.chr10 3012996\ncavPor2.s 39251\notoGar1.s 178473\nponAbe2.c 158049311\npanTro2.c 157528691\nhg18.chr6 155038619\nechTel1.s 87661\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=128047.000000\ns mm9.chr10 3012828 168 + 129993255 TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATGCACTTAGCACAGCCTGCCCTGAGGGAT----GAACACT--ATTGTTAA-AGAACTATTCCGCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT\ns cavPor2.scaffold_290371 515 166 - 39932 -----GTGGGATGTCTTGACAGCTAAATAGTcttatatttaagcatttatGAAAATAATGAGGTTATCATGGTTCGCTCTAGTAGCTCTGAGACCTTT--ATTGTCAGCAAAGCTGTTTAGC--AGGAGGCAACTTCAGGTTCCGTGGGATTCTAGTGCCATCTGCTGGTCATAT\nq cavPor2.scaffold_290371 -----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--9999999999999999999999--999999999999999999999999999999999999999999999999999\ni cavPor2.scaffold_290371 C 0 C 0\ns otoGar1.scaffold_334.1-359464 180830 161 - 359464 -----GTGGACATTCGTGACAGGCAAATAGTGTTCTATTTAAACATTTGTTGAAATGATAAACTTAGCTCAGCC--CCTT---AGAAGTG-AGAGGCT--ACTGTCAGGGAAGCGGTTTTGCG-GAGCAGCAGCCTCAGGATCTGTGGGATTTTAGCGCCATCTGCTGGTCACAG\nq otoGar1.scaffold_334.1-359464 -----999999999999999999999999999999999999999999999999999999999999999999999--9999---9999999-9999999--99999999999999999999989-996999999999999999999999999999999999999999999999999\ni otoGar1.scaffold_334.1-359464 C 0 C 0\ns ponAbe2.chr6 16160959 161 - 174210431 -----GTGGACTATCCTGACAACCAAATAGCGTTATATTTAAACATTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGTTTAGCT-AAGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAT\ni ponAbe2.chr6 C 0 C 0\ns panTro2.chr6 16379760 161 - 173908612 -----GCGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\nq panTro2.chr6 -----9999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999-------9999999999999999999-999999999999999999999999999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns hg18.chr6 15861212 161 - 170899992 -----GTGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTGTGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC\ni hg18.chr6 C 0 C 0\ns echTel1.scaffold_288249 87492 169 + 100002 TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATGAGTTTGTCATAACT-GCCTCCTCCCAAGTG-GGAAGCTGAAGCACCAA-GTACTGACTCAGC--AGTCCCTGACCTCA-CATCCATGGAAATCTAGTGACATCTGCTGGACACAT\nq echTel1.scaffold_288249 99989999998979665899999999999676899897997899979878899999999999999999999999-999999999999999-99999999999999999-9999999999999--99999999999999-999999999999999999999999999999999999\ni echTel1.scaffold_288249 N 0 I 7564\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 98097)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3012996 : 3012996 + 222],\n \"AGATGTCTGCTGTGGAGACCTGGCCAACTTTGCTTTCTTCAAAAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCATTAGGAAGGCGACCTCTAGTGCACAAACCTTGACATTTTCCCTTTTAATGGAATTTAACAGAAGTTCAGGATGTTCTTTGGGTAATTTACAATTAGGGGGCAAAAATCAAAAGTATTTCGAGCATATCAAAACTGTTAGCTATG\",\n )\n self.assertEqual(\n alignment[0],\n \"AGATGTCTGCTGTGGAGA-------CCTGGCCAACTTTG----CTT--TCTTC-----AAAAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCA-----TTAGGAAGGCGACCTCTAGTGCACAAACCTTGAC-ATTTTCCCTTTTAATGGAA-TTTAACAGAAGTTCAGGATGTTCTTTGGGTAATTTACAATT---A----GGGGGCAAAAATCAAAAGTATTTCGAGCATATCAAAACTGTTAGCTATG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_290371\")\n self.assertEqual(len(alignment.sequences[1].seq), 39932)\n self.assertEqual(\n alignment.sequences[1].seq[39074 : 39074 + 177],\n \"AAATGcctctgcttttccttttctagctgtAAATTGTTTAAATGGAATTCTGAACCTGACAGAGTcgaagaaaaaaattgcaaagctTTTCCGCTAGAGGTCACTCTCCCCACTATGTGGTGTGGTCGGCTTTAGCGCGGAAGACTGGAGTTAGCCAGCCCGTGGCTGCAGACGTCA\",\n )\n self.assertEqual(\n alignment[1],\n \"TGACGTCTGCAGCCACGG-------GCTGGCTAACTCCA--GTCTT--CCGCG-----CTAAAGCCGAC--------------------CACACCACATAGTGGGGAGAGTGACCTCTAGCGGAAAagctttgca-atttttttcttc----gAC-TCTGTCAG--GTTCAGAATTCCATTTAAACAATTTacagct---a----gaaaaggaaaagcagaggCATTT--------------------------\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999997999999999995699999999999336991774687\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 170899992)\n self.assertEqual(\n alignment.sequences[2].seq[155038435 : 155038435 + 184],\n \"ATACTCTTACCTCCCCCCACCATTACAAATTGTCTAAATGGCATTCTAAGCCTTTATGAATTCAATTAAAAAGAAAAATGCCAAGGCCTGCTCGCTAGAGGTCGCTCTCCTAACTATGGGGTCCTGTTAGTCTTATAGAGTAAGACAGCAGAGTAGGCCAAGAAAGTGATGGCAGCAGCCATCA\",\n )\n self.assertEqual(\n alignment[2],\n \"TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGC-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 14)\n self.assertEqual(alignment.sequences[3].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 173908612)\n self.assertEqual(\n alignment.sequences[3].seq[157528507 : 157528507 + 184],\n \"ATACTCTTACCTCCCCCCACCATTACAAATTGTCTAAATGGCATTCTAAGCCTTTATGAATTTAATTAAAAAGAAAAATTCCAAGGCCTGCTCGCTAGAGGTCGCTCTCCTAACCATGGGGTCCTGTTAGTCTTATAGAATAAGACAGCAGAGTAGGCCAAGAAAGTGATGGCAGCAGCCATCA\",\n )\n self.assertEqual(\n alignment[3],\n \"TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ATTCT-----ATAAGACTAAC--------------------AGGACCCCATGGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTAAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 14)\n self.assertEqual(alignment.sequences[4].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 174210431)\n self.assertEqual(\n alignment.sequences[4].seq[158049094 : 158049094 + 217],\n \"CATCATTGACAGGTTTGAATACATTCAATATTTATACTCTTACCTCCCCCCACCATTACAAATTGTCTAAATGGCATTCTAAGCCTTTATGAATTCAATTAAAAAGAAAAATTCCAAGGCCTGCTCGCTAGAGGTCGCTCTCCTAACTATGGGGTCCTGTTAGTCTTATAGAGTAAGACGGCCTAGTAGGCCAAGAAAGTGATGGCAGCAGCCATCA\",\n )\n self.assertEqual(\n alignment[4],\n \"TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTAGGCCGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTATAAATATTGAATGTAT-TCAAACCTGTCAATGATG\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 2)\n self.assertEqual(alignment.sequences[5].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[5].seq), 359464)\n self.assertEqual(\n alignment.sequences[5].seq[178247 : 178247 + 226],\n \"TAACAAGGCTGAATGCCAGCAATATTTGCACTCTCAGGTCCCCACACATACACTATGAATTGTCTAACTTGCATTTTGAGCCGTTGTAAAATTCAATTAAAAAGAAAAAAATCCAAGGCTTGTTCACCAGAGGTCGCTCTAGTAACTGCAGGGTCCGATTTTTCTTTTGTTGCAGAATTTAAGACGGTGGAGTTGGCAGGGAAAGCGGTGGTGGCGGCGGCCGTCC\",\n )\n self.assertEqual(\n alignment[5],\n \"GGACGGCCGCCGCCACCACCGCTTTCCCTGCCAACTCCACCGTCTTAAATTCTGCAACAAAAGAAAAAT--------------------CGGACCCTGCAGTTACTAGAGCGACCTCTGGTGAACAAGCCTTGGATTTTTTTCTTTTTAATTGAATTTTACAAC-GGCTCAAAATGCAAGTTAGACAATTCATAGTGTATGTGTGGGGACCTGAGAGTGCAAATATTGCTGGCAT-TCAGCCTTGTTA------\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999989999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999699999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 2931)\n self.assertEqual(alignment.sequences[6].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[6].seq), 498454)\n self.assertEqual(\n alignment.sequences[6].seq[331078 : 331078 + 159],\n \"TAATTATAAGTTGTCTAAATGGCATTTGAACCTTTATAAATTCTGTTTTAAAGAAAAATTCCAAGGTTTGCTCACTAGAGGTCTCCTCTCCCGGAGGATCCAGTTTGTCTTTCGTTGAGAGAGCTGAGTGGTCCAAGAAAGTGACAGCTGTAGCCATCA\",\n )\n self.assertEqual(\n alignment[6],\n \"TGATGGCTACAGCTGTCA---CTTTCTTGGACCACTCAGCTCTCTC--AAC-------GAAAGACAAAC--------------------TGGATCCTCCGG---GAGAGGAGACCTCTAGTGAGCAAACCTTGGA-ATTTTTCTTTAAAACAGAA-TTTATAAA-GGTTCA-AATGCCATTTAGACAACTTATAATT---A-----------------------------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"234233433332122232158211222021213444332433213323732111754365002326236241111233524253535324593652222413766453735782535545832457354545484445655854554657999679999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 4145)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 7)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3012996, 3013014, 3013014, 3013014, 3013028, 3013028,\n 3013028, 3013031, 3013031, 3013034, 3013036, 3013036,\n 3013047, 3013067, 3013074, 3013074, 3013077, 3013108,\n 3013108, 3013120, 3013124, 3013127, 3013127, 3013135,\n 3013136, 3013137, 3013142, 3013143, 3013168, 3013168,\n 3013169, 3013169, 3013184, 3013192, 3013199, 3013200,\n 3013212, 3013218],\n [ 39251, 39233, 39233, 39233, 39219, 39219,\n 39217, 39214, 39214, 39211, 39209, 39209,\n 39198, 39198, 39191, 39186, 39183, 39152,\n 39152, 39140, 39140, 39137, 39137, 39129,\n 39129, 39129, 39124, 39123, 39098, 39098,\n 39097, 39097, 39082, 39074, 39074, 39074,\n 39074, 39074],\n [155038619, 155038601, 155038601, 155038597, 155038583, 155038581,\n 155038579, 155038576, 155038576, 155038573, 155038571, 155038571,\n 155038560, 155038560, 155038553, 155038548, 155038545, 155038514,\n 155038514, 155038502, 155038498, 155038495, 155038495, 155038487,\n 155038487, 155038486, 155038481, 155038480, 155038455, 155038455,\n 155038454, 155038450, 155038435, 155038435, 155038435, 155038435,\n 155038435, 155038435],\n [157528691, 157528673, 157528673, 157528669, 157528655, 157528653,\n 157528651, 157528648, 157528648, 157528645, 157528643, 157528643,\n 157528632, 157528632, 157528625, 157528620, 157528617, 157528586,\n 157528586, 157528574, 157528570, 157528567, 157528567, 157528559,\n 157528559, 157528558, 157528553, 157528552, 157528527, 157528527,\n 157528526, 157528522, 157528507, 157528507, 157528507, 157528507,\n 157528507, 157528507],\n [158049311, 158049293, 158049293, 158049289, 158049275, 158049273,\n 158049271, 158049268, 158049268, 158049265, 158049263, 158049263,\n 158049252, 158049252, 158049245, 158049240, 158049237, 158049206,\n 158049206, 158049194, 158049190, 158049187, 158049187, 158049179,\n 158049179, 158049178, 158049173, 158049172, 158049147, 158049147,\n 158049146, 158049142, 158049127, 158049119, 158049112, 158049112,\n 158049100, 158049094],\n [ 178473, 178455, 178452, 178448, 178434, 178432,\n 178430, 178427, 178425, 178422, 178420, 178415,\n 178404, 178404, 178397, 178392, 178389, 178358,\n 178357, 178345, 178341, 178338, 178337, 178329,\n 178329, 178328, 178323, 178322, 178297, 178294,\n 178293, 178289, 178274, 178266, 178259, 178259,\n 178247, 178247],\n [ 331237, 331219, 331219, 331215, 331201, 331199,\n 331197, 331194, 331194, 331191, 331191, 331191,\n 331180, 331180, 331173, 331168, 331168, 331137,\n 331137, 331125, 331121, 331118, 331118, 331110,\n 331110, 331109, 331104, 331104, 331079, 331079,\n 331078, 331078, 331078, 331078, 331078, 331078,\n 331078, 331078],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3012996 AGATGTCTGCTGTGGAGA-------CCTGGCCAACTTTG----CTT--TCTTC-----AA\ncavPor2.s 39251 TGACGTCTGCAGCCACGG-------GCTGGCTAACTCCA--GTCTT--CCGCG-----CT\nhg18.chr6 155038619 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ACTCT-----AT\npanTro2.c 157528691 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ATTCT-----AT\nponAbe2.c 158049311 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTAGGCCGTCTT--ACTCT-----AT\notoGar1.s 178473 GGACGGCCGCCGCCACCACCGCTTTCCCTGCCAACTCCACCGTCTTAAATTCTGCAACAA\ntupBel1.s 331237 TGATGGCTACAGCTGTCA---CTTTCTTGGACCACTCAGCTCTCTC--AAC-------GA\n\nmm9.chr10 3013038 AAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCA-----TTAGGAAGGCGACCTCTAG\ncavPor2.s 39207 AAAGCCGAC--------------------CACACCACATAGTGGGGAGAGTGACCTCTAG\nhg18.chr6 155038569 AAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAG\npanTro2.c 157528641 AAGACTAAC--------------------AGGACCCCATGGTTAGGAGAGCGACCTCTAG\nponAbe2.c 158049261 AAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAG\notoGar1.s 178413 AAGAAAAAT--------------------CGGACCCTGCAGTTACTAGAGCGACCTCTGG\ntupBel1.s 331189 AAGACAAAC--------------------TGGATCCTCCGG---GAGAGGAGACCTCTAG\n\nmm9.chr10 3013093 TGCACAAACCTTGAC-ATTTTCCCTTTTAATGGAA-TTTAACAGAAGTTCAGGATGTTCT\ncavPor2.s 39167 CGGAAAagctttgca-atttttttcttc----gAC-TCTGTCAG--GTTCAGAATTCCAT\nhg18.chr6 155038529 CGAGCAGGCCTTGGC-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCAT\npanTro2.c 157528601 CGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTAAA-TTCATAAA-GGCTTAGAATGCCAT\nponAbe2.c 158049221 CGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCAT\notoGar1.s 178373 TGAACAAGCCTTGGATTTTTTTCTTTTTAATTGAATTTTACAAC-GGCTCAAAATGCAAG\ntupBel1.s 331152 TGAGCAAACCTTGGA-ATTTTTCTTTAAAACAGAA-TTTATAAA-GGTTCA-AATGCCAT\n\nmm9.chr10 3013151 TTGGGTAATTTACAATT---A----GGGGGCAAAAATCAAAAGTATTTCGAGCATATCAA\ncavPor2.s 39115 TTAAACAATTTacagct---a----gaaaaggaaaagcagaggCATTT------------\nhg18.chr6 155038472 TTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT--------------------\npanTro2.c 157528544 TTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT--------------------\nponAbe2.c 158049164 TTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTATAAATATTGAATGTAT-TCAA\notoGar1.s 178314 TTAGACAATTCATAGTGTATGTGTGGGGACCTGAGAGTGCAAATATTGCTGGCAT-TCAG\ntupBel1.s 331096 TTAGACAACTTATAATT---A---------------------------------------\n\nmm9.chr10 3013204 AACTGTTAGCTATG 3013218\ncavPor2.s 39074 -------------- 39074\nhg18.chr6 155038435 -------------- 155038435\npanTro2.c 157528507 -------------- 157528507\nponAbe2.c 158049108 ACCTGTCAATGATG 158049094\notoGar1.s 178255 CCTTGTTA------ 178247\ntupBel1.s 331078 -------------- 331078\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=98097.000000\ns mm9.chr10 3012996 222 + 129993255 AGATGTCTGCTGTGGAGA-------CCTGGCCAACTTTG----CTT--TCTTC-----AAAAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCA-----TTAGGAAGGCGACCTCTAGTGCACAAACCTTGAC-ATTTTCCCTTTTAATGGAA-TTTAACAGAAGTTCAGGATGTTCTTTGGGTAATTTACAATT---A----GGGGGCAAAAATCAAAAGTATTTCGAGCATATCAAAACTGTTAGCTATG\ns cavPor2.scaffold_290371 681 177 - 39932 TGACGTCTGCAGCCACGG-------GCTGGCTAACTCCA--GTCTT--CCGCG-----CTAAAGCCGAC--------------------CACACCACATAGTGGGGAGAGTGACCTCTAGCGGAAAagctttgca-atttttttcttc----gAC-TCTGTCAG--GTTCAGAATTCCATTTAAACAATTTacagct---a----gaaaaggaaaagcagaggCATTT--------------------------\nq cavPor2.scaffold_290371 999999999999999999-------99999999999999--99999--99999-----99999999999--------------------9999999999999999999999999999999999999999999999-999999999999----999-99999999--9999999999999999997999999999995---6----99999999999336991774687--------------------------\ni cavPor2.scaffold_290371 C 0 N 0\ns hg18.chr6 15861373 184 - 170899992 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGC-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------\ni hg18.chr6 C 0 I 14\ns panTro2.chr6 16379921 184 - 173908612 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ATTCT-----ATAAGACTAAC--------------------AGGACCCCATGGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTAAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------\nq panTro2.chr6 999999999999999999---9999999999999999999999999--99999-----99999999999--------------------9999999999999999999999999999999999999999999999-9999999999999999999-99999999-99999999999999999999999999999999---99999999999999999999----------------------------------\ni panTro2.chr6 C 0 I 14\ns ponAbe2.chr6 16161120 217 - 174210431 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTAGGCCGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTATAAATATTGAATGTAT-TCAAACCTGTCAATGATG\ni ponAbe2.chr6 C 0 I 2\ns otoGar1.scaffold_334.1-359464 180991 226 - 359464 GGACGGCCGCCGCCACCACCGCTTTCCCTGCCAACTCCACCGTCTTAAATTCTGCAACAAAAGAAAAAT--------------------CGGACCCTGCAGTTACTAGAGCGACCTCTGGTGAACAAGCCTTGGATTTTTTTCTTTTTAATTGAATTTTACAAC-GGCTCAAAATGCAAGTTAGACAATTCATAGTGTATGTGTGGGGACCTGAGAGTGCAAATATTGCTGGCAT-TCAGCCTTGTTA------\nq otoGar1.scaffold_334.1-359464 999998999999999999999999999999999999999999999999999999999999999999999--------------------999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999699999999999999999999999999-999999999999------\ni otoGar1.scaffold_334.1-359464 C 0 I 2931\ns tupBel1.scaffold_114895.1-498454 167217 159 - 498454 TGATGGCTACAGCTGTCA---CTTTCTTGGACCACTCAGCTCTCTC--AAC-------GAAAGACAAAC--------------------TGGATCCTCCGG---GAGAGGAGACCTCTAGTGAGCAAACCTTGGA-ATTTTTCTTTAAAACAGAA-TTTATAAA-GGTTCA-AATGCCATTTAGACAACTTATAATT---A-----------------------------------------------------\nq tupBel1.scaffold_114895.1-498454 234233433332122232---1582112220212134443324332--133-------23732111754--------------------365002326236---2411112335242535353245936522224-1376645373578253554-58324573-545454-8444565585455465799967999---9-----------------------------------------------------\ni tupBel1.scaffold_114895.1-498454 N 0 I 4145\ne echTel1.scaffold_288249 87661 7564 + 100002 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3013218 : 3013218 + 219],\n \"agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggatctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacacagaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAAAAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT\",\n )\n self.assertEqual(\n alignment[0],\n \"agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggatctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacacagaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAAAAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (178247, 175316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155038435, 155038421))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157528507, 157528493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158049094, 158049092))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3013218, 3013437]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3013218 agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggat\n\nmm9.chr10 3013278 ctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacaca\n\nmm9.chr10 3013338 gaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAA\n\nmm9.chr10 3013398 AAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT 3013437\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3013218 219 + 129993255 agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggatctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacacagaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAAAAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I\ne hg18.chr6 15861557 14 - 170899992 I\ne panTro2.chr6 16380105 14 - 173908612 I\ne ponAbe2.chr6 16161337 2 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['a', 'g', 'c', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't',\n 'g', 'g', 'c', 'a', 'c', 'a', 'c', 'a', 'c', 'c', 't', 't', 't',\n 'a', 'c', 't', 'c', 'c', 'c', 'a', 'g', 'c', 'a', 't', 't', 't',\n 'g', 'g', 'g', 'g', 'g', 'g', 'c', 'a', 'g', 'a', 'g', 'g', 'c',\n 'a', 'g', 'g', 't', 'g', 'g', 'a', 't', 'c', 't', 'g', 't', 'g',\n 'a', 'g', 't', 't', 't', 'g', 'a', 'g', 'g', 'c', 'c', 'a', 'g',\n 'c', 'c', 't', 'g', 'g', 't', 'c', 't', 'a', 'c', 'a', 'g', 'a',\n 'g', 'g', 'g', 'a', 'g', 't', 'c', 't', 'c', 'a', 'g', 'g', 'a',\n 'c', 'a', 'g', 'c', 'c', 'a', 'g', 'a', 'g', 'c', 't', 'a', 'c',\n 'a', 'c', 'a', 'g', 'a', 'a', 'a', 't', 'a', 'a', 'c', 'c', 't',\n 'g', 'c', 'c', 't', 'a', 'g', 'a', 'a', 'a', 'a', 'a', 'c', 'a',\n 'a', 'a', 'a', 'c', 'a', 'a', 'a', 'a', 'c', 'a', 'a', 'a', 'a',\n 'c', 'a', 't', 'c', 'a', 'a', 'a', 'a', 'c', 't', 'c', 'a', 'a',\n 'a', 'a', 'c', 'a', 'a', 'a', 'T', 'A', 'A', 'A', 'A', 'A', 'A',\n 'A', 'A', 'T', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'C', 'A',\n 'A', 'C', 'C', 'T', 'A', 'A', 'A', 'C', 'C', 'A', 'A', 'A', 'T',\n 'A', 'A', 'C', 'A', 'A', 'A', 'A', 'C', 'A', 'C', 'T']],\n dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 40604)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3013437 : 3013437 + 166],\n \"TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAAGAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCAGACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA\",\n )\n self.assertEqual(\n alignment[0],\n \"TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAAGAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCAGACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 173908612)\n self.assertEqual(\n alignment.sequences[1].seq[157528363 : 157528363 + 130],\n \"TATCAAACAGCCCATGAATGCAAAACGATACACCCATAAAATAGGATGTAATCGCCAAAATCTAATTCTATTGCATCTAGAAGATCTTTATCCACAGTGAAAAGAGTTGAACATCATTGACAGGTTTGAA\",\n )\n self.assertEqual(\n alignment[1],\n \"TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999099999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 14)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 9106)\n self.assertEqual(alignment.sequences[2].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 170899992)\n self.assertEqual(\n alignment.sequences[2].seq[155038291 : 155038291 + 130],\n \"TATCAAACAGCCCATGAATGCAAAACGATACACCCATAAAATAGGATGTAATCGCCAAAATCTAATTCTATTGCATCTAGAAGATCTTTATCCACAGTGAAAAGAGTTGAACATCATTGACAGGTTTGAA\",\n )\n self.assertEqual(\n alignment[2],\n \"TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 14)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 9085)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158048983 : 158048983 + 109],\n \"TATCAAACAGCCCATGAATGCAAAACGATACACCCATAAAATAGGATGTAATCGCCAAAATCTAATTCTATTGCATCTAGAAGATCTTTATCCACAGTGAAAAGAGTTG\",\n )\n self.assertEqual(\n alignment[3],\n \"---------------------CAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 2)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 8044)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (178247, 175316))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 4)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 3)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3013437, 3013458, 3013509, 3013545, 3013603],\n [157528493, 157528472, 157528421, 157528421, 157528363],\n [155038421, 155038400, 155038349, 155038349, 155038291],\n [158049092, 158049092, 158049041, 158049041, 158048983],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3013437 TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAA\npanTro2.c 157528493 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAA\nhg18.chr6 155038421 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAA\nponAbe2.c 158049092 ---------------------CAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAA\n\nmm9.chr10 3013497 GAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCA\npanTro2.c 157528433 TAGAATTAGATT------------------------------------TTGGCGATTACA\nhg18.chr6 155038361 TAGAATTAGATT------------------------------------TTGGCGATTACA\nponAbe2.c 158049053 TAGAATTAGATT------------------------------------TTGGCGATTACA\n\nmm9.chr10 3013557 GACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA 3013603\npanTro2.c 157528409 TCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA 157528363\nhg18.chr6 155038337 TCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA 155038291\nponAbe2.c 158049029 TCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA 158048983\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=40604.000000\ns mm9.chr10 3013437 166 + 129993255 TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAAGAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCAGACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA\ns panTro2.chr6 16380119 130 - 173908612 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\nq panTro2.chr6 999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------9999999999999999999999999999999999999099999999999999999999\ni panTro2.chr6 I 14 I 9106\ns hg18.chr6 15861571 130 - 170899992 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\ni hg18.chr6 I 14 I 9085\ns ponAbe2.chr6 16161339 109 - 174210431 ---------------------CAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA\ni ponAbe2.chr6 I 2 I 8044\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'C', 'C', 'A', 'A', 'A', 'A', 'T', 'G', 'G', 'T', 'T', 'A',\n 'G', 'C', 'T', 'A', 'T', 'G', 'C', 'C', 'C', 'A', 'A', 'C', 'T',\n 'C', 'C', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'C', 'C', 'A', 'A',\n 'G', 'A', 'A', 'A', 'A', 'T', 'A', 'T', 'C', 'C', 'T', 'A', 'A',\n 'C', 'C', 'A', 'T', 'G', 'T', 'A', 'A', 'G', 'A', 'G', 'A', 'G',\n 'C', 'T', 'A', 'G', 'C', 'C', 'T', 'G', 'T', 'T', 'G', 'G', 'T',\n 'G', 'G', 'C', 'A', 'G', 'C', 'C', 'A', 'A', 'G', 'C', 'C', 'T',\n 'G', 'A', 'T', 'G', 'G', 'T', 'G', 'G', 'C', 'A', 'G', 'A', 'C',\n 'T', 'A', 'G', 'A', 'T', 'T', 'G', 'A', 'T', 'G', 'G', 'T', 'G',\n 'C', 'C', 'A', 'G', 'A', 'C', 'T', 'A', 'C', 'T', 'T', 'T', 'A',\n 'T', 'G', 'G', 'C', 'T', 'G', 'T', 'A', 'T', 'C', 'A', 'T', 'T',\n 'T', 'T', 'C', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'T', 'G',\n 'T', 'T', 'G', 'T', 'G', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'C', 'A', 'A', 'A', 'C', 'C', 'T', 'G', 'T', 'C', 'A',\n 'A', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'C', 'A', 'A', 'C', 'T',\n 'C', 'T', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'G', 'T', 'G', 'G',\n 'A', 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'C', 'T', 'T', 'C', 'T',\n 'A', 'G', 'A', 'T', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'A', 'A',\n 'T', 'T', 'A', 'G', 'A', 'T', 'T', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'T', 'T', 'G', 'G', 'C', 'G', 'A', 'T', 'T',\n 'A', 'C', 'A', 'T', 'C', 'C', 'T', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'C', 'G', 'T', 'T',\n 'T', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'G', 'G',\n 'C', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'T', 'A'],\n ['T', 'T', 'C', 'A', 'A', 'A', 'C', 'C', 'T', 'G', 'T', 'C', 'A',\n 'A', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'C', 'A', 'A', 'C', 'T',\n 'C', 'T', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'G', 'T', 'G', 'G',\n 'A', 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'C', 'T', 'T', 'C', 'T',\n 'A', 'G', 'A', 'T', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'A', 'A',\n 'T', 'T', 'A', 'G', 'A', 'T', 'T', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'T', 'T', 'G', 'G', 'C', 'G', 'A', 'T', 'T',\n 'A', 'C', 'A', 'T', 'C', 'C', 'T', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'C', 'G', 'T', 'T',\n 'T', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'G', 'G',\n 'C', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'A', 'C', 'T',\n 'C', 'T', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'G', 'T', 'G', 'G',\n 'A', 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'C', 'T', 'T', 'C', 'T',\n 'A', 'G', 'A', 'T', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'A', 'A',\n 'T', 'T', 'A', 'G', 'A', 'T', 'T', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'T', 'T', 'G', 'G', 'C', 'G', 'A', 'T', 'T',\n 'A', 'C', 'A', 'T', 'C', 'C', 'T', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'C', 'G', 'T', 'T',\n 'T', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'G', 'G',\n 'C', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'T', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3013603 : 3013603 + 1041],\n \"CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgctgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacccgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagttcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcatacctttaatatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcgttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggattccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactagagtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagtcattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaaccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgaggttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggtcctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGTGTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCTTGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAGTATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaaaaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGATTTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCTTGTTTGTTTTGGTCAATGCAG\",\n )\n self.assertEqual(\n alignment[0],\n \"CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgctgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacccgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagttcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcatacctttaatatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcgttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggattccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactagagtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagtcattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaaccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgaggttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggtcctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGTGTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCTTGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAGTATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaaaaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGATTTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCTTGTTTGTTTTGGTCAATGCAG\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (178247, 175316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155038291, 155029206))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157528363, 157519257))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158048983, 158040939))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3013603, 3014644]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3013603 CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgc\n\nmm9.chr10 3013663 tgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacc\n\nmm9.chr10 3013723 cgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagt\n\nmm9.chr10 3013783 tcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcataccttta\n\nmm9.chr10 3013843 atatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcg\n\nmm9.chr10 3013903 ttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggatt\n\nmm9.chr10 3013963 ccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactaga\n\nmm9.chr10 3014023 gtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagt\n\nmm9.chr10 3014083 cattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaa\n\nmm9.chr10 3014143 ccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgagg\n\nmm9.chr10 3014203 ttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggt\n\nmm9.chr10 3014263 cctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGT\n\nmm9.chr10 3014323 GTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCT\n\nmm9.chr10 3014383 TGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAG\n\nmm9.chr10 3014443 TATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaa\n\nmm9.chr10 3014503 aaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGAT\n\nmm9.chr10 3014563 TTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCT\n\nmm9.chr10 3014623 TGTTTGTTTTGGTCAATGCAG 3014644\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3013603 1041 + 129993255 CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgctgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacccgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagttcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcatacctttaatatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcgttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggattccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactagagtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagtcattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaaccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgaggttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggtcctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGTGTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCTTGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAGTATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaaaaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGATTTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCTTGTTTGTTTTGGTCAATGCAG\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I\ne hg18.chr6 15861701 9085 - 170899992 I\ne panTro2.chr6 16380249 9106 - 173908612 I\ne ponAbe2.chr6 16161448 8044 - 174210431 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 19159)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014644 : 3014644 + 45],\n \"CCTGTACCCTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG\",\n )\n self.assertEqual(\n alignment[0], \"CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG\"\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155029160 : 155029160 + 46],\n \"AAAAGTTTAGGATTAAAACAAAATTCTCATAAAAGAAAGGTATAGG\",\n )\n self.assertEqual(\n alignment[1], \"CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT\"\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 9085)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157519211 : 157519211 + 46],\n \"AAAAGTTTAGGATTAAAACAAAATTCTCATAAAAGAAAGGTATAGG\",\n )\n self.assertEqual(\n alignment[2], \"CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT\"\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 9106)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[3].seq), 133105)\n self.assertEqual(\n alignment.sequences[3].seq[6182 : 6182 + 46],\n \"CCTATACCTTTCTTTCATGAGAATTTTGTTTGAATCCTAAACTTTT\",\n )\n self.assertEqual(\n alignment[3], \"CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[4].seq), 10574)\n self.assertEqual(\n alignment.sequences[4].seq[9373 : 9373 + 34],\n \"GGAAGTTTTGAATTAAAGCATAATTCTAACCAAA\",\n )\n self.assertEqual(\n alignment[4], \"------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC\"\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"9999969989999999999999998699989997\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (178247, 175316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158048983, 158040939))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 5)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 4)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3014644, 3014652, 3014652, 3014653, 3014664, 3014665,\n 3014684, 3014685, 3014689],\n [155029206, 155029198, 155029195, 155029194, 155029183, 155029183,\n 155029164, 155029164, 155029160],\n [157519257, 157519249, 157519246, 157519245, 157519234, 157519234,\n 157519215, 157519215, 157519211],\n [ 6182, 6190, 6193, 6194, 6205, 6205,\n 6224, 6224, 6228],\n [ 9407, 9407, 9407, 9407, 9396, 9396,\n 9377, 9377, 9373],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014644 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG 3014689\nhg18.chr6 155029206 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT 155029160\npanTro2.c 157519257 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT 157519211\ncalJac1.C 6182 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT 6228\nloxAfr1.s 9407 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC 9373\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=19159.000000\ns mm9.chr10 3014644 45 + 129993255 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG\ns hg18.chr6 15870786 46 - 170899992 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT\ni hg18.chr6 I 9085 C 0\ns panTro2.chr6 16389355 46 - 173908612 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT\nq panTro2.chr6 99999999999999999999999-9999999999999999999-9999\ni panTro2.chr6 I 9106 C 0\ns calJac1.Contig6394 6182 46 + 133105 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT\ni calJac1.Contig6394 N 0 C 0\ns loxAfr1.scaffold_75566 1167 34 - 10574 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC\nq loxAfr1.scaffold_75566 ------------99999699899-9999999999999869998-9997\ni loxAfr1.scaffold_75566 N 0 C 0\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I\ne ponAbe2.chr6 16161448 8044 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'C', 'T', 'G', 'T', 'A', 'C', 'C', '-', '-', '-', 'C', 'T',\n 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'G', 'A', 'A', 'T', 'T', 'T',\n 'T', 'T', 'G', 'T', 'T', 'T', 'C', 'A', 'G', 'T', 'G', 'T', 'T',\n 'A', 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G'],\n ['C', 'C', 'T', 'A', 'T', 'A', 'C', 'C', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', 'T', 'A', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'T', 'T',\n 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'C', 'T',\n 'A', 'A', 'A', 'C', '-', 'T', 'T', 'T', 'T'],\n ['C', 'C', 'T', 'A', 'T', 'A', 'C', 'C', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', 'T', 'A', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'T', 'T',\n 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'C', 'T',\n 'A', 'A', 'A', 'C', '-', 'T', 'T', 'T', 'T'],\n ['C', 'C', 'T', 'A', 'T', 'A', 'C', 'C', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', 'C', 'A', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'T', 'T',\n 'T', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'A', 'T', 'C', 'C', 'T',\n 'A', 'A', 'A', 'C', '-', 'T', 'T', 'T', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T',\n 'T', 'T', 'G', 'G', 'T', 'T', 'A', 'G', 'A', 'A', '-', 'T', 'T',\n 'A', 'T', 'G', 'C', 'T', 'T', 'T', 'A', 'A', 'T', 'T', 'C', 'A',\n 'A', 'A', 'A', 'C', '-', 'T', 'T', 'C', 'C']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 40840)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014689 : 3014689 + 53],\n \"GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCTTTGGAAAGAGTTG\",\n )\n self.assertEqual(\n alignment[0], \"GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG\"\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155029107 : 155029107 + 53],\n \"CCACTATTTCCCAAAAGATTAGATATTTCACAGATTAAATGGTTTATGATCCC\",\n )\n self.assertEqual(\n alignment[1], \"GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\"\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 401)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157519158 : 157519158 + 53],\n \"CCACTATTTCCCAAAAGATTAGATATTTCACAGATTAAATGGTTTATGATCCC\",\n )\n self.assertEqual(\n alignment[2], \"GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\"\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 400)\n self.assertEqual(alignment.sequences[3].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[3].seq), 133105)\n self.assertEqual(\n alignment.sequences[3].seq[6228 : 6228 + 53],\n \"GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTTTGGGAAACAGTGG\",\n )\n self.assertEqual(\n alignment[3], \"GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 2)\n self.assertEqual(alignment.sequences[4].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[4].seq), 359464)\n self.assertEqual(\n alignment.sequences[4].seq[175264 : 175264 + 52],\n \"CAGCTATTGCCCAAGTGATTTGATATTTCATAGATTAAAAGTTTATGCTTCC\",\n )\n self.assertEqual(\n alignment[4], \"GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG\"\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"7455455669566996656997698955556899975999984787795599\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 2931)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 2)\n self.assertEqual(alignment.sequences[5].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[5].seq), 10574)\n self.assertEqual(\n alignment.sequences[5].seq[9319 : 9319 + 54],\n \"CAGCTTTTTCCCCTGAAGATTTGGCATTTCGCAGACTAAATGGTTTATACTCCC\",\n )\n self.assertEqual(\n alignment[5], \"GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG\"\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"899989799999979999999999999999797999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 2)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158048983, 158040939))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 6)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 3)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3014689, 3014702, 3014703, 3014729, 3014729, 3014742],\n [155029160, 155029147, 155029146, 155029120, 155029120, 155029107],\n [157519211, 157519198, 157519197, 157519171, 157519171, 157519158],\n [ 6228, 6241, 6242, 6268, 6268, 6281],\n [ 175316, 175303, 175303, 175277, 175277, 175264],\n [ 9373, 9360, 9359, 9333, 9332, 9319],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014689 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG\nhg18.chr6 155029160 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\npanTro2.c 157519211 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\ncalJac1.C 6228 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG\notoGar1.s 175316 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG\nloxAfr1.s 9373 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG\n\nmm9.chr10 3014742\nhg18.chr6 155029107\npanTro2.c 157519158\ncalJac1.C 6281\notoGar1.s 175264\nloxAfr1.s 9319\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=40840.000000\ns mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG\ns hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\ni hg18.chr6 C 0 I 401\ns panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG\nq panTro2.chr6 9999999999999999999999999999999999999999-9999999999999\ni panTro2.chr6 C 0 I 400\ns calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG\ni calJac1.Contig6394 C 0 I 2\ns otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG\nq otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599\ni otoGar1.scaffold_334.1-359464 I 2931 I 2\ns loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG\nq loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999\ni loxAfr1.scaffold_75566 C 0 I 2\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne ponAbe2.chr6 16161448 8044 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['G', 'G', 'G', 'A', 'G', 'C', 'A', 'T', 'A', 'A', 'A', 'A', 'C',\n 'T', 'C', 'T', 'A', 'A', 'A', 'T', 'C', 'T', 'G', 'C', 'T', 'A',\n 'A', 'A', 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'T', 'C', 'C', 'C',\n 'T', '-', 'T', 'T', 'G', 'G', 'A', 'A', 'A', 'G', 'A', 'G', 'T',\n 'T', 'G'],\n ['G', 'G', 'G', 'A', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'C', 'C',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'G', 'T', 'G', 'A',\n 'A', 'A', 'T', 'A', 'T', 'C', 'T', 'A', 'A', 'T', 'C', 'T', 'T',\n 'T', '-', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'T', 'A', 'G', 'T',\n 'G', 'G'],\n ['G', 'G', 'G', 'A', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'C', 'C',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'G', 'T', 'G', 'A',\n 'A', 'A', 'T', 'A', 'T', 'C', 'T', 'A', 'A', 'T', 'C', 'T', 'T',\n 'T', '-', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'T', 'A', 'G', 'T',\n 'G', 'G'],\n ['G', 'G', 'G', 'A', 'T', 'C', 'A', 'T', 'A', 'A', 'G', 'C', 'C',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'G', 'T', 'G', 'A',\n 'A', 'A', 'T', 'G', 'T', 'G', 'A', 'A', 'A', 'T', 'C', 'T', 'T',\n 'T', '-', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'C', 'A', 'G', 'T',\n 'G', 'G'],\n ['G', 'G', 'A', 'A', 'G', 'C', 'A', 'T', 'A', 'A', 'A', 'C', 'T',\n '-', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'A', 'T', 'G', 'A',\n 'A', 'A', 'T', 'A', 'T', 'C', 'A', 'A', 'A', 'T', 'C', 'A', 'C',\n 'T', '-', 'T', 'G', 'G', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'C',\n 'T', 'G'],\n ['G', 'G', 'G', 'A', 'G', 'T', 'A', 'T', 'A', 'A', 'A', 'C', 'C',\n 'A', 'T', 'T', 'T', 'A', 'G', 'T', 'C', 'T', 'G', 'C', 'G', 'A',\n 'A', 'A', 'T', 'G', 'C', 'C', 'A', 'A', 'A', 'T', 'C', 'T', 'T',\n 'C', 'A', 'G', 'G', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'G', 'C',\n 'T', 'G']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 411)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014742 : 3014742 + 36],\n \"AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA\",\n )\n self.assertEqual(alignment[0], \"AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA\")\n self.assertEqual(alignment.sequences[1].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[1].seq), 133105)\n self.assertEqual(\n alignment.sequences[1].seq[6283 : 6283 + 28], \"AAATGTATGATCTCCCCATCCTGCCCTG\"\n )\n self.assertEqual(alignment[1], \"AAATGTA-----TGATCTCCCCATCCTGCCCTG---\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 2)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 54)\n self.assertEqual(alignment.sequences[2].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[2].seq), 359464)\n self.assertEqual(\n alignment.sequences[2].seq[175231 : 175231 + 31],\n \"TGCACGGAGGGGGTGAGGGCATCAGAAATCT\",\n )\n self.assertEqual(alignment[2], \"AGATTTC-----TGATGCCCTCACCCCCTCCGTGCA\")\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9996999965974999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 2)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 24)\n self.assertEqual(alignment.sequences[3].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[3].seq), 10574)\n self.assertEqual(\n alignment.sequences[3].seq[9290 : 9290 + 27], \"TGTGGGGGTGGGGGGTGGCATAAGCCT\"\n )\n self.assertEqual(alignment[3], \"AGGCTTA-----TG----CCACCCCCCACCCCCACA\")\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"], \"999999999997999999999999999\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 2)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 25)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155029107, 155028706))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157519158, 157518758))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158048983, 158040939))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 4)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 5)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[3014742, 3014749, 3014754, 3014756, 3014760, 3014775, 3014778],\n [ 6283, 6290, 6290, 6292, 6296, 6311, 6311],\n [ 175262, 175255, 175255, 175253, 175249, 175234, 175231],\n [ 9317, 9310, 9310, 9308, 9308, 9293, 9290],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014742 AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA 3014778\ncalJac1.C 6283 AAATGTA-----TGATCTCCCCATCCTGCCCTG--- 6311\notoGar1.s 175262 AGATTTC-----TGATGCCCTCACCCCCTCCGTGCA 175231\nloxAfr1.s 9317 AGGCTTA-----TG----CCACCCCCCACCCCCACA 9290\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=411.000000\ns mm9.chr10 3014742 36 + 129993255 AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA\ns calJac1.Contig6394 6283 28 + 133105 AAATGTA-----TGATCTCCCCATCCTGCCCTG---\ni calJac1.Contig6394 I 2 I 54\ns otoGar1.scaffold_334.1-359464 184202 31 - 359464 AGATTTC-----TGATGCCCTCACCCCCTCCGTGCA\nq otoGar1.scaffold_334.1-359464 9996999-----965974999999999999999999\ni otoGar1.scaffold_334.1-359464 I 2 I 24\ns loxAfr1.scaffold_75566 1257 27 - 10574 AGGCTTA-----TG----CCACCCCCCACCCCCACA\nq loxAfr1.scaffold_75566 9999999-----99----997999999999999999\ni loxAfr1.scaffold_75566 I 2 I 25\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne hg18.chr6 15870885 401 - 170899992 I\ne panTro2.chr6 16389454 400 - 173908612 I\ne ponAbe2.chr6 16161448 8044 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'A', 'G', 'T', 'T', 'C', 'C', 'C', 'T', 'C', 'C', 'A', 'T',\n 'A', 'A', 'T', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'T', 'C', 'C',\n 'C', 'A', 'C', 'C', 'C', 'C', 'C', 'A', 'C', 'A'],\n ['A', 'A', 'A', 'T', 'G', 'T', 'A', '-', '-', '-', '-', '-', 'T',\n 'G', 'A', 'T', 'C', 'T', 'C', 'C', 'C', 'C', 'A', 'T', 'C', 'C',\n 'T', 'G', 'C', 'C', 'C', 'T', 'G', '-', '-', '-'],\n ['A', 'G', 'A', 'T', 'T', 'T', 'C', '-', '-', '-', '-', '-', 'T',\n 'G', 'A', 'T', 'G', 'C', 'C', 'C', 'T', 'C', 'A', 'C', 'C', 'C',\n 'C', 'C', 'T', 'C', 'C', 'G', 'T', 'G', 'C', 'A'],\n ['A', 'G', 'G', 'C', 'T', 'T', 'A', '-', '-', '-', '-', '-', 'T',\n 'G', '-', '-', '-', '-', 'C', 'C', 'A', 'C', 'C', 'C', 'C', 'C',\n 'C', 'A', 'C', 'C', 'C', 'C', 'C', 'A', 'C', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014778 : 3014778 + 17], \"TCCCATGTCCACCCTGA\"\n )\n self.assertEqual(alignment[0], \"TCCCATGTCCACCCTGA\")\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(record.seq), 10574)\n self.assertEqual(segment, (9290, 9265))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6311, 6365))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (331078, 326933))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (175231, 175207))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155029107, 155028706))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157519158, 157518758))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158048983, 158040939))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 8)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3014778, 3014795]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014778 TCCCATGTCCACCCTGA 3014795\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3014778 17 + 129993255 TCCCATGTCCACCCTGA\ne loxAfr1.scaffold_75566 1284 25 - 10574 I\ne calJac1.Contig6394 6311 54 + 133105 I\ne tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 184233 24 - 359464 I\ne hg18.chr6 15870885 401 - 170899992 I\ne panTro2.chr6 16389454 400 - 173908612 I\ne ponAbe2.chr6 16161448 8044 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'C', 'C', 'C', 'A', 'T', 'G', 'T', 'C', 'C', 'A', 'C', 'C',\n 'C', 'T', 'G', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, -12243)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014795 : 3014795 + 47],\n \"GTTTCAGGGGCAGCTCGCTGTTAGCAGCTAAGGCATGGTGTCTCTCA\",\n )\n self.assertEqual(\n alignment[0],\n \"GTTTCAGGGGCAGCTCGCTG----------------TTAGCAG-CTAAGGCATGGTGTCTCTCA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[1].seq), 359464)\n self.assertEqual(\n alignment.sequences[1].seq[175147 : 175147 + 60],\n \"AGAAATACACCCCACCTAAACCATCTAAACCAAATATCCATGACTGCAACTTGTTCCCGA\",\n )\n self.assertEqual(\n alignment[1],\n \"---TCGGGAACAAGTTGCAGTCATGGATAT-TTGGTTTAGATGGTTTAGGTGGGGTGTATTTCT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"899999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 24)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[2].seq), 133105)\n self.assertEqual(\n alignment.sequences[2].seq[6365 : 6365 + 39],\n \"GCCATGAATATTTTAGACATGCAGGTGTGGCGTGTTTCT\",\n )\n self.assertEqual(\n alignment[2],\n \"-------------------GCCATGAATAT-----TTTAGAC-ATGCAGGTGTGGCGTGTTTCT\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 54)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155028686 : 155028686 + 20],\n \"AGAAACATGCCACACCTGCt\",\n )\n self.assertEqual(\n alignment[3],\n \"--------------------------------------------aGCAGGTGTGGCATGTTTCT\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 401)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 173908612)\n self.assertEqual(\n alignment.sequences[4].seq[157518738 : 157518738 + 20],\n \"AGAAACATGCCACACCTGCt\",\n )\n self.assertEqual(\n alignment[4],\n \"--------------------------------------------aGCAGGTGTGGCATGTTTCT\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"], \"99999999999999999999\"\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 400)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 174210431)\n self.assertEqual(\n alignment.sequences[5].seq[158040919 : 158040919 + 20],\n \"AGAAACATGCCACACCTGCt\",\n )\n self.assertEqual(\n alignment[5],\n \"--------------------------------------------aGCAGGTGTGGCATGTTTCT\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 8044)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[6].seq), 498454)\n self.assertEqual(\n alignment.sequences[6].seq[326906 : 326906 + 27],\n \"AGCGATGCGCCACACCCACATTTCTAA\",\n )\n self.assertEqual(\n alignment[6],\n \"------------------------------------TTAGAAA-TGTGGGTGTGGCGCATCGCT\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"], \"999999999999989998899999699\"\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 4145)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[7].seq), 10026)\n self.assertEqual(\n alignment.sequences[7].seq[2184 : 2184 + 26], \"GAACCATGCCACACCTAAATTTCTAA\"\n )\n self.assertEqual(\n alignment[7],\n \"------------------------------------TTAGAAA-TTTAGGTGTGGCATGGTTC-\",\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"], \"42558311324566557465575854\"\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[8].seq), 10574)\n self.assertEqual(\n alignment.sequences[8].seq[9203 : 9203 + 62],\n \"aGAGATACAGCAAACCTCAATTTCTGAAACAACGTATTGATGTCCTAAACTTGCTCTCAAAC\",\n )\n self.assertEqual(\n alignment[8],\n \"GTT-TGAGAGCAAGTTTAGGACATCAATACGTTGTTTCAGAAA-TTGAGGTTTGCTGTATCTCt\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 25)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 9)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3014795, 3014798, 3014799, 3014814, 3014815, 3014815,\n 3014815, 3014815, 3014815, 3014821, 3014822, 3014822,\n 3014841, 3014842],\n [ 175207, 175207, 175206, 175191, 175190, 175180,\n 175180, 175176, 175175, 175169, 175168, 175167,\n 175148, 175147],\n [ 6365, 6365, 6365, 6365, 6366, 6376,\n 6376, 6376, 6377, 6383, 6383, 6384,\n 6403, 6404],\n [155028706, 155028706, 155028706, 155028706, 155028706, 155028706,\n 155028706, 155028706, 155028706, 155028706, 155028706, 155028706,\n 155028687, 155028686],\n [157518758, 157518758, 157518758, 157518758, 157518758, 157518758,\n 157518758, 157518758, 157518758, 157518758, 157518758, 157518758,\n 157518739, 157518738],\n [158040939, 158040939, 158040939, 158040939, 158040939, 158040939,\n 158040939, 158040939, 158040939, 158040939, 158040939, 158040939,\n 158040920, 158040919],\n [ 326933, 326933, 326933, 326933, 326933, 326933,\n 326933, 326933, 326933, 326927, 326926, 326926,\n 326907, 326906],\n [ 2210, 2210, 2210, 2210, 2210, 2210,\n 2210, 2210, 2210, 2204, 2203, 2203,\n 2184, 2184],\n [ 9265, 9262, 9262, 9247, 9246, 9236,\n 9235, 9231, 9230, 9224, 9223, 9223,\n 9204, 9203],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014795 GTTTCAGGGGCAGCTCGCTG----------------TTAGCAG-CTAAGGCATGGTGTCT\notoGar1.s 175207 ---TCGGGAACAAGTTGCAGTCATGGATAT-TTGGTTTAGATGGTTTAGGTGGGGTGTAT\ncalJac1.C 6365 -------------------GCCATGAATAT-----TTTAGAC-ATGCAGGTGTGGCGTGT\nhg18.chr6 155028706 --------------------------------------------aGCAGGTGTGGCATGT\npanTro2.c 157518758 --------------------------------------------aGCAGGTGTGGCATGT\nponAbe2.c 158040939 --------------------------------------------aGCAGGTGTGGCATGT\ntupBel1.s 326933 ------------------------------------TTAGAAA-TGTGGGTGTGGCGCAT\ncavPor2.s 2210 ------------------------------------TTAGAAA-TTTAGGTGTGGCATGG\nloxAfr1.s 9265 GTT-TGAGAGCAAGTTTAGGACATCAATACGTTGTTTCAGAAA-TTGAGGTTTGCTGTAT\n\nmm9.chr10 3014838 CTCA 3014842\notoGar1.s 175151 TTCT 175147\ncalJac1.C 6400 TTCT 6404\nhg18.chr6 155028690 TTCT 155028686\npanTro2.c 157518742 TTCT 157518738\nponAbe2.c 158040923 TTCT 158040919\ntupBel1.s 326910 CGCT 326906\ncavPor2.s 2187 TTC- 2184\nloxAfr1.s 9207 CTCt 9203\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=-12243.000000\ns mm9.chr10 3014795 47 + 129993255 GTTTCAGGGGCAGCTCGCTG----------------TTAGCAG-CTAAGGCATGGTGTCTCTCA\ns otoGar1.scaffold_334.1-359464 184257 60 - 359464 ---TCGGGAACAAGTTGCAGTCATGGATAT-TTGGTTTAGATGGTTTAGGTGGGGTGTATTTCT\nq otoGar1.scaffold_334.1-359464 ---899999999999999999999999999-999999999999999999999999999999999\ni otoGar1.scaffold_334.1-359464 I 24 C 0\ns calJac1.Contig6394 6365 39 + 133105 -------------------GCCATGAATAT-----TTTAGAC-ATGCAGGTGTGGCGTGTTTCT\ni calJac1.Contig6394 I 54 C 0\ns hg18.chr6 15871286 20 - 170899992 --------------------------------------------aGCAGGTGTGGCATGTTTCT\ni hg18.chr6 I 401 C 0\ns panTro2.chr6 16389854 20 - 173908612 --------------------------------------------aGCAGGTGTGGCATGTTTCT\nq panTro2.chr6 --------------------------------------------99999999999999999999\ni panTro2.chr6 I 400 C 0\ns ponAbe2.chr6 16169492 20 - 174210431 --------------------------------------------aGCAGGTGTGGCATGTTTCT\ni ponAbe2.chr6 I 8044 C 0\ns tupBel1.scaffold_114895.1-498454 171521 27 - 498454 ------------------------------------TTAGAAA-TGTGGGTGTGGCGCATCGCT\nq tupBel1.scaffold_114895.1-498454 ------------------------------------9999999-99999989998899999699\ni tupBel1.scaffold_114895.1-498454 I 4145 C 0\ns cavPor2.scaffold_216473 7816 26 - 10026 ------------------------------------TTAGAAA-TTTAGGTGTGGCATGGTTC-\nq cavPor2.scaffold_216473 ------------------------------------4255831-1324566557465575854-\ni cavPor2.scaffold_216473 N 0 C 0\ns loxAfr1.scaffold_75566 1309 62 - 10574 GTT-TGAGAGCAAGTTTAGGACATCAATACGTTGTTTCAGAAA-TTGAGGTTTGCTGTATCTCt\nq loxAfr1.scaffold_75566 999-999999999999999999999999999999999999999-99999999999999999999\ni loxAfr1.scaffold_75566 I 25 C 0\ne echTel1.scaffold_288249 87661 7564 + 100002 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['G', 'T', 'T', 'T', 'C', 'A', 'G', 'G', 'G', 'G', 'C', 'A', 'G',\n 'C', 'T', 'C', 'G', 'C', 'T', 'G', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'A',\n 'G', 'C', 'A', 'G', '-', 'C', 'T', 'A', 'A', 'G', 'G', 'C', 'A',\n 'T', 'G', 'G', 'T', 'G', 'T', 'C', 'T', 'C', 'T', 'C', 'A'],\n ['-', '-', '-', 'T', 'C', 'G', 'G', 'G', 'A', 'A', 'C', 'A', 'A',\n 'G', 'T', 'T', 'G', 'C', 'A', 'G', 'T', 'C', 'A', 'T', 'G', 'G',\n 'A', 'T', 'A', 'T', '-', 'T', 'T', 'G', 'G', 'T', 'T', 'T', 'A',\n 'G', 'A', 'T', 'G', 'G', 'T', 'T', 'T', 'A', 'G', 'G', 'T', 'G',\n 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'T', 'T', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', 'G', 'C', 'C', 'A', 'T', 'G', 'A',\n 'A', 'T', 'A', 'T', '-', '-', '-', '-', '-', 'T', 'T', 'T', 'A',\n 'G', 'A', 'C', '-', 'A', 'T', 'G', 'C', 'A', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'G', 'T', 'G', 'T', 'T', 'T', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'a', 'G', 'C', 'A', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'T', 'T', 'T', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'a', 'G', 'C', 'A', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'T', 'T', 'T', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'a', 'G', 'C', 'A', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'T', 'T', 'T', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'A',\n 'G', 'A', 'A', 'A', '-', 'T', 'G', 'T', 'G', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'G', 'C', 'A', 'T', 'C', 'G', 'C', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'A',\n 'G', 'A', 'A', 'A', '-', 'T', 'T', 'T', 'A', 'G', 'G', 'T', 'G',\n 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'G', 'T', 'T', 'C', '-'],\n ['G', 'T', 'T', '-', 'T', 'G', 'A', 'G', 'A', 'G', 'C', 'A', 'A',\n 'G', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C', 'A', 'T', 'C', 'A',\n 'A', 'T', 'A', 'C', 'G', 'T', 'T', 'G', 'T', 'T', 'T', 'C', 'A',\n 'G', 'A', 'A', 'A', '-', 'T', 'T', 'G', 'A', 'G', 'G', 'T', 'T',\n 'T', 'G', 'C', 'T', 'G', 'T', 'A', 'T', 'C', 'T', 'C', 't']],\n dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 320596)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3014842 : 3014842 + 186],\n \"CTTGGGATGCTTTATAGTGGAAATGGAAAGCAATTTATTTAGATCTTAAATCATTTTGAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCTTCATTTTTAAAATATTGCATCCTATAATACACATAAATCTTGTTCTCGtttttatttttttatttatttatttttttttcttt\",\n )\n self.assertEqual(\n alignment[0],\n \"C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGATCTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCTTCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtttttatttttt----tatt-tat-----------------------ttattttttttt------------cttt\",\n )\n self.assertEqual(alignment.sequences[1].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[1].seq), 10574)\n self.assertEqual(\n alignment.sequences[1].seq[8958 : 8958 + 245],\n \"AGATTTGGCCAAAGTCAATGAAAAAAGAGAGAGAGAGTGAACTTGCTAAGACACCTGCTTAAAAAGGGAATGAGATTTTGAAAAGATGCTGTGTGTGGTATAAAACCCAATTTTTTTTTTTAAATGAGGGTATTGTTCACAGGAATATTAAAGTGAAAATTTCATTATACTTCAAAGGGATTTATGGCCAAAAGAAACAGTGTGACTTTCACTTCAGCtttaaaaaaaaaaaaaaatcaaaaata\",\n )\n self.assertEqual(\n alignment[1],\n \"tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGCCATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCCTCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATTCCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGACTTTGGCCAAATCT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[2].seq), 10026)\n self.assertEqual(\n alignment.sequences[2].seq[1986 : 1986 + 198],\n \"agagaaagagagactaaTAAACCTGCCAGAAGAAGGAAATGAGATGTTGGAAATATGCTGTATGTGGTACAAAATCCAAACTTTTTTAAATGAGGGCATTGTTAGTAGGAATATTAATGTGATCATTTTATTATACTTCAAAAGGATTTAAGTCCTAAAGAAACAGGGTGCCTTTCATTCCAACTGTGAATATCCAAA\",\n )\n self.assertEqual(\n alignment[2],\n \"---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCCTCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATTTCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt------------ctct\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"610137772001955312362668764253688587789879568878689568989568988778987788768588885664786777656586678636299978766899797899369899566878676899958889788869976598977898999989967788999979899987999997779899\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[3].seq), 498454)\n self.assertEqual(\n alignment.sequences[3].seq[326691 : 326691 + 215],\n \"AAGTCAATAGACAAAAAGGGAACTTGCTAATAAACCTGCCAAAAAAGGAAATGAGATTTTGGAAATATGCTGTACGTGGTATAAAATCCCAGATTTTGTAAAATGAGGGCATTGTTCACAGGAATAGTAAAGTGATCATTTTATTATACTTCAAAAGGATTTAAGACCTACAGACACAGTGTGCTTTTTATTTCAGCTGTAAAAAATCCAAAAGG\",\n )\n self.assertEqual(\n alignment[3],\n \"CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGTCTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCCTCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATTTCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG------------ACTT\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"98999999989999999899999999999999999999999999999999999999999999999999989999999999999999999999999998999999999999999999988999999999739999999989999999999999999799999999999999999999769984999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 174210431)\n self.assertEqual(\n alignment.sequences[4].seq[158040700 : 158040700 + 219],\n \"AAGTAAATAAGAGAGAGAGATAACTTGCTATAAATAAACCTGCCAAGAAAGGAAATGAGATTTCAGAAATATGCTGCATGTGGTATAAAATCCAGGATTTTTTTAAAAGAGGACATTGCTCACAGGAGTATTAAAGTGATCGTTTTATTATACTTCAAAAGTATTTAAGACCTAAAGAAACAGTGTGCCTTCCATTTCAGCTATAAAAAGTCCAAAAGG\",\n )\n self.assertEqual(\n alignment[4],\n \"CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCCTCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTTCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT------------ACTT\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 173908612)\n self.assertEqual(\n alignment.sequences[5].seq[157518570 : 157518570 + 168],\n \"AAATGGGATTTCAGAAATATGCTGCATGTGGTATAAAATCCAGGATTTTTTTAAAAAGAGGGCATTGTTCACAGGAGTATTAAAGTGATCATTTTTTTATACTTCAAAAGTATTTAAGACCTAAAGAAATATTGTGCCTTCCATTTCAGCTATAAAAAGTCCAAAAGG\",\n )\n self.assertEqual(\n alignment[5],\n \"CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATTT------------------------------------------------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[6].seq), 170899992)\n self.assertEqual(\n alignment.sequences[6].seq[155028517 : 155028517 + 169],\n \"AAATGAGATTTCAGAAATATGCTGCATGTGGTATAAAATCCAGGATTTTTTTTAAAAAGAGGGCATTGTTCACAGGAGTATTAAAGTGATCATTTTTTTATACTTCAAAAGTATTTAAGACCTAAAGAAATATTGTGCCTTCCATTTCAGCTATAAAAAGTCCAAAAGG\",\n )\n self.assertEqual(\n alignment[6],\n \"CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTT------------------------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[7].seq), 133105)\n self.assertEqual(\n alignment.sequences[7].seq[6404 : 6404 + 223],\n \"TCTTTTGTATTTTTTTATAGCTGAAAAGGAAGGCACACTGTCTCTTTAGGTCTTAAATACGTTTGAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCCTCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATTTCCTTTCCTGGCAGGTTTATTAATAGCAAGTTCTCTCTCTTATTTATTTATTT\",\n )\n self.assertEqual(\n alignment[7],\n \"TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGTCTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCCTCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATTTCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT------------ATTT\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[8].seq), 359464)\n self.assertEqual(\n alignment.sequences[8].seq[174925 : 174925 + 222],\n \"GAGAAAAAGAAGAAGAAAGCCGGAGAGAACTTGCTAACAAACCCGCCAAAAAGGAAATGAGATTTTGGAAATATGCTGGATCTGGTATAAAATCCAAGATTTTTTTAAATGAGGGCATTGTTCACAGGAACAGTAAAGTAATCGTTTTATTATACTTCAAAAGGATTTAAGTCCTAAAAAAACAGTGTGCCTTTCATTTCACCCATAAAAAAGCCCAAAATA\",\n )\n self.assertEqual(\n alignment[8],\n \"TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCCTCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATTT-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT------------TCTC\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"999999999999999999999999999999999799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"ornAna1.chr2\")\n self.assertEqual(len(alignment.sequences[9].seq), 54797317)\n self.assertEqual(\n alignment.sequences[9].seq[40046122 : 40046122 + 201],\n \"AAAGAGAGAACGGTTAATACAATGCACCCAAAAAGGAACTAAGATTTTGGAAATGGGCTGTATGTCGTTAAAATACAAAGATATTTTAATGAGGGCTTTGTTAGCGGGGAAATGAAGATCATAATTACAATACACTTTTAAAAAGGCTTAAGATAGAAAGAAAACAATGAGCCTTTCACTTTTGCAGTAACATTTCCAAGG\",\n )\n self.assertEqual(\n alignment[9],\n \"--CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTATCTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCCTCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGTTCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT----------------\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 5690)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 10)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3014842, 3014843, 3014843, 3014843, 3014849, 3014849,\n 3014849, 3014851, 3014852, 3014874, 3014874, 3014875,\n 3014875, 3014899, 3014899, 3014951, 3014951, 3014951,\n 3014951, 3014951, 3014969, 3014970, 3014981, 3014981,\n 3014988, 3014988, 3014996, 3014997, 3014998, 3014999,\n 3015005, 3015005, 3015009, 3015009, 3015012, 3015012,\n 3015012, 3015012, 3015012, 3015012, 3015024, 3015024,\n 3015028],\n [ 9203, 9202, 9201, 9200, 9194, 9186,\n 9185, 9183, 9182, 9160, 9156, 9155,\n 9155, 9131, 9131, 9079, 9079, 9078,\n 9077, 9076, 9058, 9057, 9046, 9045,\n 9038, 9033, 9025, 9024, 9023, 9023,\n 9017, 9013, 9009, 9009, 9006, 9006,\n 9002, 8993, 8992, 8986, 8974, 8962,\n 8958],\n [ 2184, 2184, 2184, 2184, 2178, 2178,\n 2178, 2176, 2176, 2154, 2150, 2149,\n 2149, 2125, 2125, 2073, 2073, 2073,\n 2073, 2073, 2055, 2054, 2043, 2042,\n 2035, 2030, 2022, 2021, 2020, 2019,\n 2013, 2009, 2005, 2005, 2002, 2002,\n 2002, 2002, 2002, 2002, 1990, 1990,\n 1986],\n [ 326906, 326905, 326904, 326903, 326897, 326897,\n 326897, 326895, 326894, 326872, 326868, 326867,\n 326867, 326843, 326843, 326791, 326791, 326791,\n 326791, 326790, 326772, 326771, 326760, 326759,\n 326752, 326747, 326739, 326738, 326737, 326737,\n 326731, 326727, 326723, 326723, 326720, 326720,\n 326716, 326707, 326707, 326707, 326695, 326695,\n 326691],\n [158040919, 158040918, 158040917, 158040916, 158040910, 158040910,\n 158040910, 158040908, 158040907, 158040885, 158040881, 158040880,\n 158040880, 158040856, 158040856, 158040804, 158040804, 158040804,\n 158040804, 158040803, 158040785, 158040784, 158040773, 158040772,\n 158040765, 158040760, 158040752, 158040751, 158040750, 158040750,\n 158040744, 158040740, 158040736, 158040736, 158040733, 158040730,\n 158040726, 158040717, 158040716, 158040716, 158040704, 158040704,\n 158040700],\n [157518738, 157518737, 157518736, 157518735, 157518729, 157518729,\n 157518729, 157518727, 157518726, 157518704, 157518700, 157518699,\n 157518699, 157518675, 157518675, 157518623, 157518622, 157518622,\n 157518622, 157518621, 157518603, 157518602, 157518591, 157518590,\n 157518583, 157518578, 157518570, 157518570, 157518570, 157518570,\n 157518570, 157518570, 157518570, 157518570, 157518570, 157518570,\n 157518570, 157518570, 157518570, 157518570, 157518570, 157518570,\n 157518570],\n [155028686, 155028685, 155028684, 155028683, 155028677, 155028677,\n 155028677, 155028675, 155028674, 155028652, 155028648, 155028647,\n 155028647, 155028623, 155028623, 155028571, 155028570, 155028570,\n 155028569, 155028568, 155028550, 155028549, 155028538, 155028537,\n 155028530, 155028525, 155028517, 155028517, 155028517, 155028517,\n 155028517, 155028517, 155028517, 155028517, 155028517, 155028517,\n 155028517, 155028517, 155028517, 155028517, 155028517, 155028517,\n 155028517],\n [ 6404, 6405, 6406, 6407, 6413, 6413,\n 6414, 6416, 6417, 6439, 6443, 6444,\n 6444, 6468, 6468, 6520, 6521, 6522,\n 6523, 6524, 6542, 6543, 6554, 6555,\n 6562, 6567, 6575, 6576, 6577, 6577,\n 6583, 6587, 6591, 6591, 6594, 6597,\n 6601, 6610, 6611, 6611, 6623, 6623,\n 6627],\n [ 175147, 175146, 175145, 175144, 175138, 175138,\n 175137, 175135, 175134, 175112, 175108, 175107,\n 175107, 175083, 175083, 175031, 175031, 175031,\n 175031, 175030, 175012, 175011, 175000, 174999,\n 174992, 174987, 174979, 174979, 174978, 174978,\n 174972, 174968, 174964, 174964, 174961, 174961,\n 174957, 174948, 174947, 174941, 174929, 174929,\n 174925],\n [ 40046323, 40046323, 40046323, 40046322, 40046316, 40046316,\n 40046316, 40046314, 40046313, 40046291, 40046287, 40046286,\n 40046285, 40046261, 40046260, 40046208, 40046208, 40046208,\n 40046208, 40046208, 40046190, 40046190, 40046179, 40046178,\n 40046171, 40046166, 40046158, 40046157, 40046156, 40046156,\n 40046150, 40046146, 40046142, 40046141, 40046138, 40046138,\n 40046134, 40046134, 40046134, 40046134, 40046122, 40046122,\n 40046122],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3014842 C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGAT\nloxAfr1.s 9203 tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGC\ncavPor2.s 2184 ---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGA\ntupBel1.s 326906 CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGT\nponAbe2.c 158040919 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGT\npanTro2.c 157518738 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGT\nhg18.chr6 155028686 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGT\ncalJac1.C 6404 TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGT\notoGar1.s 175147 TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGA\nornAna1.c 40046323 --CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTAT\n\nmm9.chr10 3014886 CTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCT\nloxAfr1.s 9144 CATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCC\ncavPor2.s 2138 CTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCC\ntupBel1.s 326856 CTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCC\nponAbe2.c 158040869 CTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCC\npanTro2.c 157518688 CTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCC\nhg18.chr6 155028636 CTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCC\ncalJac1.C 6455 CTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCC\notoGar1.s 175096 CTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCC\nornAna1.c 40046274 CTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCC\n\nmm9.chr10 3014945 TCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtt\nloxAfr1.s 9085 TCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATT\ncavPor2.s 2079 TCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATT\ntupBel1.s 326797 TCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATT\nponAbe2.c 158040810 TCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATT\npanTro2.c 157518629 TCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATT\nhg18.chr6 155028577 TCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATT\ncalJac1.C 6514 TCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATT\notoGar1.s 175037 TCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATT\nornAna1.c 40046214 TCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGT\n\nmm9.chr10 3014995 tttatttttt----tatt-tat-----------------------ttattttttttt---\nloxAfr1.s 9026 CCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGAC\ncavPor2.s 2023 TCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt---\ntupBel1.s 326740 TCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG---\nponAbe2.c 158040753 TCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT---\npanTro2.c 157518571 T-----------------------------------------------------------\nhg18.chr6 155028518 T-----------------------------------------------------------\ncalJac1.C 6574 TCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT---\notoGar1.s 174980 T-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT---\nornAna1.c 40046159 TCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT---\n\nmm9.chr10 3015024 ---------cttt 3015028\nloxAfr1.s 8971 TTTGGCCAAATCT 8958\ncavPor2.s 1990 ---------ctct 1986\ntupBel1.s 326695 ---------ACTT 326691\nponAbe2.c 158040704 ---------ACTT 158040700\npanTro2.c 157518570 ------------- 157518570\nhg18.chr6 155028517 ------------- 155028517\ncalJac1.C 6623 ---------ATTT 6627\notoGar1.s 174929 ---------TCTC 174925\nornAna1.c 40046122 ------------- 40046122\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=320596.000000\ns mm9.chr10 3014842 186 + 129993255 C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGATCTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCTTCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtttttatttttt----tatt-tat-----------------------ttattttttttt------------cttt\ns loxAfr1.scaffold_75566 1371 245 - 10574 tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGCCATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCCTCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATTCCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGACTTTGGCCAAATCT\nq loxAfr1.scaffold_75566 999999999999999999999999999999999999999999999999-999999999999999999999999-9999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999-99999999999999-999---999999999999999999999999999999999999999999999999\ni loxAfr1.scaffold_75566 C 0 C 0\ns cavPor2.scaffold_216473 7842 198 - 10026 ---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCCTCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATTTCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt------------ctct\nq cavPor2.scaffold_216473 ---610137---------77-200195531236266876425368858-778987956887868956898956-8988778987788768588885664786777656586678636299978766----89979789936989956687867689995888978886997659897789899998996778899997-989-----------------------998799999777------------9899\ni cavPor2.scaffold_216473 C 0 C 0\ns tupBel1.scaffold_114895.1-498454 171548 215 - 498454 CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGTCTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCCTCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATTTCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG------------ACTT\nq tupBel1.scaffold_114895.1-498454 989999999---------899999998999999999999999999999-999999999999999999999999-9999998999999999999999999999999999899999999999999999---998899999999973999999998999999999999999979999999999999-99999997699849-999---9999999999999-------999999999999------------9999\ni tupBel1.scaffold_114895.1-498454 C 0 C 0\ns ponAbe2.chr6 16169512 219 - 174210431 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCCTCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTTCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT------------ACTT\ni ponAbe2.chr6 C 0 C 0\ns panTro2.chr6 16389874 168 - 173908612 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATTT------------------------------------------------------------------------\nq panTro2.chr6 999999999---------999999999999999999999999999999-999999999999999999999999-99999999999999999999999999999999999999999999999999999--9999999999999999999999999999999999999999999999999999------------------------------------------------------------------------\ni panTro2.chr6 C 0 C 0\ns hg18.chr6 15871306 169 - 170899992 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTT------------------------------------------------------------------------\ni hg18.chr6 C 0 C 0\ns calJac1.Contig6394 6404 223 + 133105 TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGTCTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCCTCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATTTCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT------------ATTT\ni calJac1.Contig6394 C 0 C 0\ns otoGar1.scaffold_334.1-359464 184317 222 - 359464 TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCCTCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATTT-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT------------TCTC\nq otoGar1.scaffold_334.1-359464 999999999--------9999999999999999999999997999999-999999999999999999999999-9999999999999999999999999999999999999999999999999999---9999999999999999999999999999999999999999999999999999-9-99999999999999-999---99999999999999999999999999999999------------9999\ni otoGar1.scaffold_334.1-359464 C 0 C 0\ns ornAna1.chr2 14750994 201 - 54797317 --CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTATCTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCCTCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGTTCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT----------------\ni ornAna1.chr2 N 0 I 5690\ne echTel1.scaffold_288249 87661 7564 + 100002 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, -36127)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3015028 : 3015028 + 58],\n \"ccattttttattaggtatttagctcatttacatttccaatgctataccaaaagtcccc\",\n )\n self.assertEqual(\n alignment[0],\n \"ccatttt----------ttattaggtatttagctcatttacatttccaatgctatac----caaaagtcccc\",\n )\n self.assertEqual(alignment.sequences[1].id, \"loxAfr1.scaffold_75566\")\n self.assertEqual(len(alignment.sequences[1].seq), 10574)\n self.assertEqual(\n alignment.sequences[1].seq[8925 : 8925 + 33],\n \"GAGAACTTTTGTAAGGAATGGAGGTAGAAGTGA\",\n )\n self.assertEqual(\n alignment[1],\n \"TCACTTCTA---------------------------------------CCTCCATTCCTTACAAAAGTTCTC\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[2].seq), 10026)\n self.assertEqual(alignment.sequences[2].seq[1978 : 1978 + 8], \"agacacag\")\n self.assertEqual(\n alignment[2],\n \"ctgtgtc----------t------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"quality\"], \"67889899\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 1372)\n self.assertEqual(alignment.sequences[3].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[3].seq), 498454)\n self.assertEqual(alignment.sequences[3].seq[326690 : 326690 + 1], \"A\")\n self.assertEqual(\n alignment[3],\n \"T-----------------------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"quality\"], \"9\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 2374)\n self.assertEqual(alignment.sequences[4].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 174210431)\n self.assertEqual(\n alignment.sequences[4].seq[158040688 : 158040688 + 12], \"GAAAAGGCAAAA\"\n )\n self.assertEqual(\n alignment[4],\n \"TTTTGCCTTTTC------------------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 75)\n self.assertEqual(alignment.sequences[5].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[5].seq), 133105)\n self.assertEqual(\n alignment.sequences[5].seq[6627 : 6627 + 22], \"TGCTTTTTCTCAAATCTCCACT\"\n )\n self.assertEqual(\n alignment[5],\n \"TGCTTTTTCTCAAATCTCCACT--------------------------------------------------\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 3479)\n self.assertEqual(alignment.sequences[6].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[6].seq), 359464)\n self.assertEqual(\n alignment.sequences[6].seq[174889 : 174889 + 36],\n \"TGGAAGTGAATATTTGGCAAAAGTCAATAGAAAAAA\",\n )\n self.assertEqual(\n alignment[6],\n \"TTTTTTCTATT------------GACTTTTGCCAAATATTCACTTCCA------------------------\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 137)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028517, 155028517))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518570, 157518570))\n self.assertEqual(status, \"C\")\n self.assertEqual(len(alignment.sequences), 7)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 4)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3015028, 3015029, 3015035, 3015035, 3015035, 3015035,\n 3015035, 3015036, 3015040, 3015041, 3015066, 3015075,\n 3015075, 3015086],\n [ 8958, 8957, 8951, 8949, 8949, 8949,\n 8949, 8949, 8949, 8949, 8949, 8940,\n 8936, 8925],\n [ 1986, 1985, 1979, 1979, 1979, 1979,\n 1979, 1978, 1978, 1978, 1978, 1978,\n 1978, 1978],\n [ 326691, 326690, 326690, 326690, 326690, 326690,\n 326690, 326690, 326690, 326690, 326690, 326690,\n 326690, 326690],\n [158040700, 158040699, 158040693, 158040691, 158040689, 158040688,\n 158040688, 158040688, 158040688, 158040688, 158040688, 158040688,\n 158040688, 158040688],\n [ 6627, 6628, 6634, 6636, 6638, 6639,\n 6644, 6645, 6649, 6649, 6649, 6649,\n 6649, 6649],\n [ 174925, 174924, 174918, 174916, 174914, 174914,\n 174914, 174914, 174914, 174914, 174889, 174889,\n 174889, 174889],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3015028 ccatttt----------ttattaggtatttagctcatttacatttccaatgctatac---\nloxAfr1.s 8958 TCACTTCTA---------------------------------------CCTCCATTCCTT\ncavPor2.s 1986 ctgtgtc----------t------------------------------------------\ntupBel1.s 326691 T-----------------------------------------------------------\nponAbe2.c 158040700 TTTTGCCTTTTC------------------------------------------------\ncalJac1.C 6627 TGCTTTTTCTCAAATCTCCACT--------------------------------------\notoGar1.s 174925 TTTTTTCTATT------------GACTTTTGCCAAATATTCACTTCCA------------\n\nmm9.chr10 3015075 -caaaagtcccc 3015086\nloxAfr1.s 8937 ACAAAAGTTCTC 8925\ncavPor2.s 1978 ------------ 1978\ntupBel1.s 326690 ------------ 326690\nponAbe2.c 158040688 ------------ 158040688\ncalJac1.C 6649 ------------ 6649\notoGar1.s 174889 ------------ 174889\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=-36127.000000\ns mm9.chr10 3015028 58 + 129993255 ccatttt----------ttattaggtatttagctcatttacatttccaatgctatac----caaaagtcccc\ns loxAfr1.scaffold_75566 1616 33 - 10574 TCACTTCTA---------------------------------------CCTCCATTCCTTACAAAAGTTCTC\nq loxAfr1.scaffold_75566 999999999---------------------------------------999999999999999999999999\ni loxAfr1.scaffold_75566 C 0 N 0\ns cavPor2.scaffold_216473 8040 8 - 10026 ctgtgtc----------t------------------------------------------------------\nq cavPor2.scaffold_216473 6788989----------9------------------------------------------------------\ni cavPor2.scaffold_216473 C 0 I 1372\ns tupBel1.scaffold_114895.1-498454 171763 1 - 498454 T-----------------------------------------------------------------------\nq tupBel1.scaffold_114895.1-498454 9-----------------------------------------------------------------------\ni tupBel1.scaffold_114895.1-498454 C 0 I 2374\ns ponAbe2.chr6 16169731 12 - 174210431 TTTTGCCTTTTC------------------------------------------------------------\ni ponAbe2.chr6 C 0 I 75\ns calJac1.Contig6394 6627 22 + 133105 TGCTTTTTCTCAAATCTCCACT--------------------------------------------------\ni calJac1.Contig6394 C 0 I 3479\ns otoGar1.scaffold_334.1-359464 184539 36 - 359464 TTTTTTCTATT------------GACTTTTGCCAAATATTCACTTCCA------------------------\nq otoGar1.scaffold_334.1-359464 99999999999------------9999999999999999999999999------------------------\ni otoGar1.scaffold_334.1-359464 C 0 I 137\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne hg18.chr6 155028517 0 + 170899992 C\ne panTro2.chr6 157518570 0 + 173908612 C\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['c', 'c', 'a', 't', 't', 't', 't', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 't', 't', 'a', 't', 't', 'a', 'g', 'g', 't',\n 'a', 't', 't', 't', 'a', 'g', 'c', 't', 'c', 'a', 't', 't', 't',\n 'a', 'c', 'a', 't', 't', 't', 'c', 'c', 'a', 'a', 't', 'g', 'c',\n 't', 'a', 't', 'a', 'c', '-', '-', '-', '-', 'c', 'a', 'a', 'a',\n 'a', 'g', 't', 'c', 'c', 'c', 'c'],\n ['T', 'C', 'A', 'C', 'T', 'T', 'C', 'T', 'A', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'T', 'C',\n 'C', 'A', 'T', 'T', 'C', 'C', 'T', 'T', 'A', 'C', 'A', 'A', 'A',\n 'A', 'G', 'T', 'T', 'C', 'T', 'C'],\n ['c', 't', 'g', 't', 'g', 't', 'c', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 't', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-'],\n ['T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-'],\n ['T', 'T', 'T', 'T', 'G', 'C', 'C', 'T', 'T', 'T', 'T', 'C', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-'],\n ['T', 'G', 'C', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C', 'A', 'A',\n 'A', 'T', 'C', 'T', 'C', 'C', 'A', 'C', 'T', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-'],\n ['T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'T', 'T', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'A', 'C',\n 'T', 'T', 'T', 'T', 'G', 'C', 'C', 'A', 'A', 'A', 'T', 'A', 'T',\n 'T', 'C', 'A', 'C', 'T', 'T', 'C', 'C', 'A', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3015086 : 3015086 + 2572],\n \"catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcccctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccgactaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagttcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctctagctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctgtgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataagatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccctggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgtaactccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcagtcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcctaggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaatgtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataaattaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgtatccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataaggctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatatatgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaaccgccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtgttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagccattctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgattaaggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaattctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccaccttcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaagatcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcagaaactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattgctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttctcctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttgaccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagttgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctcccttgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattccattggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgtagtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagagtttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaattcgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttggcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttccatcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagatctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgagaagggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggccattgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggtttaggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaagtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaattgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagccttgtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttggctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG\",\n )\n self.assertEqual(\n alignment[0],\n \"catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcccctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccgactaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagttcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctctagctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctgtgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataagatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccctggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgtaactccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcagtcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcctaggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaatgtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataaattaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgtatccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataaggctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatatatgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaaccgccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtgttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagccattctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgattaaggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaattctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccaccttcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaagatcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcagaaactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattgctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttctcctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttgaccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagttgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctcccttgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattccattggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgtagtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagagtttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaattcgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttggcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttccatcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagatctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgagaagggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggccattgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggtttaggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaagtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaattgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagccttgtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttggctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174889, 174752))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028517, 155028517))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518570, 157518570))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040688, 158040613))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3015086, 3017658]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3015086 catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcc\n\nmm9.chr10 3015146 cctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccg\n\nmm9.chr10 3015206 actaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagt\n\nmm9.chr10 3015266 tcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctct\n\nmm9.chr10 3015326 agctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctg\n\nmm9.chr10 3015386 tgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataa\n\nmm9.chr10 3015446 gatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccct\n\nmm9.chr10 3015506 ggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgta\n\nmm9.chr10 3015566 actccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcag\n\nmm9.chr10 3015626 tcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcct\n\nmm9.chr10 3015686 aggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaat\n\nmm9.chr10 3015746 gtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataa\n\nmm9.chr10 3015806 attaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgta\n\nmm9.chr10 3015866 tccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataagg\n\nmm9.chr10 3015926 ctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatata\n\nmm9.chr10 3015986 tgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaacc\n\nmm9.chr10 3016046 gccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtg\n\nmm9.chr10 3016106 ttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagcca\n\nmm9.chr10 3016166 ttctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgatta\n\nmm9.chr10 3016226 aggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaatt\n\nmm9.chr10 3016286 ctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccacct\n\nmm9.chr10 3016346 tcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaaga\n\nmm9.chr10 3016406 tcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcaga\n\nmm9.chr10 3016466 aactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattg\n\nmm9.chr10 3016526 ctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttct\n\nmm9.chr10 3016586 cctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttga\n\nmm9.chr10 3016646 ccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagt\n\nmm9.chr10 3016706 tgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctccct\n\nmm9.chr10 3016766 tgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattcc\n\nmm9.chr10 3016826 attggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgt\n\nmm9.chr10 3016886 agtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagag\n\nmm9.chr10 3016946 tttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaatt\n\nmm9.chr10 3017006 cgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttg\n\nmm9.chr10 3017066 gcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttcc\n\nmm9.chr10 3017126 atcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagat\n\nmm9.chr10 3017186 ctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgaga\n\nmm9.chr10 3017246 agggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggcca\n\nmm9.chr10 3017306 ttgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggttta\n\nmm9.chr10 3017366 ggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaa\n\nmm9.chr10 3017426 gtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaa\n\nmm9.chr10 3017486 ttgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagcctt\n\nmm9.chr10 3017546 gtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttgg\n\nmm9.chr10 3017606 ctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG 3017658\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3015086 2572 + 129993255 catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcccctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccgactaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagttcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctctagctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctgtgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataagatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccctggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgtaactccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcagtcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcctaggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaatgtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataaattaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgtatccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataaggctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatatatgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaaccgccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtgttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagccattctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgattaaggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaattctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccaccttcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaagatcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcagaaactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattgctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttctcctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttgaccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagttgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctcccttgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattccattggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgtagtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagagtttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaattcgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttggcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttccatcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagatctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgagaagggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggccattgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggtttaggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaagtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaattgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagccttgtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttggctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184575 137 - 359464 I\ne hg18.chr6 155028517 0 + 170899992 C\ne panTro2.chr6 157518570 0 + 173908612 C\ne ponAbe2.chr6 16169743 75 - 174210431 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 12170)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3017658 : 3017658 + 85],\n \"TTTTTATTTGCAGGTTTCTTTACAGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTGTTGACCTTTATCAGATTTCTGCTTTAACC\",\n )\n self.assertEqual(\n alignment[0],\n \"TTTTTATTTGCAGGTTTCTTTAC----AGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTGTTGACCTTTATCAGATTTCTGCTTTAACC\",\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155028434 : 155028434 + 83],\n \"GGTGGAAGTGGAGATTTGGGAAAAGGCAAAAAAATAAATAAGAGAGAGAGATAACTTGCTATAAATAACCCTGCCAAGAAAGG\",\n )\n self.assertEqual(\n alignment[1],\n \"CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 53)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157518487 : 157518487 + 83],\n \"GGTGGAAGTGGAGATTTGGGAAAAGGCAAAAAAATAAATAAGAGAGAGAGATAACTTGCTATAAATAACCCTGCCAAGAAAGG\",\n )\n self.assertEqual(\n alignment[2],\n \"CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 53)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174889, 174752))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040688, 158040613))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 3)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 7)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3017658, 3017681, 3017681, 3017699, 3017705, 3017743],\n [155028517, 155028494, 155028490, 155028472, 155028472, 155028434],\n [157518570, 157518547, 157518543, 157518525, 157518525, 157518487],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3017658 TTTTTATTTGCAGGTTTCTTTAC----AGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTG\nhg18.chr6 155028517 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTT\npanTro2.c 157518570 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTT\n\nmm9.chr10 3017714 TTGACCTTTATCAGATTTCTGCTTTAACC 3017743\nhg18.chr6 155028463 TTGCCTTTTCCCAAATCTCCACTTCCACC 155028434\npanTro2.c 157518516 TTGCCTTTTCCCAAATCTCCACTTCCACC 157518487\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=12170.000000\ns mm9.chr10 3017658 85 + 129993255 TTTTTATTTGCAGGTTTCTTTAC----AGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTGTTGACCTTTATCAGATTTCTGCTTTAACC\ns hg18.chr6 15871475 83 - 170899992 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC\ni hg18.chr6 C 0 I 53\ns panTro2.chr6 16390042 83 - 173908612 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC\nq panTro2.chr6 999999999999999999999999999999999999999999999------99999999999999999999999999999999999999\ni panTro2.chr6 C 0 I 53\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184575 137 - 359464 I\ne ponAbe2.chr6 16169743 75 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'T', 'G', 'C', 'A', 'G',\n 'G', 'T', 'T', 'T', 'C', 'T', 'T', 'T', 'A', 'C', '-', '-', '-',\n '-', 'A', 'G', 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'A',\n 'T', 'T', 'C', 'T', 'T', 'C', 'T', 'C', 'C', 'T', 'C', 'T', 'T',\n 'T', 'T', 'C', 'T', 'T', 'C', 'T', 'G', 'T', 'T', 'G', 'A', 'C',\n 'C', 'T', 'T', 'T', 'A', 'T', 'C', 'A', 'G', 'A', 'T', 'T', 'T',\n 'C', 'T', 'G', 'C', 'T', 'T', 'T', 'A', 'A', 'C', 'C'],\n ['C', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'G', 'G', 'C', 'A', 'G',\n 'G', 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'T', 'A', 'G', 'C',\n 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'C', 'T', 'C', 'T', 'C', 'T',\n 'C', 'T', 'C', 'T', 'T', 'A', '-', '-', '-', '-', '-', '-', 'T',\n 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'G', 'C', 'C',\n 'T', 'T', 'T', 'T', 'C', 'C', 'C', 'A', 'A', 'A', 'T', 'C', 'T',\n 'C', 'C', 'A', 'C', 'T', 'T', 'C', 'C', 'A', 'C', 'C'],\n ['C', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'G', 'G', 'C', 'A', 'G',\n 'G', 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'T', 'A', 'G', 'C',\n 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'C', 'T', 'C', 'T', 'C', 'T',\n 'C', 'T', 'C', 'T', 'T', 'A', '-', '-', '-', '-', '-', '-', 'T',\n 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'G', 'C', 'C',\n 'T', 'T', 'T', 'T', 'C', 'C', 'C', 'A', 'A', 'A', 'T', 'C', 'T',\n 'C', 'C', 'A', 'C', 'T', 'T', 'C', 'C', 'A', 'C', 'C']],\n dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3017743 : 3017743 + 418],\n \"ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggctgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaattagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaagagagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgccagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaatctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggagacctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca\",\n )\n self.assertEqual(\n alignment[0],\n \"ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggctgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaattagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaagagagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgccagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaatctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggagacctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174889, 174752))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028434, 155028381))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518487, 157518434))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040688, 158040613))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3017743, 3018161]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3017743 ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggc\n\nmm9.chr10 3017803 tgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaa\n\nmm9.chr10 3017863 ttagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaag\n\nmm9.chr10 3017923 agagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgc\n\nmm9.chr10 3017983 cagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaat\n\nmm9.chr10 3018043 ctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggaga\n\nmm9.chr10 3018103 cctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca\n\nmm9.chr10 3018161\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3017743 418 + 129993255 ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggctgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaattagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaagagagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgccagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaatctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggagacctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184575 137 - 359464 I\ne hg18.chr6 15871558 53 - 170899992 I\ne panTro2.chr6 16390125 53 - 173908612 I\ne ponAbe2.chr6 16169743 75 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'C', 'C', 'A', 'C', 'A', 'G', 'A', 'C', 'C', 'T', 'T', 'C',\n 'T', 'G', 'T', 'T', 'T', 'A', 'G', 'T', 'C', 'C', 'A', 'A', 'A',\n 'G', 'G', 'A', 'C', 'G', 'C', 'A', 'A', 'A', 'T', 'T', 'A', 'T',\n 'G', 'T', 'A', 'T', 'C', 'C', 'A', 'C', 'T', 'T', 't', 'a', 'g',\n 't', 'a', 'g', 'g', 'a', 'g', 'g', 'c', 't', 'g', 'a', 'c', 'c',\n 'c', 'g', 'c', 'a', 'g', 'c', 'c', 't', 'a', 'c', 'a', 't', 'g',\n 'a', 'a', 'c', 'c', 'a', 'g', 'g', 't', 'a', 't', 't', 't', 'c',\n 't', 'g', 'g', 'a', 'a', 'g', 'g', 'c', 'a', 'g', 'g', 'c', 't',\n 'g', 'g', 'g', 'g', 't', 't', 'g', 'a', 'a', 'a', 'g', 'a', 'g',\n 'a', 'a', 'a', 't', 't', 'a', 'g', 'a', 't', 'g', 'g', 't', 'g',\n 'a', 'g', 'a', 'a', 'a', 'a', 'g', 'a', 'a', 't', 'a', 'a', 't',\n 'g', 'a', 'g', 'g', 'c', 'c', 'a', 'a', 'g', 'a', 'c', 'a', 'a',\n 'a', 't', 't', 't', 't', 't', 'c', 't', 'c', 't', 't', 'a', 't',\n 'c', 'a', 'a', 'g', 'g', 'c', 'c', 'c', 'a', 'a', 'g', 'a', 'g',\n 'a', 'g', 't', 't', 't', 'a', 'c', 't', 'a', 'a', 'g', 'a', 'g',\n 'a', 'c', 't', 'a', 't', 'g', 'c', 't', 't', 'a', 'a', 'a', 'a',\n 'g', 'g', 'g', 'g', 'g', 'a', 'a', 'g', 'g', 'c', 'c', 'c', 'a',\n 't', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c',\n 't', 'c', 'g', 'c', 'g', 'c', 'c', 'a', 'g', 't', 'c', 't', 'a',\n 't', 'c', 'c', 't', 't', 'g', 'g', 't', 'g', 'c', 't', 't', 't',\n 'g', 't', 'c', 'a', 'c', 'c', 'a', 't', 'g', 'c', 'c', 'a', 't',\n 'c', 'a', 'g', 'c', 'a', 'c', 't', 't', 'g', 'g', 't', 'c', 'g',\n 'g', 'c', 'a', 'g', 'g', 't', 'a', 'g', 'c', 'a', 'g', 'a', 'a',\n 't', 'c', 't', 'c', 'a', 'g', 'g', 'g', 'c', 'a', 'g', 't', 't',\n 'g', 'a', 'c', 'a', 'c', 't', 't', 'c', 'a', 'a', 'a', 'a', 'g',\n 'a', 'a', 'a', 'c', 'c', 'a', 'g', 'c', 'c', 'a', 'a', 'g', 't',\n 'c', 'a', 'g', 'a', 'a', 'a', 'g', 'c', 't', 'g', 'c', 'a', 'c',\n 't', 'g', 'c', 'a', 'g', 'g', 'a', 'g', 'a', 'c', 'c', 't', 'g',\n 'c', 'a', 'c', 't', 'c', 'a', 'g', 't', 'g', 'g', 't', 'g', 'a',\n 'c', 'a', 'a', 'g', 'g', 't', 'c', 't', 'g', 't', 'a', 'c', 'c',\n 'a', 'g', 'c', 'c', 't', 'g', 'c', 't', 't', 'c', 'a', 'g', 'g',\n 'c', 't', 'g', 'g', 'g', 'g', 'g', 'a', 'g', 'g', 'c', 't', 'a',\n 'c', 'a']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 22499)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018161 : 3018161 + 69],\n \"ATCCACAAAAGAGACAAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAATTCCATTTTATTGA\",\n )\n self.assertEqual(\n alignment[0],\n \"ATCCACAAAAGAGAC-----AAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAATTCCATTTTATTGA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 173908612)\n self.assertEqual(\n alignment.sequences[1].seq[157518369 : 157518369 + 65],\n \"TCAATAAAATAAAATTGTTTTATGGTACAAACTTTTCTTATGGTTAATTGTTTTCCTTTGTAGGT\",\n )\n self.assertEqual(\n alignment[1],\n \"ACCTACAAAGG---------AAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 53)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 170899992)\n self.assertEqual(\n alignment.sequences[2].seq[155028316 : 155028316 + 65],\n \"TCAATAAAATAAAATTGTTTTATGGTACAAACTTTTCTTGTGGTTAATTGTTTTCCTTTGTAGGT\",\n )\n self.assertEqual(\n alignment[2],\n \"ACCTACAAAGG---------AAAACAATTAACCACAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 53)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158040552 : 158040552 + 61],\n \"TCAATAAAATAAAATTGTTTTATGGTACAAACTTTTCTTATGGTTAATTGTTTTCCTTTGT\",\n )\n self.assertEqual(\n alignment[3],\n \"-------------ACAAAGGAAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 75)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 97)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174889, 174752))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 4)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3018161, 3018172, 3018174, 3018176, 3018176, 3018230],\n [157518434, 157518423, 157518423, 157518423, 157518423, 157518369],\n [155028381, 155028370, 155028370, 155028370, 155028370, 155028316],\n [158040613, 158040613, 158040613, 158040611, 158040606, 158040552],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018161 ATCCACAAAAGAGAC-----AAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAA\npanTro2.c 157518434 ACCTACAAAGG---------AAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAA\nhg18.chr6 155028381 ACCTACAAAGG---------AAAACAATTAACCACAAGAAAAGTTTGTACCATAAAACAA\nponAbe2.c 158040613 -------------ACAAAGGAAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAA\n\nmm9.chr10 3018216 TTCCATTTTATTGA 3018230\npanTro2.c 157518383 TTTTATTTTATTGA 157518369\nhg18.chr6 155028330 TTTTATTTTATTGA 155028316\nponAbe2.c 158040566 TTTTATTTTATTGA 158040552\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=22499.000000\ns mm9.chr10 3018161 69 + 129993255 ATCCACAAAAGAGAC-----AAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAATTCCATTTTATTGA\ns panTro2.chr6 16390178 65 - 173908612 ACCTACAAAGG---------AAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\nq panTro2.chr6 99999999999---------999999999999999999999999999999999999999999999999999999\ni panTro2.chr6 I 53 C 0\ns hg18.chr6 15871611 65 - 170899992 ACCTACAAAGG---------AAAACAATTAACCACAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\ni hg18.chr6 I 53 C 0\ns ponAbe2.chr6 16169818 61 - 174210431 -------------ACAAAGGAAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA\ni ponAbe2.chr6 I 75 I 97\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184575 137 - 359464 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'T', 'C', 'C', 'A', 'C', 'A', 'A', 'A', 'A', 'G', 'A', 'G',\n 'A', 'C', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'G', 'A', 'A',\n 'G', 'A', 'A', 'A', 'A', 'C', 'C', 'A', 'A', 'A', 'A', 'G', 'A',\n 'A', 'A', 'A', 'G', 'A', 'T', 'T', 'G', 'T', 'A', 'G', 'C', 'T',\n 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'C', 'C', 'A',\n 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A'],\n ['A', 'C', 'C', 'T', 'A', 'C', 'A', 'A', 'A', 'G', 'G', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'A', 'C', 'A',\n 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'T', 'A', 'A', 'G', 'A',\n 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G', 'T', 'A', 'C', 'C', 'A',\n 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A'],\n ['A', 'C', 'C', 'T', 'A', 'C', 'A', 'A', 'A', 'G', 'G', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'A', 'C', 'A',\n 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'C', 'A', 'A', 'G', 'A',\n 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G', 'T', 'A', 'C', 'C', 'A',\n 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'A', 'C', 'A', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'C', 'A',\n 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'T', 'A', 'A', 'G', 'A',\n 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G', 'T', 'A', 'C', 'C', 'A',\n 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'T', 'A',\n 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 4781)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018230 : 3018230 + 129],\n \"AGGACAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATGAATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTACAGCCCCAGC\",\n )\n self.assertEqual(\n alignment[0],\n \"AGGA-CAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATGAATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTA-CAGCCCCAGC\",\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155028221 : 155028221 + 95],\n \"CATATACCTAATAAATCTATATATGTGTAAATTCTTTTTCATAATGACTATCAGAACATTGGGAGCCAGGTTCTGATATATATTGATTGGATTAT\",\n )\n self.assertEqual(\n alignment[1],\n \"ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTATGAA----------AAAGAATTTACACATATATAGATTTATTAGGTATATG\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157518274 : 157518274 + 95],\n \"catatacctaataaatctatatatgtgtaaatTCTTTTTCACAATGACTATCAGAACATTGGGAGCCAGGTTCTGATATATATTGATTGGATTAT\",\n )\n self.assertEqual(\n alignment[2],\n \"ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTGTGAA----------AAAGAatttacacatatatagatttattaggtatatg\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174889, 174752))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040552, 158040455))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 3)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 7)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3018230, 3018234, 3018234, 3018249, 3018270, 3018289,\n 3018294, 3018313, 3018323, 3018349, 3018349, 3018359],\n [155028316, 155028312, 155028311, 155028296, 155028296, 155028277,\n 155028277, 155028258, 155028258, 155028232, 155028231, 155028221],\n [157518369, 157518365, 157518364, 157518349, 157518349, 157518330,\n 157518330, 157518311, 157518311, 157518285, 157518284, 157518274],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018230 AGGA-CAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATG\nhg18.chr6 155028316 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG\npanTro2.c 157518369 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG\n\nmm9.chr10 3018289 AATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTA\nhg18.chr6 155028277 -----TTCTGATAGTCATTATGAA----------AAAGAATTTACACATATATAGATTTA\npanTro2.c 157518330 -----TTCTGATAGTCATTGTGAA----------AAAGAatttacacatatatagattta\n\nmm9.chr10 3018349 -CAGCCCCAGC 3018359\nhg18.chr6 155028232 TTAGGTATATG 155028221\npanTro2.c 157518285 ttaggtatatg 157518274\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=4781.000000\ns mm9.chr10 3018230 129 + 129993255 AGGA-CAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATGAATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTA-CAGCCCCAGC\ns hg18.chr6 15871676 95 - 170899992 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTATGAA----------AAAGAATTTACACATATATAGATTTATTAGGTATATG\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16390243 95 - 173908612 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTGTGAA----------AAAGAatttacacatatatagatttattaggtatatg\nq panTro2.chr6 99999999999999999999---------------------9999999999999999999-----9999999999999999999----------9999999999999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184575 137 - 359464 I\ne ponAbe2.chr6 16169879 97 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'G', 'G', 'A', '-', 'C', 'A', 'A', 'A', 'A', 'T', 'A', 'A',\n 'T', 'A', 'C', 'A', 'G', 'A', 't', 't', 't', 't', 't', 't', 't',\n 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't',\n 't', 'G', 'C', 'A', 'G', 'T', 'A', 'C', 'T', 'G', 'G', 'A', 'A',\n 'A', 'T', 'G', 'G', 'A', 'A', 'T', 'G', 'A', 'A', 'T', 'G', 'T',\n 'C', 'C', 'C', 'T', 'C', 'A', 'C', 'A', 'A', 'T', 'C', 'A', 'C',\n 'T', 'A', 'T', 'C', 'A', 'A', 'G', 'G', 'T', 'C', 'C', 'C', 'T',\n 'A', 'T', 'C', 'A', 'A', 'G', 'G', 'C', 'A', 'A', 'T', 'C', 'A',\n 'C', 'T', 'C', 'T', 'G', 'T', 'C', 'A', 'C', 'C', 'G', 'A', 'G',\n 'C', 'T', 'A', '-', 'C', 'A', 'G', 'C', 'C', 'C', 'C', 'A', 'G',\n 'C'],\n ['A', 'T', 'A', 'A', 'T', 'C', 'C', 'A', 'A', 'T', 'C', 'A', 'A',\n 'T', 'A', 'T', 'A', 'T', 'A', 'T', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'C', 'A', 'G', 'A', 'A', 'C', 'C', 'T', 'G', 'G', 'C',\n 'T', 'C', 'C', 'C', 'A', 'A', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'T', 'C', 'T', 'G', 'A', 'T', 'A', 'G', 'T', 'C', 'A', 'T',\n 'T', 'A', 'T', 'G', 'A', 'A', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', 'A', 'A', 'A', 'G', 'A', 'A', 'T', 'T', 'T', 'A',\n 'C', 'A', 'C', 'A', 'T', 'A', 'T', 'A', 'T', 'A', 'G', 'A', 'T',\n 'T', 'T', 'A', 'T', 'T', 'A', 'G', 'G', 'T', 'A', 'T', 'A', 'T',\n 'G'],\n ['A', 'T', 'A', 'A', 'T', 'C', 'C', 'A', 'A', 'T', 'C', 'A', 'A',\n 'T', 'A', 'T', 'A', 'T', 'A', 'T', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'C', 'A', 'G', 'A', 'A', 'C', 'C', 'T', 'G', 'G', 'C',\n 'T', 'C', 'C', 'C', 'A', 'A', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'T', 'C', 'T', 'G', 'A', 'T', 'A', 'G', 'T', 'C', 'A', 'T',\n 'T', 'G', 'T', 'G', 'A', 'A', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', 'A', 'A', 'A', 'G', 'A', 'a', 't', 't', 't', 'a',\n 'c', 'a', 'c', 'a', 't', 'a', 't', 'a', 't', 'a', 'g', 'a', 't',\n 't', 't', 'a', 't', 't', 'a', 'g', 'g', 't', 'a', 't', 'a', 't',\n 'g']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 61520)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018359 : 3018359 + 123],\n \"TTCAAACATGCATACATGCATTCATGTCTCATAATAATTATTAACATTGTCTTAGGCCAGAGGCTCGACTGCCCCAAAGCAATCCACTTAAACTGTCCCTGAGAAAGTCAttcctctccctaa\",\n )\n self.assertEqual(\n alignment[0],\n \"TT-CAAACATGCATACATGCATTCATGTCTCATAA-TAATTATTAACA-TTGTCTTAGGCCAGAGGCTCGACTGCCCCAAAGCAATCCACT-------TAAACTGTCCCTGAGAA-AGTCAttcctctccctaa\",\n )\n self.assertEqual(alignment.sequences[1].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 173908612)\n self.assertEqual(\n alignment.sequences[1].seq[157518143 : 157518143 + 131],\n \"AAAGAAAAGGATGACCCTTCCCGGAGAGAATATAAAATATGGATGGCTTAGTTTGTATCACTCAGGCCACTGACCTAAGATGACTGTTAATAATTATTTATGAGacatacacatatatttgtacatttata\",\n )\n self.assertEqual(\n alignment[1],\n \"-tataaatgtacaaatatatgtgtatgtCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 2400)\n self.assertEqual(alignment.sequences[2].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 170899992)\n self.assertEqual(\n alignment.sequences[2].seq[155028090 : 155028090 + 131],\n \"AAAGAAAAGGATGACCCTTCCCGGAGAGAATATAAAATATGGATGGCTTAGTTTGTATCATTCAGGCCACTGACCTAAGATGACTGTTAATAATTATTTATGAGACATACACATATATTTGTACGTTTATA\",\n )\n self.assertEqual(\n alignment[2],\n \"-TATAAACGTACAAATATATGTGTATGTCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAATGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 2402)\n self.assertEqual(alignment.sequences[3].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[3].seq), 359464)\n self.assertEqual(\n alignment.sequences[3].seq[174625 : 174625 + 127],\n \"TCAGAAGAAAGGATGACCCTTCACACAGGGAGGATAGGATGGGTTAGCTTGTGTCACTCGGGCCTCTAACCTAAGACAAATGTTAATAATTACTTACAGGACCTACATTTACACATACATGTATAAA\",\n )\n self.assertEqual(\n alignment[3],\n \"TT-TATACATGTATGTGTAAATGTAGGTCCTGTAAGTAATTATTAACATTTGTCTTAGGTTAGAGGCCCGAGTGACACAAGCTAACCCATCC------TATCCTCCCTGTGTGAAGGGTCATCCTTTCTTCTGA\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999667736999999999999999999999999999995666677755798899998999967967999999999589\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 137)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 2731)\n self.assertEqual(alignment.sequences[4].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 174210431)\n self.assertEqual(\n alignment.sequences[4].seq[158040326 : 158040326 + 129],\n \"AAAGAAAAGGATGACCCTTCCCAGAGAGAATATAAAATATGGATGGCTTAGTTTCTATCACTCAGGCCACTGACCTAAGATGACTGTTAATAATtatttatgacacatacacatatatttgtacattta\",\n )\n self.assertEqual(\n alignment[4],\n \"---taaatgtacaaatatatgtgtatgtgtcataaataATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATAGAAACTAAGCCATCCATATTTTATATTCTCTCTGGGAAGGGTCATCCTTTTCTTT--\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 97)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 2523)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 5)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 5)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3018359, 3018360, 3018361, 3018361, 3018393, 3018393,\n 3018405, 3018405, 3018447, 3018447, 3018447, 3018464,\n 3018464, 3018480, 3018482],\n [157518274, 157518274, 157518273, 157518272, 157518240, 157518239,\n 157518227, 157518226, 157518184, 157518183, 157518177, 157518160,\n 157518159, 157518143, 157518143],\n [155028221, 155028221, 155028220, 155028219, 155028187, 155028186,\n 155028174, 155028173, 155028131, 155028130, 155028124, 155028107,\n 155028106, 155028090, 155028090],\n [ 174752, 174751, 174750, 174750, 174718, 174717,\n 174705, 174704, 174662, 174661, 174661, 174644,\n 174643, 174627, 174625],\n [158040455, 158040455, 158040455, 158040455, 158040423, 158040422,\n 158040410, 158040409, 158040367, 158040366, 158040360, 158040343,\n 158040342, 158040326, 158040326],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018359 TT-CAAACATGCATACATGCATTCATGTCTCATAA-TAATTATTAACA-TTGTCTTAGGC\npanTro2.c 157518274 -tataaatgtacaaatatatgtgtatgtCTCATAAATAATTATTAACAGTCATCTTAGGT\nhg18.chr6 155028221 -TATAAACGTACAAATATATGTGTATGTCTCATAAATAATTATTAACAGTCATCTTAGGT\notoGar1.s 174752 TT-TATACATGTATGTGTAAATGTAGGTCCTGTAAGTAATTATTAACATTTGTCTTAGGT\nponAbe2.c 158040455 ---taaatgtacaaatatatgtgtatgtgtcataaataATTATTAACAGTCATCTTAGGT\n\nmm9.chr10 3018416 CAGAGGCTCGACTGCCCCAAAGCAATCCACT-------TAAACTGTCCCTGAGAA-AGTC\npanTro2.c 157518215 CAGTGGCCTGAGTGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTC\nhg18.chr6 155028162 CAGTGGCCTGAATGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTC\notoGar1.s 174693 TAGAGGCCCGAGTGACACAAGCTAACCCATCC------TATCCTCCCTGTGTGAAGGGTC\nponAbe2.c 158040398 CAGTGGCCTGAGTGATAGAAACTAAGCCATCCATATTTTATATTCTCTCTGGGAAGGGTC\n\nmm9.chr10 3018468 Attcctctccctaa 3018482\npanTro2.c 157518155 ATCCTTTTCTTT-- 157518143\nhg18.chr6 155028102 ATCCTTTTCTTT-- 155028090\notoGar1.s 174639 ATCCTTTCTTCTGA 174625\nponAbe2.c 158040338 ATCCTTTTCTTT-- 158040326\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=61520.000000\ns mm9.chr10 3018359 123 + 129993255 TT-CAAACATGCATACATGCATTCATGTCTCATAA-TAATTATTAACA-TTGTCTTAGGCCAGAGGCTCGACTGCCCCAAAGCAATCCACT-------TAAACTGTCCCTGAGAA-AGTCAttcctctccctaa\ns panTro2.chr6 16390338 131 - 173908612 -tataaatgtacaaatatatgtgtatgtCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--\nq panTro2.chr6 -99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--\ni panTro2.chr6 C 0 I 2400\ns hg18.chr6 15871771 131 - 170899992 -TATAAACGTACAAATATATGTGTATGTCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAATGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--\ni hg18.chr6 C 0 I 2402\ns otoGar1.scaffold_334.1-359464 184712 127 - 359464 TT-TATACATGTATGTGTAAATGTAGGTCCTGTAAGTAATTATTAACATTTGTCTTAGGTTAGAGGCCCGAGTGACACAAGCTAACCCATCC------TATCCTCCCTGTGTGAAGGGTCATCCTTTCTTCTGA\nq otoGar1.scaffold_334.1-359464 99-99999999999999999999999999999999999999999999999999667736999999999999999999999999999995666------677755798899998999967967999999999589\ni otoGar1.scaffold_334.1-359464 I 137 I 2731\ns ponAbe2.chr6 16169976 129 - 174210431 ---taaatgtacaaatatatgtgtatgtgtcataaataATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATAGAAACTAAGCCATCCATATTTTATATTCTCTCTGGGAAGGGTCATCCTTTTCTTT--\ni ponAbe2.chr6 I 97 I 2523\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'T', '-', 'C', 'A', 'A', 'A', 'C', 'A', 'T', 'G', 'C', 'A',\n 'T', 'A', 'C', 'A', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T',\n 'G', 'T', 'C', 'T', 'C', 'A', 'T', 'A', 'A', '-', 'T', 'A', 'A',\n 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', '-', 'T', 'T', 'G',\n 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'C', 'C', 'A', 'G', 'A', 'G',\n 'G', 'C', 'T', 'C', 'G', 'A', 'C', 'T', 'G', 'C', 'C', 'C', 'C',\n 'A', 'A', 'A', 'G', 'C', 'A', 'A', 'T', 'C', 'C', 'A', 'C', 'T',\n '-', '-', '-', '-', '-', '-', '-', 'T', 'A', 'A', 'A', 'C', 'T',\n 'G', 'T', 'C', 'C', 'C', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'A',\n 'G', 'T', 'C', 'A', 't', 't', 'c', 'c', 't', 'c', 't', 'c', 'c',\n 'c', 't', 'a', 'a'],\n ['-', 't', 'a', 't', 'a', 'a', 'a', 't', 'g', 't', 'a', 'c', 'a',\n 'a', 'a', 't', 'a', 't', 'a', 't', 'g', 't', 'g', 't', 'a', 't',\n 'g', 't', 'C', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'T', 'A', 'A',\n 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'G', 'T', 'C', 'A',\n 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'T', 'G',\n 'G', 'C', 'C', 'T', 'G', 'A', 'G', 'T', 'G', 'A', 'T', 'A', 'C',\n 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'G', 'C', 'C', 'A', 'T', 'C',\n 'C', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'T', 'T',\n 'C', 'T', 'C', 'T', 'C', 'C', 'G', 'G', 'G', 'A', 'A', 'G', 'G',\n 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', '-', '-'],\n ['-', 'T', 'A', 'T', 'A', 'A', 'A', 'C', 'G', 'T', 'A', 'C', 'A',\n 'A', 'A', 'T', 'A', 'T', 'A', 'T', 'G', 'T', 'G', 'T', 'A', 'T',\n 'G', 'T', 'C', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'T', 'A', 'A',\n 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'G', 'T', 'C', 'A',\n 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'T', 'G',\n 'G', 'C', 'C', 'T', 'G', 'A', 'A', 'T', 'G', 'A', 'T', 'A', 'C',\n 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'G', 'C', 'C', 'A', 'T', 'C',\n 'C', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'T', 'T',\n 'C', 'T', 'C', 'T', 'C', 'C', 'G', 'G', 'G', 'A', 'A', 'G', 'G',\n 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', '-', '-'],\n ['T', 'T', '-', 'T', 'A', 'T', 'A', 'C', 'A', 'T', 'G', 'T', 'A',\n 'T', 'G', 'T', 'G', 'T', 'A', 'A', 'A', 'T', 'G', 'T', 'A', 'G',\n 'G', 'T', 'C', 'C', 'T', 'G', 'T', 'A', 'A', 'G', 'T', 'A', 'A',\n 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'T', 'T', 'T', 'G',\n 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'T', 'A', 'G', 'A', 'G',\n 'G', 'C', 'C', 'C', 'G', 'A', 'G', 'T', 'G', 'A', 'C', 'A', 'C',\n 'A', 'A', 'G', 'C', 'T', 'A', 'A', 'C', 'C', 'C', 'A', 'T', 'C',\n 'C', '-', '-', '-', '-', '-', '-', 'T', 'A', 'T', 'C', 'C', 'T',\n 'C', 'C', 'C', 'T', 'G', 'T', 'G', 'T', 'G', 'A', 'A', 'G', 'G',\n 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'C', 'T', 'T',\n 'C', 'T', 'G', 'A'],\n ['-', '-', '-', 't', 'a', 'a', 'a', 't', 'g', 't', 'a', 'c', 'a',\n 'a', 'a', 't', 'a', 't', 'a', 't', 'g', 't', 'g', 't', 'a', 't',\n 'g', 't', 'g', 't', 'c', 'a', 't', 'a', 'a', 'a', 't', 'a', 'A',\n 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'G', 'T', 'C', 'A',\n 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'T', 'G',\n 'G', 'C', 'C', 'T', 'G', 'A', 'G', 'T', 'G', 'A', 'T', 'A', 'G',\n 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'G', 'C', 'C', 'A', 'T', 'C',\n 'C', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'T', 'T',\n 'C', 'T', 'C', 'T', 'C', 'T', 'G', 'G', 'G', 'A', 'A', 'G', 'G',\n 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'T', 'C', 'T',\n 'T', 'T', '-', '-']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018482 : 3018482 + 162],\n \"tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtccttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatggggagaggaggaaaggaggagaggggaggagaggaggggagGTAT\",\n )\n self.assertEqual(\n alignment[0],\n \"tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtccttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatggggagaggaggaaaggaggagaggggaggagaggaggggagGTAT\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3018482, 3018644]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018482 tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtcc\n\nmm9.chr10 3018542 ttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatgggg\n\nmm9.chr10 3018602 agaggaggaaaggaggagaggggaggagaggaggggagGTAT 3018644\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3018482 162 + 129993255 tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtccttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatggggagaggaggaaaggaggagaggggaggagaggaggggagGTAT\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['t', 'c', 't', 't', 'c', 'a', 't', 'c', 't', 'c', 'c', 't', 'c',\n 't', 't', 't', 't', 'c', 'c', 't', 'c', 'c', 't', 't', 't', 't',\n 't', 't', 't', 't', 't', 't', 'c', 't', 'c', 'a', 't', 't', 't',\n 'c', 't', 'c', 't', 't', 't', 'c', 't', 'c', 't', 't', 't', 'c',\n 't', 't', 't', 't', 'g', 't', 'c', 'c', 't', 't', 't', 't', 'c',\n 'c', 't', 't', 'T', 'A', 'T', 'A', 'G', 'C', 'A', 'A', 'G', 'C',\n 'A', 'A', 'G', 'G', 'C', 'A', 'A', 'G', 'T', 'A', 'G', 'T', 'C',\n 'T', 'C', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'A', 'A', 'G', 'G',\n 'C', 'A', 'T', 'g', 'g', 'a', 'g', 'a', 'g', 'a', 'a', 't', 'g',\n 'g', 'g', 'g', 'a', 'g', 'a', 'g', 'g', 'a', 'g', 'g', 'a', 'a',\n 'a', 'g', 'g', 'a', 'g', 'g', 'a', 'g', 'a', 'g', 'g', 'g', 'g',\n 'a', 'g', 'g', 'a', 'g', 'a', 'g', 'g', 'a', 'g', 'g', 'g', 'g',\n 'a', 'g', 'G', 'T', 'A', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 1520)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018644 : 3018644 + 178],\n \"AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTCTGAGTGTCAGTGATGTTCATGAGATTATCACCAGCAAGGATGGCTGACGGGAACTGCAAGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATGCACTGTTTCAGCATCT\",\n )\n self.assertEqual(\n alignment[0],\n \"AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTC---TGAGTGTCAGTGATGTTCA-TGAGATTATCACCAGCAAGGATG--GCTGACGGGAACTG---CAAGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATG--------------------------CACTGTTTCAGCATCT\",\n )\n self.assertEqual(alignment.sequences[1].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[1].seq), 125616256)\n self.assertEqual(\n alignment.sequences[1].seq[47545632 : 47545632 + 204],\n \"AAATTCTTCAATAGGGAAATTTTATATTTCATATTACAATTCTATTCTATCCATGATCTTTCCTCTCATTTTAGAGTTCTGGCTGGTGGTATTTGCTTCTGATTCCATCAACCGCATCCTTAGGAGAGGATCTCAGTATCCATCACTTACACGCATGTGAATAAACTCAATGTGCTATCCCTCCCAGGGGCATTTGCCTTTTCT\",\n )\n self.assertEqual(\n alignment[1],\n \"AGAAAAGGCAAATGCCCCTGGGAGGGA-----TAGCACATTGA--GTTTATTCACATGCGTGTAAGTGATGGATACTGAGATCCTCTCC--TAAGGATGCGGTTGATGGAATCAGAAGCAAATACCACCAGCCAGAACTCTAAAATGAGAGGAAAGATCATGGATAGAATAGAATTGTAATATGAAATATAAAATTTCCCTATTGAAGAATTT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 160)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 2)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3018644, 3018671, 3018676, 3018687, 3018689, 3018697,\n 3018697, 3018716, 3018716, 3018729, 3018731, 3018739,\n 3018739, 3018753, 3018753, 3018806, 3018806, 3018822],\n [47545836, 47545809, 47545809, 47545798, 47545798, 47545790,\n 47545787, 47545768, 47545767, 47545754, 47545754, 47545746,\n 47545744, 47545730, 47545727, 47545674, 47545648, 47545632],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018644 AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTC---TGAG\n 0 ||...||||.||...||.|||||.|.|-----|.|.|.|.|||--||.|.|||---||.|\ncanFam2.c 47545836 AGAAAAGGCAAATGCCCCTGGGAGGGA-----TAGCACATTGA--GTTTATTCACATGCG\n\nmm9.chr10 3018701 TGTCAGTGATGTTCA-TGAGATTATCACCAGCAAGGATG--GCTGACGGGAACTG---CA\n 60 |||.|||||||...|-||||||..||.||--.|||||||--|.|||.||.|.|.|---||\ncanFam2.c 47545783 TGTAAGTGATGGATACTGAGATCCTCTCC--TAAGGATGCGGTTGATGGAATCAGAAGCA\n\nmm9.chr10 3018755 AGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATG---------\n 120 |....||....||.||..||||||......|||||..|||..||.||.||.---------\ncanFam2.c 47545725 AATACCACCAGCCAGAACTCTAAAATGAGAGGAAAGATCATGGATAGAATAGAATTGTAA\n\nmm9.chr10 3018806 -----------------CACTGTTTCAGCATCT 3018822\n 180 -----------------|.||.||..||.||.| 213\ncanFam2.c 47545665 TATGAAATATAAAATTTCCCTATTGAAGAATTT 47545632\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=1520.000000\ns mm9.chr10 3018644 178 + 129993255 AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTC---TGAGTGTCAGTGATGTTCA-TGAGATTATCACCAGCAAGGATG--GCTGACGGGAACTG---CAAGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATG--------------------------CACTGTTTCAGCATCT\ns canFam2.chr1 78070420 204 - 125616256 AGAAAAGGCAAATGCCCCTGGGAGGGA-----TAGCACATTGA--GTTTATTCACATGCGTGTAAGTGATGGATACTGAGATCCTCTCC--TAAGGATGCGGTTGATGGAATCAGAAGCAAATACCACCAGCCAGAACTCTAAAATGAGAGGAAAGATCATGGATAGAATAGAATTGTAATATGAAATATAAAATTTCCCTATTGAAGAATTT\nq canFam2.chr1 999999999999999999999999999-----99999999999--99999999999999999999999999999999999999999999--99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni canFam2.chr1 N 0 I 160\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'G', 'G', 'G', 'T', 'A', 'G', 'G', 'C', 'C', 'A', 'A', 'G',\n 'T', 'G', 'C', 'C', 'T', 'T', 'G', 'G', 'G', 'A', 'A', 'G', 'T',\n 'A', 'G', 'T', 'T', 'G', 'T', 'T', 'G', 'G', 'T', 'A', 'G', 'A',\n 'C', 'T', 'G', 'A', 'A', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'T',\n 'C', '-', '-', '-', 'T', 'G', 'A', 'G', 'T', 'G', 'T', 'C', 'A',\n 'G', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'C', 'A', '-', 'T', 'G',\n 'A', 'G', 'A', 'T', 'T', 'A', 'T', 'C', 'A', 'C', 'C', 'A', 'G',\n 'C', 'A', 'A', 'G', 'G', 'A', 'T', 'G', '-', '-', 'G', 'C', 'T',\n 'G', 'A', 'C', 'G', 'G', 'G', 'A', 'A', 'C', 'T', 'G', '-', '-',\n '-', 'C', 'A', 'A', 'G', 'A', 'G', 'G', 'C', 'A', 'T', 'A', 'G',\n 'C', 'C', 'C', 'T', 'G', 'A', 'G', 'T', 'T', 'C', 'T', 'A', 'A',\n 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'G', 'A', 'A', 'A', 'C',\n 'G', 'T', 'C', 'A', 'C', 'A', 'G', 'A', 'A', 'A', 'G', 'G', 'A',\n 'T', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'C', 'A', 'C', 'T', 'G', 'T', 'T', 'T', 'C', 'A', 'G',\n 'C', 'A', 'T', 'C', 'T'],\n ['A', 'G', 'A', 'A', 'A', 'A', 'G', 'G', 'C', 'A', 'A', 'A', 'T',\n 'G', 'C', 'C', 'C', 'C', 'T', 'G', 'G', 'G', 'A', 'G', 'G', 'G',\n 'A', '-', '-', '-', '-', '-', 'T', 'A', 'G', 'C', 'A', 'C', 'A',\n 'T', 'T', 'G', 'A', '-', '-', 'G', 'T', 'T', 'T', 'A', 'T', 'T',\n 'C', 'A', 'C', 'A', 'T', 'G', 'C', 'G', 'T', 'G', 'T', 'A', 'A',\n 'G', 'T', 'G', 'A', 'T', 'G', 'G', 'A', 'T', 'A', 'C', 'T', 'G',\n 'A', 'G', 'A', 'T', 'C', 'C', 'T', 'C', 'T', 'C', 'C', '-', '-',\n 'T', 'A', 'A', 'G', 'G', 'A', 'T', 'G', 'C', 'G', 'G', 'T', 'T',\n 'G', 'A', 'T', 'G', 'G', 'A', 'A', 'T', 'C', 'A', 'G', 'A', 'A',\n 'G', 'C', 'A', 'A', 'A', 'T', 'A', 'C', 'C', 'A', 'C', 'C', 'A',\n 'G', 'C', 'C', 'A', 'G', 'A', 'A', 'C', 'T', 'C', 'T', 'A', 'A',\n 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'A', 'A', 'G',\n 'A', 'T', 'C', 'A', 'T', 'G', 'G', 'A', 'T', 'A', 'G', 'A', 'A',\n 'T', 'A', 'G', 'A', 'A', 'T', 'T', 'G', 'T', 'A', 'A', 'T', 'A',\n 'T', 'G', 'A', 'A', 'A', 'T', 'A', 'T', 'A', 'A', 'A', 'A', 'T',\n 'T', 'T', 'C', 'C', 'C', 'T', 'A', 'T', 'T', 'G', 'A', 'A', 'G',\n 'A', 'A', 'T', 'T', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 1986)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018822 : 3018822 + 110],\n \"CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACAGAAGAGAACCTAACTTGCTTAGGAGCATATGTACAGTTAATCAAGACAAAAATAAGAATGGAGACt\",\n )\n self.assertEqual(\n alignment[0],\n \"CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACA----GAAGAGAACCTAACTTG-CTTAGGAGCATATGTACAGTTAATCAAGAC-----AAAAATAAGAATGGAGACt\",\n )\n self.assertEqual(alignment.sequences[1].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[1].seq), 125616256)\n self.assertEqual(\n alignment.sequences[1].seq[47545353 : 47545353 + 119],\n \"ATTTTCCATACTTATTTTTAGTTGATCTTGCTAAATTGTGTGCATCTCTAGAAGTCGATTTGAATTCCCTTTACAATGTGGAGAATTTTAAGTGAGTAATAATGGGCAGGGAAAAAAAG\",\n )\n self.assertEqual(\n alignment[1],\n \"CTTTTTTTCCCTGCCCATTATTACTCACTTAAAATTCTCC-ACATTGTAAAGGGAATTCAAATCGACTTCTAGAGATGCACACAATTTAGCAAGATCAACTAAAAATAAGTATGGAAAAT\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 160)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 2)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3018822, 3018862, 3018863, 3018866, 3018866, 3018883,\n 3018883, 3018913, 3018913, 3018932],\n [47545472, 47545432, 47545432, 47545429, 47545425, 47545408,\n 47545407, 47545377, 47545372, 47545353],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018822 CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACA----GAAGAGAACCTA\n 0 ||...||.|..|.|...|||.|..|||||||.||..||||-|||----.|||.|||...|\ncanFam2.c 47545472 CTTTTTTTCCCTGCCCATTATTACTCACTTAAAATTCTCC-ACATTGTAAAGGGAATTCA\n\nmm9.chr10 3018878 ACTTG-CTTAGGAGCATATGTACAGTTAATCAAGAC-----AAAAATAAGAATGGAGACt\n 60 |.|.|-|||......||....|||.||.|.|||||.-----|||||||||.|||||.|..\ncanFam2.c 47545413 AATCGACTTCTAGAGATGCACACAATTTAGCAAGATCAACTAAAAATAAGTATGGAAAAT\n\nmm9.chr10 3018932 \n 120 \ncanFam2.c 47545353 \n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=1986.000000\ns mm9.chr10 3018822 110 + 129993255 CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACA----GAAGAGAACCTAACTTG-CTTAGGAGCATATGTACAGTTAATCAAGAC-----AAAAATAAGAATGGAGACt\ns canFam2.chr1 78070784 119 - 125616256 CTTTTTTTCCCTGCCCATTATTACTCACTTAAAATTCTCC-ACATTGTAAAGGGAATTCAAATCGACTTCTAGAGATGCACACAATTTAGCAAGATCAACTAAAAATAAGTATGGAAAAT\nq canFam2.chr1 9999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999\ni canFam2.chr1 I 160 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'T', 'G', 'C', 'C', 'T', 'T', 'C', 'C', 'A', 'T', 'T', 'A',\n 'C', 'G', 'A', 'T', 'T', 'T', 'A', 'C', 'T', 'G', 'A', 'T', 'C',\n 'A', 'C', 'T', 'T', 'A', 'C', 'A', 'A', 'C', 'C', 'C', 'T', 'C',\n 'C', 'C', 'A', 'C', 'A', '-', '-', '-', '-', 'G', 'A', 'A', 'G',\n 'A', 'G', 'A', 'A', 'C', 'C', 'T', 'A', 'A', 'C', 'T', 'T', 'G',\n '-', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'G', 'C', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'C', 'A', 'G', 'T', 'T', 'A', 'A', 'T', 'C',\n 'A', 'A', 'G', 'A', 'C', '-', '-', '-', '-', '-', 'A', 'A', 'A',\n 'A', 'A', 'T', 'A', 'A', 'G', 'A', 'A', 'T', 'G', 'G', 'A', 'G',\n 'A', 'C', 't'],\n ['C', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'C', 'C', 'T', 'G',\n 'C', 'C', 'C', 'A', 'T', 'T', 'A', 'T', 'T', 'A', 'C', 'T', 'C',\n 'A', 'C', 'T', 'T', 'A', 'A', 'A', 'A', 'T', 'T', 'C', 'T', 'C',\n 'C', '-', 'A', 'C', 'A', 'T', 'T', 'G', 'T', 'A', 'A', 'A', 'G',\n 'G', 'G', 'A', 'A', 'T', 'T', 'C', 'A', 'A', 'A', 'T', 'C', 'G',\n 'A', 'C', 'T', 'T', 'C', 'T', 'A', 'G', 'A', 'G', 'A', 'T', 'G',\n 'C', 'A', 'C', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'A', 'G', 'C',\n 'A', 'A', 'G', 'A', 'T', 'C', 'A', 'A', 'C', 'T', 'A', 'A', 'A',\n 'A', 'A', 'T', 'A', 'A', 'G', 'T', 'A', 'T', 'G', 'G', 'A', 'A',\n 'A', 'A', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3018932 : 3018932 + 339],\n \"gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaaaaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtgggggcatggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatccaaaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacccacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaatggcaccactcctggtccaagaatatacaaaccatgaca\",\n )\n self.assertEqual(\n alignment[0],\n \"gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaaaaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtgggggcatggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatccaaaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacccacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaatggcaccactcctggtccaagaatatacaaaccatgaca\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47545353, 47545353))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][9]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 10)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3018932, 3019271]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3018932 gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaa\n\nmm9.chr10 3018992 aaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtggggg\n\nmm9.chr10 3019052 catggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatcca\n\nmm9.chr10 3019112 aaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacc\n\nmm9.chr10 3019172 cacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaa\n\nmm9.chr10 3019232 tggcaccactcctggtccaagaatatacaaaccatgaca 3019271\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3018932 339 + 129993255 gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaaaaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtgggggcatggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatccaaaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacccacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaatggcaccactcctggtccaagaatatacaaaccatgaca\ne canFam2.chr1 47545353 0 + 125616256 C\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['g', 't', 'c', 't', 'g', 'a', 'g', 't', 't', 'a', 'g', 'g', 'g',\n 't', 't', 't', 't', 'a', 'c', 't', 'g', 'c', 't', 'g', 't', 'g',\n 'a', 'a', 'c', 'a', 'g', 'a', 'c', 'a', 'c', 'c', 'a', 't', 'g',\n 'a', 'c', 'c', 'a', 'a', 'g', 'g', 'c', 'a', 't', 'g', 't', 'c',\n 't', 't', 'a', 't', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 't',\n 't', 't', 'a', 'a', 't', 't', 'a', 'g', 'g', 'g', 'c', 't', 'g',\n 'g', 'c', 't', 't', 'a', 'c', 'a', 'g', 'a', 't', 't', 'c', 'a',\n 'g', 'a', 'g', 'g', 't', 't', 'c', 'a', 'g', 't', 'g', 'g', 'g',\n 'a', 'g', 'c', 'a', 't', 'c', 'a', 'a', 'g', 'g', 't', 'g', 'g',\n 'g', 'g', 'g', 'c', 'a', 't', 'g', 'g', 'c', 'a', 'g', 'c', 'a',\n 't', 'c', 'c', 'a', 'g', 'g', 'c', 'a', 'g', 'g', 'c', 'a', 't',\n 'g', 'g', 't', 'g', 'c', 'a', 'g', 'g', 'c', 'a', 'g', 'a', 'g',\n 'c', 't', 'g', 'a', 'g', 'a', 'g', 't', 't', 'c', 't', 'a', 'c',\n 'a', 't', 'c', 't', 't', 'c', 'a', 't', 'c', 'c', 'a', 'a', 'a',\n 'g', 'g', 'c', 't', 't', 'c', 't', 'a', 'g', 't', 'g', 'g', 'a',\n 'a', 'g', 'a', 'c', 't', 'g', 'a', 'c', 't', 't', 'c', 'c', 'a',\n 'g', 'g', 'c', 'a', 'c', 'c', 't', 'a', 'g', 'g', 'g', 't', 'g',\n 'a', 'g', 'g', 'g', 't', 'c', 't', 't', 'a', 'a', 'g', 'c', 'c',\n 'c', 'a', 'c', 'a', 'c', 'c', 'c', 'a', 'c', 'a', 'g', 't', 'g',\n 'a', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'a', 't', 't', 'c', 'c',\n 'a', 'a', 'c', 'c', 'a', 'g', 'g', 't', 'c', 'a', 'c', 'a', 'c',\n 'c', 't', 'a', 't', 't', 'c', 'c', 'a', 'a', 'c', 'a', 'a', 'g',\n 'g', 'c', 'c', 'a', 't', 'a', 'c', 'c', 't', 'c', 'c', 'a', 'a',\n 'a', 't', 'g', 'g', 'c', 'a', 'c', 'c', 'a', 'c', 't', 'c', 'c',\n 't', 'g', 'g', 't', 'c', 'c', 'a', 'a', 'g', 'a', 'a', 't', 'a',\n 't', 'a', 'c', 'a', 'a', 'a', 'c', 'c', 'a', 't', 'g', 'a', 'c',\n 'a']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 228)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019271 : 3019271 + 106],\n \"GAGACCAAATGTGGCGCTCACGTGAGGCCAGGAGTAAATCGCACACACAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG\",\n )\n self.assertEqual(\n alignment[0],\n \"GAGACCAAATG------------TGGCGCTCACG-TGAGGCCAGGAGTAAATCGCACACACAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[1].seq), 125616256)\n self.assertEqual(\n alignment.sequences[1].seq[47545247 : 47545247 + 106],\n \"CCAGGTTTGGGACCTATGTGTGTCAAGTGAATAGAAGCAGGTGGGACAGCATGTGCGTCACACATGGACACAGCCTGGACATCGTGGGGCATTTTCCATTTGCCTC\",\n )\n self.assertEqual(\n alignment[1],\n \"GAGGC-AAATGGAAAATGCCCCACGATGTCCAGGCTGTGTCCATGTGTGA--CGCACATGCTGTCC----------CACCTGCTTCTATTCACTTGACACACATAGGTCCCAAACCTGG\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 2)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019271, 3019276, 3019277, 3019282, 3019282, 3019293,\n 3019293, 3019308, 3019310, 3019324, 3019334, 3019377],\n [47545353, 47545348, 47545348, 47545343, 47545331, 47545320,\n 47545319, 47545304, 47545304, 47545290, 47545290, 47545247],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019271 GAGACCAAATG------------TGGCGCTCACG-TGAGGCCAGGAGTAAATCGCACACA\n 0 |||.|-|||||------------.|..|..||.|-||.|.|||.|.||.|--||||||..\ncanFam2.c 47545353 GAGGC-AAATGGAAAATGCCCCACGATGTCCAGGCTGTGTCCATGTGTGA--CGCACATG\n\nmm9.chr10 3019318 CAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG\n 60 |.|.||----------||.|||||....|.|.||.||.......|||...|.|||||||\ncanFam2.c 47545296 CTGTCC----------CACCTGCTTCTATTCACTTGACACACATAGGTCCCAAACCTGG\n\nmm9.chr10 3019377\n 119\ncanFam2.c 47545247\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=228.000000\ns mm9.chr10 3019271 106 + 129993255 GAGACCAAATG------------TGGCGCTCACG-TGAGGCCAGGAGTAAATCGCACACACAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG\ns canFam2.chr1 78070903 106 - 125616256 GAGGC-AAATGGAAAATGCCCCACGATGTCCAGGCTGTGTCCATGTGTGA--CGCACATGCTGTCC----------CACCTGCTTCTATTCACTTGACACACATAGGTCCCAAACCTGG\nq canFam2.chr1 99999-99999999999999999999999999999999999999999999--99999999999999----------9999999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['G', 'A', 'G', 'A', 'C', 'C', 'A', 'A', 'A', 'T', 'G', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'G', 'G',\n 'C', 'G', 'C', 'T', 'C', 'A', 'C', 'G', '-', 'T', 'G', 'A', 'G',\n 'G', 'C', 'C', 'A', 'G', 'G', 'A', 'G', 'T', 'A', 'A', 'A', 'T',\n 'C', 'G', 'C', 'A', 'C', 'A', 'C', 'A', 'C', 'A', 'G', 'C', 'C',\n 'C', 'A', 'T', 'G', 'C', 'T', 'T', 'T', 'C', 'A', 'C', 'C', 'A',\n 'T', 'C', 'T', 'G', 'C', 'T', 'A', 'G', 'G', 'G', 'T', 'G', 'C',\n 'T', 'C', 'T', 'G', 'G', 'A', 'G', 'C', 'A', 'G', 'G', 'G', 'C',\n 'A', 'G', 'G', 'C', 'T', 'T', 'C', 'T', 'A', 'A', 'C', 'C', 'T',\n 'G', 'G'],\n ['G', 'A', 'G', 'G', 'C', '-', 'A', 'A', 'A', 'T', 'G', 'G', 'A',\n 'A', 'A', 'A', 'T', 'G', 'C', 'C', 'C', 'C', 'A', 'C', 'G', 'A',\n 'T', 'G', 'T', 'C', 'C', 'A', 'G', 'G', 'C', 'T', 'G', 'T', 'G',\n 'T', 'C', 'C', 'A', 'T', 'G', 'T', 'G', 'T', 'G', 'A', '-', '-',\n 'C', 'G', 'C', 'A', 'C', 'A', 'T', 'G', 'C', 'T', 'G', 'T', 'C',\n 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A',\n 'C', 'C', 'T', 'G', 'C', 'T', 'T', 'C', 'T', 'A', 'T', 'T', 'C',\n 'A', 'C', 'T', 'T', 'G', 'A', 'C', 'A', 'C', 'A', 'C', 'A', 'T',\n 'A', 'G', 'G', 'T', 'C', 'C', 'C', 'A', 'A', 'A', 'C', 'C', 'T',\n 'G', 'G']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 10938)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019377 : 3019377 + 88],\n \"CCCCAGCATTCTGGCAGACACAGTGAAAAGAGACAGATGGTCACTAATAAAATCTGTATAAATTAGATCTCAGAGGATGGATGGACCA\",\n )\n self.assertEqual(\n alignment[0],\n \"CCCCAGCATTCTGGCAGACACAGTG-AAAAGAGACAGATGGTCACTAATAAAATCTGT-ATAAATTAG-ATCTCAGAGGATGGATGGACCA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[1].seq), 119354)\n self.assertEqual(\n alignment.sequences[1].seq[46757 : 46757 + 88],\n \"GAGTCCCATCCTCTGAGATTCTAGTTCACCACAAAGCTTACTGGTGGGCACATGCTTCTTTTTCACATTAGCTATCAGAACACTTGGG\",\n )\n self.assertEqual(\n alignment[1],\n \"CCCAAGTGTTCTGATAGCTAATGTGAAAAAGAAGCATGTGCCCACCAGTAAGCTTTGTGGTGAACTAGAATCTCAGAGGATG---GGACTC\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[2].seq), 125616256)\n self.assertEqual(\n alignment.sequences[2].seq[47545159 : 47545159 + 88],\n \"gagtcccatcctctgagattctaggtcattgcaaatctTATTAGCGGGCCCATGTTTCTTTTTCACAGAGGCAATCAGAACACTTGGG\",\n )\n self.assertEqual(\n alignment[2],\n \"CCCAAGTGTTCTGATTGCCTCTGTGAAAAAGAAACATGGGCCCGCTAATAagatttgcaatgacctagaatctcagaggatg---ggactc\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (6649, 10128))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155028090, 155025688))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157518143, 157515743))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 3)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019377, 3019402, 3019402, 3019434, 3019434, 3019443,\n 3019443, 3019456, 3019459, 3019465],\n [ 46845, 46820, 46819, 46787, 46786, 46777,\n 46776, 46763, 46763, 46757],\n [47545247, 47545222, 47545221, 47545189, 47545188, 47545179,\n 47545178, 47545165, 47545165, 47545159],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019377 CCCCAGCATTCTGGCAGACACAGTG-AAAAGAGACAGATGGTCACTAATAAAATCTGT-A\nfelCat3.s 46845 CCCAAGTGTTCTGATAGCTAATGTGAAAAAGAAGCATGTGCCCACCAGTAAGCTTTGTGG\ncanFam2.c 47545247 CCCAAGTGTTCTGATTGCCTCTGTGAAAAAGAAACATGGGCCCGCTAATAagatttgcaa\n\nmm9.chr10 3019435 TAAATTAG-ATCTCAGAGGATGGATGGACCA 3019465\nfelCat3.s 46785 TGAACTAGAATCTCAGAGGATG---GGACTC 46757\ncanFam2.c 47545187 tgacctagaatctcagaggatg---ggactc 47545159\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=10938.000000\ns mm9.chr10 3019377 88 + 129993255 CCCCAGCATTCTGGCAGACACAGTG-AAAAGAGACAGATGGTCACTAATAAAATCTGT-ATAAATTAG-ATCTCAGAGGATGGATGGACCA\ns felCat3.scaffold_205680 72509 88 - 119354 CCCAAGTGTTCTGATAGCTAATGTGAAAAAGAAGCATGTGCCCACCAGTAAGCTTTGTGGTGAACTAGAATCTCAGAGGATG---GGACTC\nq felCat3.scaffold_205680 9999999999999999999999999999999999999999999999999999999999999999999999999999999999---999999\ni felCat3.scaffold_205680 N 0 C 0\ns canFam2.chr1 78071009 88 - 125616256 CCCAAGTGTTCTGATTGCCTCTGTGAAAAAGAAACATGGGCCCGCTAATAagatttgcaatgacctagaatctcagaggatg---ggactc\nq canFam2.chr1 9999999999999999999999999999999999999999999999999999999999999999999999999999999999---999999\ni canFam2.chr1 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 6649 3479 + 133105 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 15871902 2402 - 170899992 I\ne panTro2.chr6 16390469 2400 - 173908612 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'C', 'C', 'C', 'A', 'G', 'C', 'A', 'T', 'T', 'C', 'T', 'G',\n 'G', 'C', 'A', 'G', 'A', 'C', 'A', 'C', 'A', 'G', 'T', 'G', '-',\n 'A', 'A', 'A', 'A', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'A', 'T',\n 'G', 'G', 'T', 'C', 'A', 'C', 'T', 'A', 'A', 'T', 'A', 'A', 'A',\n 'A', 'T', 'C', 'T', 'G', 'T', '-', 'A', 'T', 'A', 'A', 'A', 'T',\n 'T', 'A', 'G', '-', 'A', 'T', 'C', 'T', 'C', 'A', 'G', 'A', 'G',\n 'G', 'A', 'T', 'G', 'G', 'A', 'T', 'G', 'G', 'A', 'C', 'C', 'A'],\n ['C', 'C', 'C', 'A', 'A', 'G', 'T', 'G', 'T', 'T', 'C', 'T', 'G',\n 'A', 'T', 'A', 'G', 'C', 'T', 'A', 'A', 'T', 'G', 'T', 'G', 'A',\n 'A', 'A', 'A', 'A', 'G', 'A', 'A', 'G', 'C', 'A', 'T', 'G', 'T',\n 'G', 'C', 'C', 'C', 'A', 'C', 'C', 'A', 'G', 'T', 'A', 'A', 'G',\n 'C', 'T', 'T', 'T', 'G', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'C',\n 'T', 'A', 'G', 'A', 'A', 'T', 'C', 'T', 'C', 'A', 'G', 'A', 'G',\n 'G', 'A', 'T', 'G', '-', '-', '-', 'G', 'G', 'A', 'C', 'T', 'C'],\n ['C', 'C', 'C', 'A', 'A', 'G', 'T', 'G', 'T', 'T', 'C', 'T', 'G',\n 'A', 'T', 'T', 'G', 'C', 'C', 'T', 'C', 'T', 'G', 'T', 'G', 'A',\n 'A', 'A', 'A', 'A', 'G', 'A', 'A', 'A', 'C', 'A', 'T', 'G', 'G',\n 'G', 'C', 'C', 'C', 'G', 'C', 'T', 'A', 'A', 'T', 'A', 'a', 'g',\n 'a', 't', 't', 't', 'g', 'c', 'a', 'a', 't', 'g', 'a', 'c', 'c',\n 't', 'a', 'g', 'a', 'a', 't', 'c', 't', 'c', 'a', 'g', 'a', 'g',\n 'g', 'a', 't', 'g', '-', '-', '-', 'g', 'g', 'a', 'c', 't', 'c']],\n dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 36924)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019465 : 3019465 + 47],\n \"AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT\",\n )\n self.assertEqual(\n alignment[0], \"AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT\"\n )\n self.assertEqual(alignment.sequences[1].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[1].seq), 133105)\n self.assertEqual(\n alignment.sequences[1].seq[10128 : 10128 + 47],\n \"aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC\",\n )\n self.assertEqual(\n alignment[1], \"aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC\"\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 3479)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157515703 : 157515703 + 40],\n \"AAAACAcatcagaataacatgaaaagccatttcaaaatat\",\n )\n self.assertEqual(\n alignment[2], \"-------atattttgaaatggcttttcatgttattctgatgTGTTTT\"\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 2400)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155025648 : 155025648 + 40],\n \"AAAACAcatcagaataacatgaaaagccatttcaaaatat\",\n )\n self.assertEqual(\n alignment[3], \"-------atattttgaaatggcttttcatgttattctgatgTGTTTT\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 2402)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[4].seq), 125616256)\n self.assertEqual(\n alignment.sequences[4].seq[47545115 : 47545115 + 44],\n \"aacacacattagaacaacatgaagagctatttttaaatatacct\",\n )\n self.assertEqual(\n alignment[4], \"---aggtatatttaaaaatagctcttcatgttgttctaatgtgtgtt\"\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[5].seq), 119354)\n self.assertEqual(\n alignment.sequences[5].seq[46714 : 46714 + 43],\n \"AACACACATCAGAACAACATGAAAACTATTTTTAAAAACACGT\",\n )\n self.assertEqual(\n alignment[5], \"---ACGTGTTTTTAAAAATAG-TTTTCATGTTGTTCTGATGTGTGTT\"\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 193)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 6)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019465, 3019468, 3019472, 3019486, 3019487, 3019512],\n [ 10128, 10131, 10135, 10149, 10150, 10175],\n [157515743, 157515743, 157515743, 157515729, 157515728, 157515703],\n [155025688, 155025688, 155025688, 155025674, 155025673, 155025648],\n [ 47545159, 47545159, 47545155, 47545141, 47545140, 47545115],\n [ 46757, 46757, 46753, 46739, 46739, 46714],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019465 AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT 3019512\ncalJac1.C 10128 aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC 10175\npanTro2.c 157515743 -------atattttgaaatggcttttcatgttattctgatgTGTTTT 157515703\nhg18.chr6 155025688 -------atattttgaaatggcttttcatgttattctgatgTGTTTT 155025648\ncanFam2.c 47545159 ---aggtatatttaaaaatagctcttcatgttgttctaatgtgtgtt 47545115\nfelCat3.s 46757 ---ACGTGTTTTTAAAAATAG-TTTTCATGTTGTTCTGATGTGTGTT 46714\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=36924.000000\ns mm9.chr10 3019465 47 + 129993255 AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT\ns calJac1.Contig6394 10128 47 + 133105 aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC\ni calJac1.Contig6394 I 3479 C 0\ns panTro2.chr6 16392869 40 - 173908612 -------atattttgaaatggcttttcatgttattctgatgTGTTTT\nq panTro2.chr6 -------9999999999999999999999999999999999999999\ni panTro2.chr6 I 2400 C 0\ns hg18.chr6 15874304 40 - 170899992 -------atattttgaaatggcttttcatgttattctgatgTGTTTT\ni hg18.chr6 I 2402 C 0\ns canFam2.chr1 78071097 44 - 125616256 ---aggtatatttaaaaatagctcttcatgttgttctaatgtgtgtt\nq canFam2.chr1 ---99999999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ns felCat3.scaffold_205680 72597 43 - 119354 ---ACGTGTTTTTAAAAATAG-TTTTCATGTTGTTCTGATGTGTGTT\nq felCat3.scaffold_205680 ---999999999999999999-9999999999999999999999999\ni felCat3.scaffold_205680 C 0 I 193\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'A', 'G', 'A', 'T', 'A', 'G', 'A', 'T', 'A', 'T', 'T', 'T',\n 'A', 'G', 'A', 'A', 'G', 'T', 'A', 'G', 'C', 'T', 'T', 'T', 'T',\n 'T', 'A', 'T', 'G', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'G', 'A',\n 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'T'],\n ['a', 'a', 'c', 'a', 'T', 'C', 'T', 'A', 'T', 'A', 'T', 'T', 'T',\n 'T', 'G', 'A', 'A', 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'T', 'T',\n 'C', 'A', 'T', 'G', 'T', 'T', 'A', 'C', 'T', 'C', 'T', 'G', 'A',\n 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'C'],\n ['-', '-', '-', '-', '-', '-', '-', 'a', 't', 'a', 't', 't', 't',\n 't', 'g', 'a', 'a', 'a', 't', 'g', 'g', 'c', 't', 't', 't', 't',\n 'c', 'a', 't', 'g', 't', 't', 'a', 't', 't', 'c', 't', 'g', 'a',\n 't', 'g', 'T', 'G', 'T', 'T', 'T', 'T'],\n ['-', '-', '-', '-', '-', '-', '-', 'a', 't', 'a', 't', 't', 't',\n 't', 'g', 'a', 'a', 'a', 't', 'g', 'g', 'c', 't', 't', 't', 't',\n 'c', 'a', 't', 'g', 't', 't', 'a', 't', 't', 'c', 't', 'g', 'a',\n 't', 'g', 'T', 'G', 'T', 'T', 'T', 'T'],\n ['-', '-', '-', 'a', 'g', 'g', 't', 'a', 't', 'a', 't', 't', 't',\n 'a', 'a', 'a', 'a', 'a', 't', 'a', 'g', 'c', 't', 'c', 't', 't',\n 'c', 'a', 't', 'g', 't', 't', 'g', 't', 't', 'c', 't', 'a', 'a',\n 't', 'g', 't', 'g', 't', 'g', 't', 't'],\n ['-', '-', '-', 'A', 'C', 'G', 'T', 'G', 'T', 'T', 'T', 'T', 'T',\n 'A', 'A', 'A', 'A', 'A', 'T', 'A', 'G', '-', 'T', 'T', 'T', 'T',\n 'C', 'A', 'T', 'G', 'T', 'T', 'G', 'T', 'T', 'C', 'T', 'G', 'A',\n 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 20303)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019512 : 3019512 + 92],\n \"TGCATCATTAAGACTAGAGTTCCTTTCTGTCTTTGCTTTCTTGACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg\",\n )\n self.assertEqual(\n alignment[0],\n \"TGCATCATTAAGACTAGAGTTCCT---------------TTCTGTCTT---TGCTTTCTTG--------ACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg\",\n )\n self.assertEqual(alignment.sequences[1].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[1].seq), 133105)\n self.assertEqual(\n alignment.sequences[1].seq[10175 : 10175 + 86],\n \"CCTCATGAAGGCCCAAGTTCCTAAAACATTAATTCTCTTCCTATTTCCTAGCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC\",\n )\n self.assertEqual(\n alignment[1],\n \"--CCTCATGAAGGCCCAAGTTCCTAAA-----ACATTAATTCTCTTCC---TATTTCCTAGCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC----------------------\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157515610 : 157515610 + 93],\n \"CCAATACCCATGTGGGAATTGCTGGCGGGCAAGACCTCTTTTCTAGAAAAGAGGAAGAGAATGAATGTTTTAGGAACTTGGGCCTTAATGAAG\",\n )\n self.assertEqual(\n alignment[2],\n \"--CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155025555 : 155025555 + 93],\n \"CCAATACCCATGTGGGAATTGCTGGCGGGCAAGACCTCTTTTCTAGAAAAGAGGAAGAGAATGAATGTTTTAGGAACTTGGGCCTTAATGAAG\",\n )\n self.assertEqual(\n alignment[3],\n \"--CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[4].seq), 125616256)\n self.assertEqual(\n alignment.sequences[4].seq[47545018 : 47545018 + 97],\n \"CCGAACAAAGTAGGAATGACTGGCAGGCAAGACACTGATGAGGAAGGGTTGAAGAAAGAAAAAATATAAGCCTGTAAGAACCTGGGTTTAGATGAGG\",\n )\n self.assertEqual(\n alignment[4],\n \"--CCTCATCTAAACCCAGGTTCTTACAGGCTTATATTTTTTCTTTCTTCAACCCTTCCTCA--------TCAGTGTCTTGCCTGCCAGTCATTCCTAC-----------TTTGTTCGG\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (46714, 46521))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 5)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 7)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019512, 3019514, 3019536, 3019536, 3019536, 3019536,\n 3019545, 3019545, 3019555, 3019555, 3019555, 3019582,\n 3019584, 3019595, 3019604],\n [ 10175, 10175, 10197, 10200, 10200, 10207,\n 10216, 10216, 10226, 10232, 10234, 10261,\n 10261, 10261, 10261],\n [157515703, 157515703, 157515681, 157515678, 157515678, 157515671,\n 157515662, 157515662, 157515652, 157515652, 157515650, 157515623,\n 157515621, 157515610, 157515610],\n [155025648, 155025648, 155025626, 155025623, 155025623, 155025616,\n 155025607, 155025607, 155025597, 155025597, 155025595, 155025568,\n 155025566, 155025555, 155025555],\n [ 47545115, 47545115, 47545093, 47545090, 47545085, 47545078,\n 47545069, 47545066, 47545056, 47545056, 47545056, 47545029,\n 47545027, 47545027, 47545018],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019512 TGCATCATTAAGACTAGAGTTCCT---------------TTCTGTCTT---TGCTTTCTT\ncalJac1.C 10175 --CCTCATGAAGGCCCAAGTTCCTAAA-----ACATTAATTCTCTTCC---TATTTCCTA\npanTro2.c 157515703 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTA\nhg18.chr6 155025648 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTA\ncanFam2.c 47545115 --CCTCATCTAAACCCAGGTTCTTACAGGCTTATATTTTTTCTTTCTTCAACCCTTCCTC\n\nmm9.chr10 3019554 G--------ACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg\ncalJac1.C 10225 GCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC----------------------\npanTro2.c 157515653 G------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\nhg18.chr6 155025598 G------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\ncanFam2.c 47545057 A--------TCAGTGTCTTGCCTGCCAGTCATTCCTAC-----------TTTGTTCGG\n\nmm9.chr10 3019604\ncalJac1.C 10261\npanTro2.c 157515610\nhg18.chr6 155025555\ncanFam2.c 47545018\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=20303.000000\ns mm9.chr10 3019512 92 + 129993255 TGCATCATTAAGACTAGAGTTCCT---------------TTCTGTCTT---TGCTTTCTTG--------ACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg\ns calJac1.Contig6394 10175 86 + 133105 --CCTCATGAAGGCCCAAGTTCCTAAA-----ACATTAATTCTCTTCC---TATTTCCTAGCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC----------------------\ni calJac1.Contig6394 C 0 C 0\ns panTro2.chr6 16392909 93 - 173908612 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\nq panTro2.chr6 --9999999999999999999999999-----9999999999999999---9999999999------999999999999999999999999999999999999999999---------\ni panTro2.chr6 C 0 C 0\ns hg18.chr6 15874344 93 - 170899992 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------\ni hg18.chr6 C 0 C 0\ns canFam2.chr1 78071141 97 - 125616256 --CCTCATCTAAACCCAGGTTCTTACAGGCTTATATTTTTTCTTTCTTCAACCCTTCCTCA--------TCAGTGTCTTGCCTGCCAGTCATTCCTAC-----------TTTGTTCGG\nq canFam2.chr1 --99999999999999999999999999999999999999999999999999999999999--------99999999999999999999999999999-----------999999999\ni canFam2.chr1 C 0 C 0\ne felCat3.scaffold_205680 72640 193 - 119354 I\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'G', 'C', 'A', 'T', 'C', 'A', 'T', 'T', 'A', 'A', 'G', 'A',\n 'C', 'T', 'A', 'G', 'A', 'G', 'T', 'T', 'C', 'C', 'T', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'T', 'T', 'C', 'T', 'G', 'T', 'C', 'T', 'T', '-', '-', '-', 'T',\n 'G', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'G', '-', '-', '-', '-',\n '-', '-', '-', '-', 'A', 'C', 'A', 'G', 'G', 'G', 'C', 'C', 'A',\n 'T', 'G', 'C', 'T', 'C', 'G', 'G', 'C', 'A', 'G', 'T', 'C', 'A',\n 'T', 'T', 'C', 'T', 'T', 'A', 'G', 'A', 'C', 'T', 'G', 'C', 'T',\n 'T', 'T', 'T', 'T', 'G', 'T', 'T', 'T', 'g', 't', 't', 't', 'g',\n 'g'],\n ['-', '-', 'C', 'C', 'T', 'C', 'A', 'T', 'G', 'A', 'A', 'G', 'G',\n 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'A', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'T', 'T', 'A', 'A',\n 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'C', 'C', '-', '-', '-', 'T',\n 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'G', 'C', 'T', 'G', 'T',\n 'C', 'T', 'C', 'G', 'C', 'C', 'T', 'A', 'G', 'G', 'C', 'C', 'T',\n 'T', 'G', 'C', 'C', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A',\n 'T', 'T', 'C', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-'],\n ['-', '-', 'C', 'T', 'T', 'C', 'A', 'T', 'T', 'A', 'A', 'G', 'G',\n 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'A', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'T', 'T', 'C', 'A',\n 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'C', 'C', '-', '-', '-', 'T',\n 'C', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'G', '-', '-', '-', '-',\n '-', '-', 'A', 'A', 'A', 'A', 'G', 'A', 'G', 'G', 'T', 'C', 'T',\n 'T', 'G', 'C', 'C', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A',\n 'T', 'T', 'C', 'C', 'C', 'A', 'C', 'A', 'T', 'G', 'G', 'G', 'T',\n 'A', 'T', 'T', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-',\n '-'],\n ['-', '-', 'C', 'T', 'T', 'C', 'A', 'T', 'T', 'A', 'A', 'G', 'G',\n 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'A', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'T', 'T', 'C', 'A',\n 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'C', 'C', '-', '-', '-', 'T',\n 'C', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'G', '-', '-', '-', '-',\n '-', '-', 'A', 'A', 'A', 'A', 'G', 'A', 'G', 'G', 'T', 'C', 'T',\n 'T', 'G', 'C', 'C', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A',\n 'T', 'T', 'C', 'C', 'C', 'A', 'C', 'A', 'T', 'G', 'G', 'G', 'T',\n 'A', 'T', 'T', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-',\n '-'],\n ['-', '-', 'C', 'C', 'T', 'C', 'A', 'T', 'C', 'T', 'A', 'A', 'A',\n 'C', 'C', 'C', 'A', 'G', 'G', 'T', 'T', 'C', 'T', 'T', 'A', 'C',\n 'A', 'G', 'G', 'C', 'T', 'T', 'A', 'T', 'A', 'T', 'T', 'T', 'T',\n 'T', 'T', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'C', 'A', 'A', 'C',\n 'C', 'C', 'T', 'T', 'C', 'C', 'T', 'C', 'A', '-', '-', '-', '-',\n '-', '-', '-', '-', 'T', 'C', 'A', 'G', 'T', 'G', 'T', 'C', 'T',\n 'T', 'G', 'C', 'C', 'T', 'G', 'C', 'C', 'A', 'G', 'T', 'C', 'A',\n 'T', 'T', 'C', 'C', 'T', 'A', 'C', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'T', 'T', 'T', 'G', 'T', 'T', 'C', 'G',\n 'G']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019604 : 3019604 + 98],\n \"tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctggaactcactttgtagaccagactggccttgaactcagaaa\",\n )\n self.assertEqual(\n alignment[0],\n \"tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctggaactcactttgtagaccagactggccttgaactcagaaa\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (46714, 46521))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47545018, 47545018))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (10261, 10261))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155025555, 155025555))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][9]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157515610, 157515610))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][10]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 11)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3019604, 3019702]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019604 tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctgga\n\nmm9.chr10 3019664 actcactttgtagaccagactggccttgaactcagaaa 3019702\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3019604 98 + 129993255 tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctggaactcactttgtagaccagactggccttgaactcagaaa\ne felCat3.scaffold_205680 72640 193 - 119354 I\ne canFam2.chr1 47545018 0 + 125616256 C\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 10261 0 + 133105 C\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 155025555 0 + 170899992 C\ne panTro2.chr6 157515610 0 + 173908612 C\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['t', 't', 't', 'g', 'g', 't', 't', 't', 'g', 'g', 't', 't', 't',\n 'g', 'g', 't', 't', 't', 't', 't', 't', 'c', 'a', 'a', 'g', 'a',\n 'c', 'a', 'g', 'g', 'g', 't', 't', 't', 'c', 't', 't', 't', 'g',\n 't', 'a', 't', 'a', 'g', 't', 'c', 'c', 't', 'a', 'g', 'c', 't',\n 'g', 't', 'c', 'c', 't', 'g', 'g', 'a', 'a', 'c', 't', 'c', 'a',\n 'c', 't', 't', 't', 'g', 't', 'a', 'g', 'a', 'c', 'c', 'a', 'g',\n 'a', 'c', 't', 'g', 'g', 'c', 'c', 't', 't', 'g', 'a', 'a', 'c',\n 't', 'c', 'a', 'g', 'a', 'a', 'a']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 45)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019702 : 3019702 + 42],\n \"tctgcctgcctctgcctcccaagtcctgggattaaaggcgtg\",\n )\n self.assertEqual(\n alignment[0],\n \"tctgcctgcctctgcctcccaag--------------------------------tcctgggattaaaggcgtg\",\n )\n self.assertEqual(alignment.sequences[1].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[1].seq), 119354)\n self.assertEqual(\n alignment.sequences[1].seq[46447 : 46447 + 74],\n \"TAAACCTTTAAGAACTTGAGTTTGTTTGTTTGGttttttttaatgtttatttttgagagagagagagagacaga\",\n )\n self.assertEqual(\n alignment[1],\n \"tctgtctctctctctctctcaaaaataaacattaaaaaaaaCCAAACAAACAAACTCAAGTTCTTAAAGGTTTA\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 193)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47545018, 47545018))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (10261, 10261))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (326690, 324316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (174625, 171894))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155025555, 155025555))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157515610, 157515610))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][9]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158040326, 158037803))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 2)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 10)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n # fmt: off\n np.array([[3019702, 3019725, 3019725, 3019744],\n [ 46521, 46498, 46466, 46447],\n ])\n # fmt: on\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019702 tctgcctgcctctgcctcccaag--------------------------------tcctg\n 0 ||||.||..||||..|||.|||.--------------------------------.....\nfelCat3.s 46521 tctgtctctctctctctctcaaaaataaacattaaaaaaaaCCAAACAAACAAACTCAAG\n\nmm9.chr10 3019730 ggattaaaggcgtg 3019744\n 60 .............. 74\nfelCat3.s 46461 TTCTTAAAGGTTTA 46447\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=45.000000\ns mm9.chr10 3019702 42 + 129993255 tctgcctgcctctgcctcccaag--------------------------------tcctgggattaaaggcgtg\ns felCat3.scaffold_205680 72833 74 - 119354 tctgtctctctctctctctcaaaaataaacattaaaaaaaaCCAAACAAACAAACTCAAGTTCTTAAAGGTTTA\nq felCat3.scaffold_205680 99999999999999999999999999999999999999999999999999999999999999999999999999\ni felCat3.scaffold_205680 I 193 C 0\ne canFam2.chr1 47545018 0 + 125616256 C\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 10261 0 + 133105 C\ne tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I\ne hg18.chr6 155025555 0 + 170899992 C\ne panTro2.chr6 157515610 0 + 173908612 C\ne ponAbe2.chr6 16170105 2523 - 174210431 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['t', 'c', 't', 'g', 'c', 'c', 't', 'g', 'c', 'c', 't', 'c', 't',\n 'g', 'c', 'c', 't', 'c', 'c', 'c', 'a', 'a', 'g', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', 't', 'c', 'c', 't', 'g', 'g', 'g', 'a', 't', 't',\n 'a', 'a', 'a', 'g', 'g', 'c', 'g', 't', 'g'],\n ['t', 'c', 't', 'g', 't', 'c', 't', 'c', 't', 'c', 't', 'c', 't',\n 'c', 't', 'c', 't', 'c', 't', 'c', 'a', 'a', 'a', 'a', 'a', 't',\n 'a', 'a', 'a', 'c', 'a', 't', 't', 'a', 'a', 'a', 'a', 'a', 'a',\n 'a', 'a', 'C', 'C', 'A', 'A', 'A', 'C', 'A', 'A', 'A', 'C', 'A',\n 'A', 'A', 'C', 'T', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'T', 'T',\n 'A', 'A', 'A', 'G', 'G', 'T', 'T', 'T', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, -16865)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019744 : 3019744 + 33],\n \"cgccaccactgccctgcCTTAAACTGCTCTTAA\",\n )\n self.assertEqual(\n alignment[0],\n \"-----------------cgccaccactgccctgcCT------------TAAACTGCTCTTAA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 174210431)\n self.assertEqual(\n alignment.sequences[1].seq[158037776 : 158037776 + 27],\n \"CCAATACCCATGTGGGAATTGCTGGCG\",\n )\n self.assertEqual(\n alignment[1],\n \"-----------------CGCCAGCAATTCC------------------CACATGGGTATTGG\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 2523)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[2].seq), 498454)\n self.assertEqual(alignment.sequences[2].seq[324312 : 324312 + 4], \"TCAA\")\n self.assertEqual(\n alignment[2],\n \"----------------------------------------------------------TTGA\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"quality\"], \"9999\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 2374)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[3].seq), 133105)\n self.assertEqual(\n alignment.sequences[3].seq[10261 : 10261 + 13], \"ACATGGCTACTGG\"\n )\n self.assertEqual(\n alignment[3],\n \"-------------------------------------------------ACATGGCTACTGG\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[4].seq), 359464)\n self.assertEqual(\n alignment.sequences[4].seq[171883 : 171883 + 11], \"TCAACACCAAT\"\n )\n self.assertEqual(\n alignment[4],\n \"---------------------------------------------------ATTGGTGTTGA\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"quality\"], \"87784564678\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 2731)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[5].seq), 4726)\n self.assertEqual(\n alignment.sequences[5].seq[4493 : 4493 + 41],\n \"TCAACACCCCTATGGGACCTGAGACAGGCAAGACAATGGTG\",\n )\n self.assertEqual(\n alignment[5],\n \"--------------------CACCATTGTCTTGCCTGTC-TCAGGTCCCATAGGGGTGTTGA\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[6].seq), 119354)\n self.assertEqual(\n alignment.sequences[6].seq[46385 : 46385 + 62],\n \"TCTACACCAATGTGGGAATGACTGAAAGACAAGACACTGATGAGTAAGAGAAAGAGAAATCA\",\n )\n self.assertEqual(\n alignment[6],\n \"TGATTTCTCTTTCTCTTACTCATCAGTGTCTTGTCTTTCAGTCATTCCCACATTGGTGTAGA\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47545018, 47545018))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155025555, 155025555))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157515610, 157515610))\n self.assertEqual(status, \"C\")\n self.assertEqual(len(alignment.sequences), 7)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019744, 3019744, 3019747, 3019757, 3019763, 3019763,\n 3019763, 3019763, 3019764, 3019766, 3019773, 3019777],\n [158037803, 158037803, 158037800, 158037790, 158037790, 158037790,\n 158037790, 158037790, 158037789, 158037787, 158037780, 158037776],\n [ 324316, 324316, 324316, 324316, 324316, 324316,\n 324316, 324316, 324316, 324316, 324316, 324312],\n [ 10261, 10261, 10261, 10261, 10261, 10261,\n 10261, 10261, 10261, 10263, 10270, 10274],\n [ 171894, 171894, 171894, 171894, 171894, 171894,\n 171894, 171894, 171894, 171894, 171887, 171883],\n [ 4534, 4534, 4534, 4524, 4518, 4515,\n 4515, 4507, 4506, 4504, 4497, 4493],\n [ 46447, 46430, 46427, 46417, 46411, 46408,\n 46407, 46399, 46398, 46396, 46389, 46385],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019744 -----------------cgccaccactgccctgcCT------------TAAACTGCTCTT\nponAbe2.c 158037803 -----------------CGCCAGCAATTCC------------------CACATGGGTATT\ntupBel1.s 324316 ----------------------------------------------------------TT\ncalJac1.C 10261 -------------------------------------------------ACATGGCTACT\notoGar1.s 171894 ---------------------------------------------------ATTGGTGTT\noryCun1.s 4534 --------------------CACCATTGTCTTGCCTGTC-TCAGGTCCCATAGGGGTGTT\nfelCat3.s 46447 TGATTTCTCTTTCTCTTACTCATCAGTGTCTTGTCTTTCAGTCATTCCCACATTGGTGTA\n\nmm9.chr10 3019775 AA 3019777\nponAbe2.c 158037778 GG 158037776\ntupBel1.s 324314 GA 324312\ncalJac1.C 10272 GG 10274\notoGar1.s 171885 GA 171883\noryCun1.s 4495 GA 4493\nfelCat3.s 46387 GA 46385\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=-16865.000000\ns mm9.chr10 3019744 33 + 129993255 -----------------cgccaccactgccctgcCT------------TAAACTGCTCTTAA\ns ponAbe2.chr6 16172628 27 - 174210431 -----------------CGCCAGCAATTCC------------------CACATGGGTATTGG\ni ponAbe2.chr6 I 2523 C 0\ns tupBel1.scaffold_114895.1-498454 174138 4 - 498454 ----------------------------------------------------------TTGA\nq tupBel1.scaffold_114895.1-498454 ----------------------------------------------------------9999\ni tupBel1.scaffold_114895.1-498454 I 2374 C 0\ns calJac1.Contig6394 10261 13 + 133105 -------------------------------------------------ACATGGCTACTGG\ni calJac1.Contig6394 C 0 C 0\ns otoGar1.scaffold_334.1-359464 187570 11 - 359464 ---------------------------------------------------ATTGGTGTTGA\nq otoGar1.scaffold_334.1-359464 ---------------------------------------------------87784564678\ni otoGar1.scaffold_334.1-359464 I 2731 C 0\ns oryCun1.scaffold_156751 192 41 - 4726 --------------------CACCATTGTCTTGCCTGTC-TCAGGTCCCATAGGGGTGTTGA\nq oryCun1.scaffold_156751 --------------------9999999999999999999-9999999999999999999999\ni oryCun1.scaffold_156751 N 0 C 0\ns felCat3.scaffold_205680 72907 62 - 119354 TGATTTCTCTTTCTCTTACTCATCAGTGTCTTGTCTTTCAGTCATTCCCACATTGGTGTAGA\nq felCat3.scaffold_205680 99999999999999999999999999999999999999999999999999999999999999\ni felCat3.scaffold_205680 C 0 C 0\ne canFam2.chr1 47545018 0 + 125616256 C\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne hg18.chr6 155025555 0 + 170899992 C\ne panTro2.chr6 157515610 0 + 173908612 C\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'c', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c',\n 't', 'g', 'c', 'c', 'c', 't', 'g', 'c', 'C', 'T', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'A', 'A', 'A',\n 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'A', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A',\n 'T', 'T', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'C', 'A',\n 'T', 'G', 'G', 'G', 'T', 'A', 'T', 'T', 'G', 'G'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', 'T', 'T', 'G', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'C', 'A',\n 'T', 'G', 'G', 'C', 'T', 'A', 'C', 'T', 'G', 'G'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A',\n 'T', 'T', 'G', 'G', 'T', 'G', 'T', 'T', 'G', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'C', 'C', 'A', 'T',\n 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'C', 'C', 'T', 'G', 'T', 'C',\n '-', 'T', 'C', 'A', 'G', 'G', 'T', 'C', 'C', 'C', 'A', 'T', 'A',\n 'G', 'G', 'G', 'G', 'T', 'G', 'T', 'T', 'G', 'A'],\n ['T', 'G', 'A', 'T', 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'T', 'C',\n 'T', 'C', 'T', 'T', 'A', 'C', 'T', 'C', 'A', 'T', 'C', 'A', 'G',\n 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'T', 'C', 'T', 'T', 'T', 'C',\n 'A', 'G', 'T', 'C', 'A', 'T', 'T', 'C', 'C', 'C', 'A', 'C', 'A',\n 'T', 'T', 'G', 'G', 'T', 'G', 'T', 'A', 'G', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 367532)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019777 : 3019777 + 183],\n \"GGCAATGTCAGGCTATGCGTTCTAGACAGGGCACAAGAAAAGCTTTTAGCAGCAGAATAAACTTTTAAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGATACAGTGGAAAGAGGCCTTTGAGAATGCATGAGAGAATATTTCCTGTAAGAGTTGAACAATTTAGAATTTACc\",\n )\n self.assertEqual(\n alignment[0],\n \"GGCAATGTCA-GGCTATGCGT------TCTAGACAGGGCACAAGAAAAGCTTTTAGCAGCAGAATAAACTTTT-AAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGA-TACAGT------GGAAAG-----A----------GGCCTTTGAGAAT---GCATGAGAGAATAT---TTCCTGTA------AGAGTTGAACAATTTAGAATTTACc\",\n )\n self.assertEqual(alignment.sequences[1].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[1].seq), 4726)\n self.assertEqual(\n alignment.sequences[1].seq[4300 : 4300 + 193],\n \"AATCCTAAACTATTTAGCTCTGAGAAATAGGGGAAGTAATATTATTCCATCCTGATTCCCAAAAGGCTTTTTTTTTCTTTGTTGTATCACTTTGAACACTTGATTACTAGCAAGGGAAGCAGTTTCCTCTAAAGGCTTATTCTACTGGAAAAAGCTTTTCCTGTCCCTTAGAACATAAGGTCATGATGTTGCC\",\n )\n self.assertEqual(\n alignment[1],\n \"GGCAACATCATGACCTTATGT------TCTAA----GGGACAGGAAAAGCTTTTTCCAGTAGAATAAGCCTTT-AGAGGAAACTGCTTCCCTTGCTAGTAATCAAGTGTTCAAAGTGA-TACAACAAAGAAAAAAAA-----A----------GCCTTTTGGGAAT-CAGGATGGAATAATATTACTTCCCCTATTTCTCAGAGCTAAATAGTTTAGGATT----\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999899999999989999999999999999999999999999999999999999999999999999898999999989979999999999999997999999998978998999999999999999978999999979689999999999999999979\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 37)\n self.assertEqual(alignment.sequences[2].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 170899992)\n self.assertEqual(\n alignment.sequences[2].seq[155025365 : 155025365 + 190],\n \"AATCCTAAATTGTTTAACTCTTAGAAATAAGGGAAATAATATTATTCTATCCTGCATTCTCAAAAAAATTTTTCTTCATCTCACTTTGGTGACCTGATTGCTATCAAGGAAAGCAATTCCCTTTAACATTTTATTCCACTGCAAAAAGCTTTTCCTGTACTTTATCTTGAATATGTATCATGGTGTTGCC\",\n )\n self.assertEqual(\n alignment[2],\n \"GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGGAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A----------TTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 173908612)\n self.assertEqual(\n alignment.sequences[3].seq[157515419 : 157515419 + 191],\n \"AATCCTAAATTGTTTAACTCTTAGAAATAAGGGAAATAATATTATTCTATCCTGCATTCTCAAAAAAAATTTTTCTTCATCTCACTTTGGTGACCTGATTGCTATCAAGGAAAGCAATTTCCTTTAACATTTTATTCCACTGCAAAAAGCTTTTCCTGTACTTTATCTTGAATATGTATCATGGTGTTGCC\",\n )\n self.assertEqual(\n alignment[3],\n \"GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 174210431)\n self.assertEqual(\n alignment.sequences[4].seq[158037586 : 158037586 + 190],\n \"AATCCTAAATTGTTTAACTCTAGAAATAAGGGAAATAATATTATTCTGTGCTGCATTCTCAAAAAGAATTTTTCTTCATCTCACTTTGGTGACCTGATTGCTATCAAGGAAAGCAATTTCCTTTAACATTTTATTCCACCGCAAAAAGCTTTTCCTGTACTTTATCTTGAATATGTATCATGGTGTTGCC\",\n )\n self.assertEqual(\n alignment[4],\n \"GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCGGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTCTTTTTGAGAATGCAGCACAGAATAATATTATTTCCCTTATTTCT-AGAGTTAAACAATTTAGGATT----\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 21)\n self.assertEqual(alignment.sequences[5].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[5].seq), 133105)\n self.assertEqual(\n alignment.sequences[5].seq[10274 : 10274 + 187],\n \"GGCAACACCGTGATACATATCCGAGATAAAGTACAGGAAAAGCTTTTGCAGTGGACGAAAATGTTGAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGAGATGAAGAAAGTTTTTTGAGAATGTGGGATAGAATAATATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT\",\n )\n self.assertEqual(\n alignment[5],\n \"GGCAACACCGTGA-TACATAT------CCGAGATAAAGTACAGGAAAAGC-TTTTGCAGTGGACGAAAATGTT-GAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAA-----------------GTTTTTTGAGAATGTGGGATAGAATAATATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT----\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 21)\n self.assertEqual(alignment.sequences[6].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[6].seq), 359464)\n self.assertEqual(\n alignment.sequences[6].seq[171686 : 171686 + 197],\n \"AATCCTGAATTATTTAACTCTGAAATGGAGGGTGGATAAAATTATTCTTTCCAGCATTCTCAAAACATTTTTTCTTTATAATCACTTTGGTCACCTGATTGCTATCAAGAAAAGCAATTTCCTTTAACCTTTTATTCTACCGTAAAGGGCTTTTCCTGCACTTTGTCTTTATCTACAGCAAGGATCACGGCGTTGCC\",\n )\n self.assertEqual(\n alignment[6],\n \"GGCAACGCCGTGA-TCCTTGCTGTAGATAAAGACAAAGTGCAGGAAAAGCCCTTTACGGTAGAATAAAAGGTT-AAAGGAAATTGCTTTTCTTGATAGCAATCAGGTGACCAAAGTGATTATAA-------AGAAAA-----A----------ATGTTTTGAGAATGCTGGAAAGAATAATTTTATCCACCCTCCATTTCAGAGTTAAATAATTCAGGATT----\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"54667653455648997776896979788699699955776666776867789776453646557877552667697777697779896767576676677696675376877786786858478887756858859779666569356677477759968759378767656876769557597655596536566\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 358)\n self.assertEqual(alignment.sequences[7].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[7].seq), 498454)\n self.assertEqual(\n alignment.sequences[7].seq[324116 : 324116 + 196],\n \"AAGCCCAAGTTATTTAACTTAGACATAGGGAAAATAATATGCTTCTATACTGCATCCACAAAAGTTTGTTTTTGTTTTTTTTTTCAGTATGACTTTGGTCACCTGATTGCTGTCAAGGAAGGCAATTTCCTTTAAAAGTTTATCCTACTGCAAAAAGCTTTTCCTGTACTTTATCTAGAACATTCATGACATTGCC\",\n )\n self.assertEqual(\n alignment[7],\n \"GGCAATGTCATGA----ATGT------TCTAGATAAAGTACAGGAAAAGCTTTTTGCAGTAGGATAAACTTTT-AAAGGAAATTGCCTTCCTTGACAGCAATCAGGTGACCAAAGTCATACTGA-------AAAAAA-----AAACAAAAACAAACTTTTGTGGATGCAGTATAGAAGCATATTATTTTCCCTATGTCT--AAGTTAAATAACTTGGGCTT----\",\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 623)\n self.assertEqual(alignment.sequences[8].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[8].seq), 119354)\n self.assertEqual(\n alignment.sequences[8].seq[46199 : 46199 + 186],\n \"aattttaaattatttaaCTCTTAGATGTAGGGGAAATAATATTATTGTATCCTGTATTCTCAAAAAAAATTCCCTTTATATTACTTTAATCACCTAATGTCTCTTGAAGAAAGCAATTTCCTACAACATTTTATTCTACTCAAAATGCTTTTCCTGCACTTTATCTAGAATGTACTTTATGATGTC\",\n )\n self.assertEqual(\n alignment[8],\n \"GACATC---ATAA-AGTACAT------TCTAGATAAAGTGCAGGAAAAGCATTTTG-AGTAGAATAAAATGTT-GTAGGAAATTGCTTTCTTCAAGAGACATTAGGTGATTAAAGTAA-TATAA-------AGGGAA-----T----------TTTTTTTGAGAATACAGGATACAATAATATTATTTCCCCTACATCTAAGAGttaaataatttaaaatt----\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 27)\n self.assertEqual(alignment.sequences[9].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[9].seq), 125616256)\n self.assertEqual(\n alignment.sequences[9].seq[47544825 : 47544825 + 193],\n \"attaaattttaaattatttaaCTCTTAGAAGTAAGGGAAACAATATTATTCTAACTTGGATTCACTGAACTTTGTTTTTTCCCTTTATATTCCTTCAATCACCTGATTGCTCTCAAAGAAAGTAATTTCCTATTAACATTTTATCCTGTTCAAAATCCTTTTGTTGTACTTTACCCGGAATTTACATCATGAT\",\n )\n self.assertEqual(\n alignment[9],\n \"------ATCATGA-TGTAAAT------TCCGGGTAAAGTACAACAAAAGGATTTTG-AACAGGATAAAATGTTAATAGGAAATTACTTTCTTTGAGAGCAATCAGGTGATTGAAGGAA-TATAA-------AGGGAAAAAACA----------AAGTTCAGTGAATCCAAGTTAGAATAATATTGTTTCCCTTACTTCTAAGAGttaaataatttaaaatttaat\",\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 10)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 3)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3019777, 3019783, 3019786, 3019787, 3019787, 3019789,\n 3019790, 3019793, 3019797, 3019797, 3019802, 3019806,\n 3019820, 3019821, 3019826, 3019827, 3019843, 3019843,\n 3019887, 3019887, 3019892, 3019893, 3019893, 3019898,\n 3019899, 3019899, 3019900, 3019900, 3019900, 3019913,\n 3019913, 3019913, 3019927, 3019927, 3019935, 3019935,\n 3019935, 3019936, 3019956, 3019960],\n [ 4493, 4487, 4484, 4483, 4482, 4480,\n 4479, 4476, 4472, 4472, 4467, 4467,\n 4453, 4452, 4447, 4446, 4430, 4430,\n 4386, 4386, 4381, 4380, 4374, 4369,\n 4368, 4368, 4367, 4367, 4367, 4354,\n 4354, 4352, 4338, 4335, 4327, 4322,\n 4321, 4320, 4300, 4300],\n [155025555, 155025549, 155025546, 155025545, 155025544, 155025542,\n 155025542, 155025539, 155025535, 155025535, 155025530, 155025526,\n 155025512, 155025511, 155025506, 155025505, 155025489, 155025489,\n 155025445, 155025445, 155025440, 155025440, 155025440, 155025435,\n 155025434, 155025434, 155025433, 155025433, 155025433, 155025420,\n 155025419, 155025417, 155025403, 155025400, 155025392, 155025387,\n 155025386, 155025385, 155025365, 155025365],\n [157515610, 157515604, 157515601, 157515600, 157515599, 157515597,\n 157515597, 157515594, 157515590, 157515590, 157515585, 157515581,\n 157515567, 157515566, 157515561, 157515560, 157515544, 157515544,\n 157515500, 157515500, 157515495, 157515495, 157515495, 157515490,\n 157515489, 157515489, 157515488, 157515488, 157515487, 157515474,\n 157515473, 157515471, 157515457, 157515454, 157515446, 157515441,\n 157515440, 157515439, 157515419, 157515419],\n [158037776, 158037770, 158037767, 158037766, 158037765, 158037763,\n 158037763, 158037760, 158037756, 158037756, 158037751, 158037747,\n 158037733, 158037732, 158037727, 158037726, 158037710, 158037710,\n 158037666, 158037666, 158037661, 158037661, 158037661, 158037656,\n 158037655, 158037655, 158037654, 158037654, 158037653, 158037640,\n 158037639, 158037637, 158037623, 158037620, 158037612, 158037607,\n 158037607, 158037606, 158037586, 158037586],\n [ 10274, 10280, 10283, 10284, 10285, 10287,\n 10287, 10290, 10294, 10294, 10299, 10303,\n 10317, 10317, 10322, 10323, 10339, 10339,\n 10383, 10383, 10388, 10388, 10388, 10393,\n 10393, 10393, 10393, 10393, 10393, 10406,\n 10407, 10409, 10423, 10426, 10434, 10439,\n 10440, 10441, 10461, 10461],\n [ 171883, 171877, 171874, 171873, 171872, 171870,\n 171870, 171867, 171863, 171857, 171852, 171848,\n 171834, 171833, 171828, 171827, 171811, 171811,\n 171767, 171766, 171761, 171761, 171761, 171756,\n 171755, 171755, 171754, 171754, 171754, 171741,\n 171740, 171738, 171724, 171721, 171713, 171708,\n 171707, 171706, 171686, 171686],\n [ 324312, 324306, 324303, 324302, 324301, 324299,\n 324299, 324299, 324295, 324295, 324290, 324286,\n 324272, 324271, 324266, 324265, 324249, 324249,\n 324205, 324204, 324199, 324199, 324199, 324194,\n 324193, 324193, 324192, 324183, 324182, 324169,\n 324168, 324166, 324152, 324149, 324141, 324136,\n 324136, 324136, 324116, 324116],\n [ 46385, 46379, 46379, 46378, 46377, 46375,\n 46375, 46372, 46368, 46368, 46363, 46359,\n 46345, 46344, 46339, 46339, 46323, 46323,\n 46279, 46279, 46274, 46274, 46274, 46269,\n 46268, 46268, 46267, 46267, 46267, 46254,\n 46253, 46251, 46237, 46234, 46226, 46221,\n 46220, 46219, 46199, 46199],\n [ 47545018, 47545018, 47545015, 47545014, 47545013, 47545011,\n 47545011, 47545008, 47545004, 47545004, 47544999, 47544995,\n 47544981, 47544980, 47544975, 47544975, 47544959, 47544958,\n 47544914, 47544914, 47544909, 47544909, 47544909, 47544904,\n 47544903, 47544898, 47544897, 47544897, 47544897, 47544884,\n 47544883, 47544881, 47544867, 47544864, 47544856, 47544851,\n 47544850, 47544849, 47544829, 47544825],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019777 GGCAATGTCA-GGCTATGCGT------TCTAGACAGGGCACAAGAAAAGCTTTTAGCAGC\noryCun1.s 4493 GGCAACATCATGACCTTATGT------TCTAA----GGGACAGGAAAAGCTTTTTCCAGT\nhg18.chr6 155025555 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGT\npanTro2.c 157515610 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGT\nponAbe2.c 158037776 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCGGT\ncalJac1.C 10274 GGCAACACCGTGA-TACATAT------CCGAGATAAAGTACAGGAAAAGC-TTTTGCAGT\notoGar1.s 171883 GGCAACGCCGTGA-TCCTTGCTGTAGATAAAGACAAAGTGCAGGAAAAGCCCTTTACGGT\ntupBel1.s 324312 GGCAATGTCATGA----ATGT------TCTAGATAAAGTACAGGAAAAGCTTTTTGCAGT\nfelCat3.s 46385 GACATC---ATAA-AGTACAT------TCTAGATAAAGTGCAGGAAAAGCATTTTG-AGT\ncanFam2.c 47545018 ------ATCATGA-TGTAAAT------TCCGGGTAAAGTACAACAAAAGGATTTTG-AAC\n\nmm9.chr10 3019830 AGAATAAACTTTT-AAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGA-T\noryCun1.s 4443 AGAATAAGCCTTT-AGAGGAAACTGCTTCCCTTGCTAGTAATCAAGTGTTCAAAGTGA-T\nhg18.chr6 155025502 GGAATAAAATGTT-AAAGGGAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-G\npanTro2.c 157515557 GGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-G\nponAbe2.c 158037723 GGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-G\ncalJac1.C 10326 GGACGAAAATGTT-GAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGA-G\notoGar1.s 171824 AGAATAAAAGGTT-AAAGGAAATTGCTTTTCTTGATAGCAATCAGGTGACCAAAGTGATT\ntupBel1.s 324262 AGGATAAACTTTT-AAAGGAAATTGCCTTCCTTGACAGCAATCAGGTGACCAAAGTCATA\nfelCat3.s 46336 AGAATAAAATGTT-GTAGGAAATTGCTTTCTTCAAGAGACATTAGGTGATTAAAGTAA-T\ncanFam2.c 47544972 AGGATAAAATGTTAATAGGAAATTACTTTCTTTGAGAGCAATCAGGTGATTGAAGGAA-T\n\nmm9.chr10 3019888 ACAGT------GGAAAG-----A----------GGCCTTTGAGAAT---GCATGAGAGAA\noryCun1.s 4385 ACAACAAAGAAAAAAAA-----A----------GCCTTTTGGGAAT-CAGGATGGAATAA\nhg18.chr6 155025444 ATGA-------AGAAAA-----A----------TTTTTTTGAGAATGCAGGATAGAATAA\npanTro2.c 157515499 ATGA-------AGAAAA-----A---------TTTTTTTTGAGAATGCAGGATAGAATAA\nponAbe2.c 158037665 ATGA-------AGAAAA-----A---------TTCTTTTTGAGAATGCAGCACAGAATAA\ncalJac1.C 10384 ATGA-------AGAAA-----------------GTTTTTTGAGAATGTGGGATAGAATAA\notoGar1.s 171765 ATAA-------AGAAAA-----A----------ATGTTTTGAGAATGCTGGAAAGAATAA\ntupBel1.s 324203 CTGA-------AAAAAA-----AAACAAAAACAAACTTTTGTGGATGCAGTATAGAAGCA\nfelCat3.s 46278 ATAA-------AGGGAA-----T----------TTTTTTTGAGAATACAGGATACAATAA\ncanFam2.c 47544913 ATAA-------AGGGAAAAAACA----------AAGTTCAGTGAATCCAAGTTAGAATAA\n\nmm9.chr10 3019924 TAT---TTCCTGTA------AGAGTTGAACAATTTAGAATTTACc 3019960\noryCun1.s 4341 TATTACTTCCCCTATTTCTCAGAGCTAAATAGTTTAGGATT---- 4300\nhg18.chr6 155025406 TATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT---- 155025365\npanTro2.c 157515460 TATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT---- 157515419\nponAbe2.c 158037626 TATTATTTCCCTTATTTCT-AGAGTTAAACAATTTAGGATT---- 158037586\ncalJac1.C 10420 TATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT---- 10461\notoGar1.s 171727 TTTTATCCACCCTCCATTTCAGAGTTAAATAATTCAGGATT---- 171686\ntupBel1.s 324155 TATTATTTTCCCTATGTCT--AAGTTAAATAACTTGGGCTT---- 324116\nfelCat3.s 46240 TATTATTTCCCCTACATCTAAGAGttaaataatttaaaatt---- 46199\ncanFam2.c 47544870 TATTGTTTCCCTTACTTCTAAGAGttaaataatttaaaatttaat 47544825\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=367532.000000\ns mm9.chr10 3019777 183 + 129993255 GGCAATGTCA-GGCTATGCGT------TCTAGACAGGGCACAAGAAAAGCTTTTAGCAGCAGAATAAACTTTT-AAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGA-TACAGT------GGAAAG-----A----------GGCCTTTGAGAAT---GCATGAGAGAATAT---TTCCTGTA------AGAGTTGAACAATTTAGAATTTACc\ns oryCun1.scaffold_156751 233 193 - 4726 GGCAACATCATGACCTTATGT------TCTAA----GGGACAGGAAAAGCTTTTTCCAGTAGAATAAGCCTTT-AGAGGAAACTGCTTCCCTTGCTAGTAATCAAGTGTTCAAAGTGA-TACAACAAAGAAAAAAAA-----A----------GCCTTTTGGGAAT-CAGGATGGAATAATATTACTTCCCCTATTTCTCAGAGCTAAATAGTTTAGGATT----\nq oryCun1.scaffold_156751 999999999999999999999------99999----9999999999989999999998999999999999999-99999999999999999999999999999999999998989999-999899799999999999-----9----------9997999999998-978998999999999999999978999999979689999999999999999979----\ni oryCun1.scaffold_156751 C 0 I 37\ns hg18.chr6 15874437 190 - 170899992 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGGAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A----------TTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16393002 191 - 173908612 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----\nq panTro2.chr6 9999999999999-9999999------9999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999-99999-------999999-----9---------999999999999999999999999999999999999999999999999999999999999999999999----\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16172655 190 - 174210431 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCGGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTCTTTTTGAGAATGCAGCACAGAATAATATTATTTCCCTTATTTCT-AGAGTTAAACAATTTAGGATT----\ni ponAbe2.chr6 C 0 I 21\ns calJac1.Contig6394 10274 187 + 133105 GGCAACACCGTGA-TACATAT------CCGAGATAAAGTACAGGAAAAGC-TTTTGCAGTGGACGAAAATGTT-GAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAA-----------------GTTTTTTGAGAATGTGGGATAGAATAATATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT----\ni calJac1.Contig6394 C 0 I 21\ns otoGar1.scaffold_334.1-359464 187581 197 - 359464 GGCAACGCCGTGA-TCCTTGCTGTAGATAAAGACAAAGTGCAGGAAAAGCCCTTTACGGTAGAATAAAAGGTT-AAAGGAAATTGCTTTTCTTGATAGCAATCAGGTGACCAAAGTGATTATAA-------AGAAAA-----A----------ATGTTTTGAGAATGCTGGAAAGAATAATTTTATCCACCCTCCATTTCAGAGTTAAATAATTCAGGATT----\nq otoGar1.scaffold_334.1-359464 5466765345564-89977768969797886996999557766667768677897764536465578775526-67697777697779896767576676677696675376877786786858-------478887-----7----------56858859779666569356677477759968759378767656876769557597655596536566----\ni otoGar1.scaffold_334.1-359464 C 0 I 358\ns tupBel1.scaffold_114895.1-498454 174142 196 - 498454 GGCAATGTCATGA----ATGT------TCTAGATAAAGTACAGGAAAAGCTTTTTGCAGTAGGATAAACTTTT-AAAGGAAATTGCCTTCCTTGACAGCAATCAGGTGACCAAAGTCATACTGA-------AAAAAA-----AAACAAAAACAAACTTTTGTGGATGCAGTATAGAAGCATATTATTTTCCCTATGTCT--AAGTTAAATAACTTGGGCTT----\nq tupBel1.scaffold_114895.1-498454 9999999999999----9999------9999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999-------999999-----999999999999999999999999999999999999999999999999999999999--99999999999999999999----\ni tupBel1.scaffold_114895.1-498454 C 0 I 623\ns felCat3.scaffold_205680 72969 186 - 119354 GACATC---ATAA-AGTACAT------TCTAGATAAAGTGCAGGAAAAGCATTTTG-AGTAGAATAAAATGTT-GTAGGAAATTGCTTTCTTCAAGAGACATTAGGTGATTAAAGTAA-TATAA-------AGGGAA-----T----------TTTTTTTGAGAATACAGGATACAATAATATTATTTCCCCTACATCTAAGAGttaaataatttaaaatt----\nq felCat3.scaffold_205680 999999---9999-9999999------99999999999999999999999999999-9999999999999999-99999999999999999999999999999999999999999999-99999-------999999-----9----------99999999999999999999999999999999999999999999999999999999999999999999----\ni felCat3.scaffold_205680 C 0 I 27\ns canFam2.chr1 78071238 193 - 125616256 ------ATCATGA-TGTAAAT------TCCGGGTAAAGTACAACAAAAGGATTTTG-AACAGGATAAAATGTTAATAGGAAATTACTTTCTTTGAGAGCAATCAGGTGATTGAAGGAA-TATAA-------AGGGAAAAAACA----------AAGTTCAGTGAATCCAAGTTAGAATAATATTGTTTCCCTTACTTCTAAGAGttaaataatttaaaatttaat\nq canFam2.chr1 ------9999999-9999999------99999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999-99999-------999999999999----------999999999999999999999999999999999999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3019960 : 3019960 + 757],\n \"actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacagttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgagggatgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaatgcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactcaggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttgctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgcagatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggatggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccggggactaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagcagaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagagaaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccctcttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggagggagaacatttgaaatgtaaataaataaaataataaaaaa\",\n )\n self.assertEqual(\n alignment[0],\n \"actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacagttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgagggatgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaatgcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactcaggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttgctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgcagatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggatggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccggggactaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagcagaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagagaaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccctcttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggagggagaacatttgaaatgtaaataaataaaataataaaaaa\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (46199, 46172))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47544825, 47544825))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (10461, 10482))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171686, 171328))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155025365, 155025365))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][9]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157515419, 157515419))\n self.assertEqual(status, \"C\")\n empty = alignment.annotations[\"empty\"][10]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158037586, 158037565))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][11]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(record.seq), 4726)\n self.assertEqual(segment, (4300, 4263))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 12)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3019960, 3020717]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3019960 actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacag\n\nmm9.chr10 3020020 ttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgaggg\n\nmm9.chr10 3020080 atgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaat\n\nmm9.chr10 3020140 gcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactca\n\nmm9.chr10 3020200 ggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttg\n\nmm9.chr10 3020260 ctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgc\n\nmm9.chr10 3020320 agatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggat\n\nmm9.chr10 3020380 ggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccgggga\n\nmm9.chr10 3020440 ctaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagc\n\nmm9.chr10 3020500 agaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagag\n\nmm9.chr10 3020560 aaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccct\n\nmm9.chr10 3020620 cttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggaggga\n\nmm9.chr10 3020680 gaacatttgaaatgtaaataaataaaataataaaaaa 3020717\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3019960 757 + 129993255 actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacagttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgagggatgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaatgcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactcaggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttgctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgcagatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggatggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccggggactaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagcagaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagagaaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccctcttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggagggagaacatttgaaatgtaaataaataaaataataaaaaa\ne felCat3.scaffold_205680 73155 27 - 119354 I\ne canFam2.chr1 47544825 0 + 125616256 C\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 10461 21 + 133105 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 187778 358 - 359464 I\ne hg18.chr6 155025365 0 + 170899992 C\ne panTro2.chr6 157515419 0 + 173908612 C\ne ponAbe2.chr6 16172845 21 - 174210431 I\ne oryCun1.scaffold_156751 426 37 - 4726 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['a', 'c', 't', 'a', 'g', 'g', 'g', 'a', 't', 'g', 'g', 'g', 'a',\n 'g', 'a', 'g', 'g', 'c', 't', 'c', 'c', 'c', 'a', 'g', 'a', 'a',\n 'c', 'c', 'c', 'a', 'g', 't', 'a', 'a', 't', 'g', 'a', 't', 'g',\n 'a', 'c', 'a', 't', 't', 'a', 'a', 'g', 'a', 'a', 'a', 't', 'a',\n 'c', 'a', 'c', 'a', 'a', 'c', 'a', 'g', 't', 't', 'g', 'g', 'g',\n 'a', 'a', 'a', 't', 'g', 'g', 'a', 'a', 'c', 'c', 'c', 'a', 'a',\n 'a', 'g', 'a', 'g', 'a', 'a', 'c', 'a', 'c', 'c', 't', 'c', 'c',\n 'a', 'g', 't', 'a', 'g', 'a', 't', 'a', 'a', 'g', 'c', 'a', 't',\n 'g', 'a', 'c', 'c', 'c', 'c', 'c', 'a', 'g', 't', 't', 'g', 'a',\n 'g', 'g', 'g', 'a', 't', 'g', 'g', 'g', 'c', 'c', 'c', 'a', 't',\n 'g', 'c', 'a', 'c', 'c', 'c', 'a', 't', 'c', 't', 't', 'a', 'a',\n 'a', 'a', 't', 't', 't', 't', 'g', 'g', 'a', 'c', 'c', 'c', 'a',\n 'g', 'a', 'a', 't', 't', 'a', 't', 't', 'c', 't', 't', 'c', 't',\n 'c', 'a', 'a', 'a', 'a', 'g', 'g', 'a', 'a', 'a', 't', 'g', 'c',\n 'a', 'g', 'g', 'g', 'a', 't', 'g', 'a', 'a', 'a', 'a', 't', 'g',\n 'g', 'a', 'g', 'c', 'a', 'g', 'a', 'g', 'a', 'c', 't', 'g', 'g',\n 'a', 'a', 'g', 'a', 'a', 'a', 'g', 'g', 'c', 'c', 'a', 'a', 'c',\n 'c', 'a', 'g', 'a', 'g', 'a', 'c', 't', 'g', 'c', 'c', 'c', 't',\n 'a', 'a', 'c', 't', 'c', 'a', 'g', 'g', 'a', 't', 'c', 'c', 'a',\n 't', 'c', 'g', 'c', 'a', 't', 'g', 't', 'g', 'c', 'a', 'g', 'g',\n 'c', 'a', 'c', 'c', 'a', 'a', 'c', 'c', 'c', 'c', 'a', 'a', 'c',\n 'a', 'c', 't', 'a', 't', 't', 'g', 'c', 't', 'g', 'a', 't', 'g',\n 'c', 'c', 'a', 't', 'g', 't', 't', 'g', 't', 'a', 'c', 't', 't',\n 'g', 'c', 't', 'g', 'a', 't', 'g', 'g', 'a', 'a', 'g', 'c', 'c',\n 't', 'g', 'g', 'c', 'a', 't', 'g', 'g', 'c', 't', 'g', 't', 'c',\n 'c', 't', 'c', 't', 'g', 'a', 'g', 'a', 'g', 't', 'c', 't', 'c',\n 'a', 'a', 'a', 't', 'g', 'a', 'g', 'g', 'c', 'a', 'c', 'c', 't',\n 'g', 'a', 'c', 'a', 'g', 'a', 't', 'g', 'c', 'a', 'g', 'a', 't',\n 'a', 'c', 't', 't', 'a', 'c', 'a', 'g', 'c', 'c', 'a', 'a', 'c',\n 'c', 'a', 'a', 't', 'g', 'g', 'a', 'c', 't', 'g', 'a', 'g', 'c',\n 'c', 'c', 'c', 'g', 'g', 'g', 'a', 'c', 'c', 't', 'c', 'a', 'a',\n 't', 'a', 'a', 'a', 'a', 'g', 'a', 'a', 't', 'g', 'a', 'g', 'g',\n 'g', 'g', 'a', 't', 'g', 'g', 'c', 'a', 'a', 'c', 'c', 'c', 'c',\n 'a', 't', 'a', 'g', 'g', 'a', 'a', 'g', 'a', 'a', 'c', 'a', 'a',\n 'c', 'a', 'g', 't', 'a', 't', 'c', 'a', 'a', 'c', 't', 'c', 'c',\n 'c', 't', 'g', 'g', 'a', 'c', 't', 'c', 'c', 't', 'c', 'a', 'g',\n 'a', 'g', 'c', 't', 'c', 'c', 'c', 'g', 'g', 'g', 'g', 'a', 'c',\n 't', 'a', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'a', 'c', 't',\n 'a', 'a', 'a', 'g', 'a', 'g', 'c', 'a', 't', 'a', 'c', 'a', 't',\n 'a', 'g', 'g', 'c', 't', 'g', 'c', 't', 'c', 't', 'g', 'a', 'g',\n 'g', 'c', 'c', 'c', 'c', 'a', 'g', 'a', 't', 'a', 'c', 'a', 't',\n 'a', 't', 'g', 't', 'a', 'g', 'c', 'a', 'g', 'a', 'g', 'g', 'a',\n 'c', 't', 'g', 'c', 'c', 't', 'c', 'a', 'g', 't', 'g', 'g', 'g',\n 'a', 'g', 'g', 'g', 'g', 'a', 't', 'g', 't', 'g', 'c', 't', 't',\n 'g', 'g', 't', 'c', 't', 't', 'g', 't', 'g', 'a', 'a', 'g', 'g',\n 'c', 't', 't', 'g', 'a', 't', 'g', 'c', 't', 'c', 'c', 'a', 'g',\n 'a', 'g', 'a', 'a', 'g', 'g', 'a', 'g', 'g', 'a', 't', 'g', 'c',\n 't', 'a', 'g', 'a', 'g', 'g', 'g', 'g', 't', 'g', 'a', 'g', 'g',\n 't', 'g', 'g', 'g', 'a', 'g', 't', 'g', 'g', 'a', 't', 'g', 'g',\n 'g', 't', 'g', 'g', 'g', 't', 'g', 'g', 'g', 'c', 'a', 'g', 'g',\n 'g', 'g', 'a', 'g', 'c', 'a', 'c', 'c', 'c', 't', 'c', 't', 't',\n 'a', 'g', 'a', 'g', 'g', 'a', 'c', 'a', 'a', 'g', 'g', 'g', 'c',\n 't', 'c', 't', 'g', 'g', 'g', 'g', 't', 'g', 'g', 'g', 'g', 'g',\n 'a', 'g', 'c', 't', 'c', 'a', 't', 'g', 'g', 'a', 'g', 'g', 'g',\n 'g', 'g', 'a', 'a', 'c', 't', 'g', 'g', 'g', 'a', 'a', 'g', 'g',\n 'a', 'g', 'g', 'g', 'a', 'g', 'a', 'a', 'c', 'a', 't', 't', 't',\n 'g', 'a', 'a', 'a', 't', 'g', 't', 'a', 'a', 'a', 't', 'a', 'a',\n 'a', 't', 'a', 'a', 'a', 'a', 't', 'a', 'a', 't', 'a', 'a', 'a',\n 'a', 'a', 'a']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 8951)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3020717 : 3020717 + 44],\n \"TGTCAAACATGCATAAAGATATACTGAGGAGCCCATGAATTTTA\",\n )\n self.assertEqual(alignment[0], \"TGTCAAACATGCATAAAGATATACT-GAGGAGCCCATGAATTTTA\")\n self.assertEqual(alignment.sequences[1].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[1].seq), 125616256)\n self.assertEqual(\n alignment.sequences[1].seq[47544792 : 47544792 + 33],\n \"TAAAATTCATGGGCCCCTCTATTATGTTAAACa\",\n )\n self.assertEqual(alignment[1], \"tGTT------------TAACATAATAGAGGGGCCCATGAATTTTA\")\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157515381 : 157515381 + 38],\n \"TAAAATTCATGGACCCCTCTAGTATATTTAAAATTTTT\",\n )\n self.assertEqual(alignment[2], \"----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA\")\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 11)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155025327 : 155025327 + 38],\n \"TAAAATTCATGGACCCCTCTAGTATATTTAAAATTTTT\",\n )\n self.assertEqual(alignment[3], \"----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 11)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (46199, 46172))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (10461, 10482))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171686, 171328))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158037586, 158037565))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(record.seq), 4726)\n self.assertEqual(segment, (4300, 4263))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 4)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 9)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3020717, 3020721, 3020727, 3020730, 3020733, 3020742,\n 3020742, 3020761],\n [ 47544825, 47544821, 47544821, 47544821, 47544821, 47544812,\n 47544811, 47544792],\n [157515419, 157515419, 157515413, 157515413, 157515410, 157515401,\n 157515400, 157515381],\n [155025365, 155025365, 155025359, 155025359, 155025356, 155025347,\n 155025346, 155025327],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3020717 TGTCAAACATGCATAAAGATATACT-GAGGAGCCCATGAATTTTA 3020761\ncanFam2.c 47544825 tGTT------------TAACATAATAGAGGGGCCCATGAATTTTA 47544792\npanTro2.c 157515419 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA 157515381\nhg18.chr6 155025365 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA 155025327\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=8951.000000\ns mm9.chr10 3020717 44 + 129993255 TGTCAAACATGCATAAAGATATACT-GAGGAGCCCATGAATTTTA\ns canFam2.chr1 78071431 33 - 125616256 tGTT------------TAACATAATAGAGGGGCCCATGAATTTTA\nq canFam2.chr1 9999------------99999999999999999999999999999\ni canFam2.chr1 C 0 I 9\ns panTro2.chr6 16393193 38 - 173908612 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA\nq panTro2.chr6 ----999999---99999999999999999999999999999999\ni panTro2.chr6 C 0 I 11\ns hg18.chr6 15874627 38 - 170899992 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA\ni hg18.chr6 C 0 I 11\ne felCat3.scaffold_205680 73155 27 - 119354 I\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 10461 21 + 133105 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 187778 358 - 359464 I\ne ponAbe2.chr6 16172845 21 - 174210431 I\ne oryCun1.scaffold_156751 426 37 - 4726 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'G', 'T', 'C', 'A', 'A', 'A', 'C', 'A', 'T', 'G', 'C', 'A',\n 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'A', 'T', 'A', 'C', 'T', '-',\n 'G', 'A', 'G', 'G', 'A', 'G', 'C', 'C', 'C', 'A', 'T', 'G', 'A',\n 'A', 'T', 'T', 'T', 'T', 'A'],\n ['t', 'G', 'T', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', 'T', 'A', 'A', 'C', 'A', 'T', 'A', 'A', 'T', 'A',\n 'G', 'A', 'G', 'G', 'G', 'G', 'C', 'C', 'C', 'A', 'T', 'G', 'A',\n 'A', 'T', 'T', 'T', 'T', 'A'],\n ['-', '-', '-', '-', 'A', 'A', 'A', 'A', 'A', 'T', '-', '-', '-',\n 'T', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'A', 'C', 'T', 'A',\n 'G', 'A', 'G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A',\n 'A', 'T', 'T', 'T', 'T', 'A'],\n ['-', '-', '-', '-', 'A', 'A', 'A', 'A', 'A', 'T', '-', '-', '-',\n 'T', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'A', 'C', 'T', 'A',\n 'G', 'A', 'G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A',\n 'A', 'T', 'T', 'T', 'T', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 0)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3020761 : 3020761 + 157],\n \"TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaagattttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaagtgctgagatcatacctctgcaccatcctgcccACCT\",\n )\n self.assertEqual(\n alignment[0],\n \"TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaagattttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaagtgctgagatcatacctctgcaccatcctgcccACCT\",\n )\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (46199, 46172))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"canFam2.chr1\")\n self.assertEqual(len(record.seq), 125616256)\n self.assertEqual(segment, (47544792, 47544783))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (10461, 10482))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][6]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (1978, 606))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][7]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171686, 171328))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][8]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"hg18.chr6\")\n self.assertEqual(len(record.seq), 170899992)\n self.assertEqual(segment, (155025327, 155025316))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][9]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"panTro2.chr6\")\n self.assertEqual(len(record.seq), 173908612)\n self.assertEqual(segment, (157515381, 157515370))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][10]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ponAbe2.chr6\")\n self.assertEqual(len(record.seq), 174210431)\n self.assertEqual(segment, (158037586, 158037565))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][11]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(record.seq), 4726)\n self.assertEqual(segment, (4300, 4263))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 1)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 12)\n self.assertTrue(\n np.array_equal(alignment.coordinates, np.array([[3020761, 3020918]]))\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3020761 TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaag\n\nmm9.chr10 3020821 attttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaa\n\nmm9.chr10 3020881 gtgctgagatcatacctctgcaccatcctgcccACCT 3020918\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=0.000000\ns mm9.chr10 3020761 157 + 129993255 TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaagattttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaagtgctgagatcatacctctgcaccatcctgcccACCT\ne felCat3.scaffold_205680 73155 27 - 119354 I\ne canFam2.chr1 78071464 9 - 125616256 I\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne calJac1.Contig6394 10461 21 + 133105 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 8048 1372 - 10026 I\ne otoGar1.scaffold_334.1-359464 187778 358 - 359464 I\ne hg18.chr6 15874665 11 - 170899992 I\ne panTro2.chr6 16393231 11 - 173908612 I\ne ponAbe2.chr6 16172845 21 - 174210431 I\ne oryCun1.scaffold_156751 426 37 - 4726 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'A', 'T', 'A', 'T', 'A', 'T', 'G', 'C', 'T', 'A', 'T', 'C',\n 'C', 'G', 'T', 'G', 'T', 'G', 'C', 'T', 'G', 'T', 'G', 'A', 'T',\n 'T', 'T', 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'A', 'A', 'T',\n 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'G', 'T', 'A',\n 'T', 'A', 'T', 'G', 'c', 'a', 'a', 'g', 'a', 't', 't', 't', 't',\n 'g', 'c', 'a', 't', 't', 'g', 't', 'a', 'g', 'c', 'a', 'g', 'a',\n 'a', 'g', 'g', 't', 'g', 'g', 'c', 't', 't', 'c', 'a', 'a', 'a',\n 'c', 't', 'c', 'a', 'c', 'g', 'a', 't', 'c', 'c', 't', 'c', 'c',\n 't', 'g', 'c', 'c', 't', 'c', 'a', 'g', 'c', 'c', 't', 't', 'c',\n 'c', 'a', 'a', 'g', 't', 'g', 'c', 't', 'g', 'a', 'g', 'a', 't',\n 'c', 'a', 't', 'a', 'c', 'c', 't', 'c', 't', 'g', 'c', 'a', 'c',\n 'c', 'a', 't', 'c', 'c', 't', 'g', 'c', 'c', 'c', 'A', 'C', 'C',\n 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 85471)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3020918 : 3020918 + 96],\n \"GAGGTTTGTGACTTTTAATACTGATTGTTATCTAACATCACAGAATTCTCAGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA\",\n )\n self.assertEqual(\n alignment[0],\n \"GAGGTTTGTGACTTTTAATA----------CTGATTGTTATCTAACATCACAGAATTCTCAGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 170899992)\n self.assertEqual(\n alignment.sequences[1].seq[155025243 : 155025243 + 73],\n \"TTGTCCTAAATAATTAATAAGTCAAACATGTTTTTCCTTAAAAGCTGAGGATTGTGCAGTATTAAATAACCAT\",\n )\n self.assertEqual(\n alignment[1],\n \"---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 11)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157515297 : 157515297 + 73],\n \"TTGTCCTAAATAATTAATAAGTCAAACATGTTTTTCCTTAAAAGCTGAGGATTGTGCAGTATTAAATAACCAT\",\n )\n self.assertEqual(\n alignment[2],\n \"---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 11)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[3].seq), 125616256)\n self.assertEqual(\n alignment.sequences[3].seq[47544708 : 47544708 + 75],\n \"TTGTCCTAAGTAATTAACAAATCACTTTTTCCTTAAGAGCTGAGAACTTCATAATGGTACAGAATTATTTTATTA\",\n )\n self.assertEqual(\n alignment[3],\n \"--------------------------TAATAAAATAATTCTGTACCATTATGAAGTTCTCAGCTCTTAAGGAAAAA-----GTGATTTGTTAATTACTTAGGACAA\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[4].seq), 119354)\n self.assertEqual(\n alignment.sequences[4].seq[46096 : 46096 + 76],\n \"TTGTCCTAAATAATTAATAAATTACTTTGTGATATTAAAGAATTATTTCATTACTTCACCATTAAAATTCATGGAC\",\n )\n self.assertEqual(\n alignment[4],\n \"---GTCCATGAATTTTAATGGTGAAGTAATGAAATAATTCTTTAATATCAC----------------------AAA-----GTAATTTATTAATTATTTAGGACAA\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"9999899999999999999999999999999999999999999999999999999999999999999999999769\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 27)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[5].seq), 10026)\n self.assertEqual(\n alignment.sequences[5].seq[524 : 524 + 82],\n \"tttaaaaaaatcacactttTTCCATCAGAACTGAAAACTTTGTAATATTAatcttcttttcctattaaaATTTGCAGAACTC\",\n )\n self.assertEqual(\n alignment[5],\n \"GAGTTCTGCAAATtttaata----------ggaaaagaagatTAATATTACAAAGTTTTCAGTTCTGATGGAAaaa----------gtgtgatttttttaaa----\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9967996679966856646585678288383465687882688656636765583677657766676965686997776684\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 1372)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 28)\n self.assertEqual(alignment.sequences[6].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[6].seq), 4726)\n self.assertEqual(\n alignment.sequences[6].seq[4161 : 4161 + 102],\n \"TCATCCCAAGTCATTAACAAGTCAAACACTTTTTTCCTTAAGACTTGAGGATTTTCCAACATTAAATAATTATCTCATTGCTTTATTAAAATTCATGGATCT\",\n )\n self.assertEqual(\n alignment[6],\n \"-AGATCCATGAATTTTAATA---AAGCAATGAGATAATTATTTAATGTTGGAAAATCCTCAAGTCTTAAGGAAAAAAGTGTTTGACTTGTTAATGACTTGGGATGA\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"999999799999999999999999999999999999999999999999999998677999969999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 37)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[7].seq), 133105)\n self.assertEqual(\n alignment.sequences[7].seq[10482 : 10482 + 100],\n \"GGGGTCCATGAATTTTAATAGTAACAAAATGGTTATTCAATATTGCAAAATCCTCAGCTTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA\",\n )\n self.assertEqual(\n alignment[7],\n \"GGGGTCCATGAATTTTAATA-----GTAACAAAATGGTTATTCAATATTGCAAAATCCTCAGC-TTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 21)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[8].seq), 174210431)\n self.assertEqual(\n alignment.sequences[8].seq[158037464 : 158037464 + 101],\n \"TTGTCCTAAATAATTAATAAGTCAAACACGTTTTTCCTTAAAAGCTGAGGATTTTGCAATATTAAATAACCATTTTATTACTATTAAAATTCATGGACCCC\",\n )\n self.assertEqual(\n alignment[8],\n \"GGGGTCCATGAATTTTAATA-----GTAATAAAATGGTTATTTAATATTGCAAAATCCTCAGCTTTTAAGGAAAAACGTGTTTGACTTATTAATTATTTAGGACAA\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 21)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171686, 171328))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 9)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 4)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3020918, 3020919, 3020921, 3020938, 3020938, 3020938,\n 3020938, 3020938, 3020941, 3020959, 3020971, 3020972,\n 3020981, 3020984, 3020989, 3020994, 3021010, 3021014],\n [155025316, 155025316, 155025316, 155025316, 155025316, 155025316,\n 155025316, 155025316, 155025316, 155025298, 155025286, 155025285,\n 155025276, 155025273, 155025268, 155025263, 155025247, 155025243],\n [157515370, 157515370, 157515370, 157515370, 157515370, 157515370,\n 157515370, 157515370, 157515370, 157515352, 157515340, 157515339,\n 157515330, 157515327, 157515322, 157515317, 157515301, 157515297],\n [ 47544783, 47544783, 47544783, 47544783, 47544783, 47544783,\n 47544783, 47544779, 47544776, 47544758, 47544746, 47544745,\n 47544736, 47544733, 47544733, 47544728, 47544712, 47544708],\n [ 46172, 46172, 46172, 46155, 46152, 46150,\n 46149, 46145, 46142, 46124, 46124, 46124,\n 46124, 46121, 46121, 46116, 46100, 46096],\n [ 606, 605, 603, 586, 586, 586,\n 586, 586, 583, 565, 553, 552,\n 543, 540, 540, 540, 524, 524],\n [ 4263, 4263, 4261, 4244, 4244, 4242,\n 4241, 4237, 4234, 4216, 4204, 4203,\n 4194, 4191, 4186, 4181, 4165, 4161],\n [ 10482, 10483, 10485, 10502, 10502, 10502,\n 10503, 10507, 10510, 10528, 10540, 10540,\n 10549, 10552, 10557, 10562, 10578, 10582],\n [158037565, 158037564, 158037562, 158037545, 158037545, 158037545,\n 158037544, 158037540, 158037537, 158037519, 158037507, 158037506,\n 158037497, 158037494, 158037489, 158037484, 158037468, 158037464],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3020918 GAGGTTTGTGACTTTTAATA----------CTGATTGTTATCTAACATCACAGAATTCTC\nhg18.chr6 155025316 ---------------------------------ATGGTTATTTAATACTGCACAATCCTC\npanTro2.c 157515370 ---------------------------------ATGGTTATTTAATACTGCACAATCCTC\ncanFam2.c 47544783 --------------------------TAATAAAATAATTCTGTACCATTATGAAGTTCTC\nfelCat3.s 46172 ---GTCCATGAATTTTAATGGTGAAGTAATGAAATAATTCTTTAATATCAC---------\ncavPor2.s 606 GAGTTCTGCAAATtttaata----------ggaaaagaagatTAATATTACAAAGTTTTC\noryCun1.s 4263 -AGATCCATGAATTTTAATA---AAGCAATGAGATAATTATTTAATGTTGGAAAATCCTC\ncalJac1.C 10482 GGGGTCCATGAATTTTAATA-----GTAACAAAATGGTTATTCAATATTGCAAAATCCTC\nponAbe2.c 158037565 GGGGTCCATGAATTTTAATA-----GTAATAAAATGGTTATTTAATATTGCAAAATCCTC\n\nmm9.chr10 3020968 AGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA 3021014\nhg18.chr6 155025289 AGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA 155025243\npanTro2.c 157515343 AGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA 157515297\ncanFam2.c 47544749 AGCTCTTAAGGAAAAA-----GTGATTTGTTAATTACTTAGGACAA 47544708\nfelCat3.s 46124 -------------AAA-----GTAATTTATTAATTATTTAGGACAA 46096\ncavPor2.s 556 AGTTCTGATGGAAaaa----------gtgtgatttttttaaa---- 524\noryCun1.s 4207 AAGTCTTAAGGAAAAAAGTGTTTGACTTGTTAATGACTTGGGATGA 4161\ncalJac1.C 10537 AGC-TTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA 10582\nponAbe2.c 158037510 AGCTTTTAAGGAAAAACGTGTTTGACTTATTAATTATTTAGGACAA 158037464\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=85471.000000\ns mm9.chr10 3020918 96 + 129993255 GAGGTTTGTGACTTTTAATA----------CTGATTGTTATCTAACATCACAGAATTCTCAGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA\ns hg18.chr6 15874676 73 - 170899992 ---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA\ni hg18.chr6 I 11 C 0\ns panTro2.chr6 16393242 73 - 173908612 ---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA\nq panTro2.chr6 ---------------------------------9999999999999999999999999999999999999999999999999999999999999999999999999\ni panTro2.chr6 I 11 C 0\ns canFam2.chr1 78071473 75 - 125616256 --------------------------TAATAAAATAATTCTGTACCATTATGAAGTTCTCAGCTCTTAAGGAAAAA-----GTGATTTGTTAATTACTTAGGACAA\nq canFam2.chr1 --------------------------99999999999999999999999999999999999999999999999999-----9999999999999999999999999\ni canFam2.chr1 I 9 C 0\ns felCat3.scaffold_205680 73182 76 - 119354 ---GTCCATGAATTTTAATGGTGAAGTAATGAAATAATTCTTTAATATCAC----------------------AAA-----GTAATTTATTAATTATTTAGGACAA\nq felCat3.scaffold_205680 ---999989999999999999999999999999999999999999999999----------------------999-----9999999999999999999999769\ni felCat3.scaffold_205680 I 27 C 0\ns cavPor2.scaffold_216473 9420 82 - 10026 GAGTTCTGCAAATtttaata----------ggaaaagaagatTAATATTACAAAGTTTTCAGTTCTGATGGAAaaa----------gtgtgatttttttaaa----\nq cavPor2.scaffold_216473 99679966799668566465----------8567828838346568788268865663676558367765776667----------6965686997776684----\ni cavPor2.scaffold_216473 I 1372 I 28\ns oryCun1.scaffold_156751 463 102 - 4726 -AGATCCATGAATTTTAATA---AAGCAATGAGATAATTATTTAATGTTGGAAAATCCTCAAGTCTTAAGGAAAAAAGTGTTTGACTTGTTAATGACTTGGGATGA\nq oryCun1.scaffold_156751 -9999997999999999999---99999999999999999999999999999999998677999969999999999999999999999999999999999999999\ni oryCun1.scaffold_156751 I 37 C 0\ns calJac1.Contig6394 10482 100 + 133105 GGGGTCCATGAATTTTAATA-----GTAACAAAATGGTTATTCAATATTGCAAAATCCTCAGC-TTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA\ni calJac1.Contig6394 I 21 C 0\ns ponAbe2.chr6 16172866 101 - 174210431 GGGGTCCATGAATTTTAATA-----GTAATAAAATGGTTATTTAATATTGCAAAATCCTCAGCTTTTAAGGAAAAACGTGTTTGACTTATTAATTATTTAGGACAA\ni ponAbe2.chr6 I 21 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne otoGar1.scaffold_334.1-359464 187778 358 - 359464 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['G', 'A', 'G', 'G', 'T', 'T', 'T', 'G', 'T', 'G', 'A', 'C', 'T',\n 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'C', 'T', 'G', 'A', 'T', 'T', 'G', 'T', 'T',\n 'A', 'T', 'C', 'T', 'A', 'A', 'C', 'A', 'T', 'C', 'A', 'C', 'A',\n 'G', 'A', 'A', 'T', 'T', 'C', 'T', 'C', 'A', 'G', 'T', 'T', 'C',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'C', 'A', 'A', 'T',\n 'T', 'G', 'T', 'T', 'C', 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'T',\n 'A', 'T', 'T', 'T', 'G', 'T', 'C', 'T', 'A', 'G', 'G', 'A', 'G',\n 'G', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', 'A', 'T', 'G', 'G', 'T', 'T',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'C', 'T', 'G', 'C', 'A',\n 'C', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'T',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'A',\n 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'A', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', 'A', 'T', 'G', 'G', 'T', 'T',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'C', 'T', 'G', 'C', 'A',\n 'C', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'T',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'A',\n 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'A', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n 'T', 'A', 'A', 'T', 'A', 'A', 'A', 'A', 'T', 'A', 'A', 'T', 'T',\n 'C', 'T', 'G', 'T', 'A', 'C', 'C', 'A', 'T', 'T', 'A', 'T', 'G',\n 'A', 'A', 'G', 'T', 'T', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'C',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', '-', '-',\n '-', '-', '-', 'G', 'T', 'G', 'A', 'T', 'T', 'T', 'G', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A'],\n ['-', '-', '-', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T',\n 'T', 'T', 'T', 'A', 'A', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G',\n 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'A', 'T', 'A', 'A', 'T', 'T',\n 'C', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'T', 'C', 'A', 'C', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', '-', '-',\n '-', '-', '-', 'G', 'T', 'A', 'A', 'T', 'T', 'T', 'A', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A'],\n ['G', 'A', 'G', 'T', 'T', 'C', 'T', 'G', 'C', 'A', 'A', 'A', 'T',\n 't', 't', 't', 'a', 'a', 't', 'a', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', 'g', 'g', 'a', 'a', 'a', 'a', 'g', 'a', 'a',\n 'g', 'a', 't', 'T', 'A', 'A', 'T', 'A', 'T', 'T', 'A', 'C', 'A',\n 'A', 'A', 'G', 'T', 'T', 'T', 'T', 'C', 'A', 'G', 'T', 'T', 'C',\n 'T', 'G', 'A', 'T', 'G', 'G', 'A', 'A', 'a', 'a', 'a', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', 'g', 't', 'g', 't', 'g',\n 'a', 't', 't', 't', 't', 't', 't', 't', 'a', 'a', 'a', '-', '-',\n '-', '-'],\n ['-', 'A', 'G', 'A', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T',\n 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', 'A', 'A', 'G',\n 'C', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T', 'A', 'A', 'T', 'T',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'G', 'T', 'T', 'G', 'G', 'A',\n 'A', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'A', 'G', 'T', 'C',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'A', 'G',\n 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'G', 'T', 'T',\n 'A', 'A', 'T', 'G', 'A', 'C', 'T', 'T', 'G', 'G', 'G', 'A', 'T',\n 'G', 'A'],\n ['G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T',\n 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-', 'G',\n 'T', 'A', 'A', 'C', 'A', 'A', 'A', 'A', 'T', 'G', 'G', 'T', 'T',\n 'A', 'T', 'T', 'C', 'A', 'A', 'T', 'A', 'T', 'T', 'G', 'C', 'A',\n 'A', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', '-', 'T',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'A',\n 'T', 'A', 'T', 'T', 'T', 'G', 'A', 'T', 'T', 'T', 'G', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A'],\n ['G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T',\n 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-', 'G',\n 'T', 'A', 'A', 'T', 'A', 'A', 'A', 'A', 'T', 'G', 'G', 'T', 'T',\n 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'T', 'T', 'G', 'C', 'A',\n 'A', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'T',\n 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'G',\n 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'A', 'T', 'T',\n 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C',\n 'A', 'A']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 105724)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021014 : 3021014 + 40],\n \"ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG\",\n )\n self.assertEqual(alignment[0], \"ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG\")\n self.assertEqual(alignment.sequences[1].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[1].seq), 4726)\n self.assertEqual(\n alignment.sequences[1].seq[4121 : 4121 + 40],\n \"AATTCCTAAATCATCCAAGTTGGAATGACTTCATCAAGAT\",\n )\n self.assertEqual(alignment[1], \"ATCTTGATGAAGTCATTCCAACTTGGATGATTTAGGAATT\")\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999969999699999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[2].seq), 359464)\n self.assertEqual(\n alignment.sequences[2].seq[171288 : 171288 + 40],\n \"CATTCCTAAATCACATAAATTGGAATAACTTCACCAAGAT\",\n )\n self.assertEqual(alignment[2], \"ATCTTGGTGAAGTTATTCCAATTTATGTGATTTAGGAATG\")\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 358)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[3].seq), 133105)\n self.assertEqual(\n alignment.sequences[3].seq[10582 : 10582 + 40],\n \"ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG\",\n )\n self.assertEqual(alignment[3], \"ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 170899992)\n self.assertEqual(\n alignment.sequences[4].seq[155025203 : 155025203 + 40],\n \"CATTCCTAAGCCATGCAAGTTGGAATAACTTCACCAAAAT\",\n )\n self.assertEqual(alignment[4], \"ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 173908612)\n self.assertEqual(\n alignment.sequences[5].seq[157515257 : 157515257 + 40],\n \"CATTCCTAAGCCATGCAAGTTGGAATAACTTCACCAAAAT\",\n )\n self.assertEqual(alignment[5], \"ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\")\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[6].seq), 174210431)\n self.assertEqual(\n alignment.sequences[6].seq[158037424 : 158037424 + 40],\n \"CATTCCTAAGCCATGCAAGTTGGAATAACTTCACCAAAAT\",\n )\n self.assertEqual(alignment[6], \"ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[7].seq), 125616256)\n self.assertEqual(\n alignment.sequences[7].seq[47544668 : 47544668 + 40],\n \"CATTCCTAAATCATGCGAGTCAGAATGACTTCACTGAGAT\",\n )\n self.assertEqual(alignment[7], \"ATCTCAGTGAAGTCATTCTGACTCGCATGATTTAGGAATG\")\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[8].seq), 119354)\n self.assertEqual(\n alignment.sequences[8].seq[46056 : 46056 + 40],\n \"CATACCTAAATCATGCAAGTCAGAATAACTTCACTGAGAT\",\n )\n self.assertEqual(alignment[8], \"ATCTCAGTGAAGTTATTCTGACTTGCATGATTTAGGTATG\")\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"9999989999989988999997999979997996167779\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[9].seq), 10470)\n self.assertEqual(\n alignment.sequences[9].seq[7314 : 7314 + 40],\n \"CATCGCTCAGTCATACGAGTCGGAATGATTTCACTGATGT\",\n )\n self.assertEqual(alignment[9], \"ACATCAGTGAAATCATTCCGACTCGTATGACTGAGCGATG\")\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"9759855999977756667495765475885678385647\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(record.seq), 10026)\n self.assertEqual(segment, (524, 496))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 10)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 4)\n self.assertTrue(\n np.array_equal(\n # fmt: off\n alignment.coordinates, np.array([[ 3021014, 3021054],\n [ 4161, 4121],\n [ 171328, 171288],\n [ 10582, 10622],\n [155025243, 155025203],\n [157515297, 157515257],\n [158037464, 158037424],\n [ 47544708, 47544668],\n [ 46096, 46056],\n [ 7354, 7314],\n ])\n # fmt: on\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021014 ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG 3021054\noryCun1.s 4161 ATCTTGATGAAGTCATTCCAACTTGGATGATTTAGGAATT 4121\notoGar1.s 171328 ATCTTGGTGAAGTTATTCCAATTTATGTGATTTAGGAATG 171288\ncalJac1.C 10582 ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG 10622\nhg18.chr6 155025243 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG 155025203\npanTro2.c 157515297 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG 157515257\nponAbe2.c 158037464 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG 158037424\ncanFam2.c 47544708 ATCTCAGTGAAGTCATTCTGACTCGCATGATTTAGGAATG 47544668\nfelCat3.s 46096 ATCTCAGTGAAGTTATTCTGACTTGCATGATTTAGGTATG 46056\ndasNov1.s 7354 ACATCAGTGAAATCATTCCGACTCGTATGACTGAGCGATG 7314\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=105724.000000\ns mm9.chr10 3021014 40 + 129993255 ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG\ns oryCun1.scaffold_156751 565 40 - 4726 ATCTTGATGAAGTCATTCCAACTTGGATGATTTAGGAATT\nq oryCun1.scaffold_156751 9999999999999969999699999999999999999999\ni oryCun1.scaffold_156751 C 0 C 0\ns otoGar1.scaffold_334.1-359464 188136 40 - 359464 ATCTTGGTGAAGTTATTCCAATTTATGTGATTTAGGAATG\nq otoGar1.scaffold_334.1-359464 9999999999999999999999999999999999999999\ni otoGar1.scaffold_334.1-359464 I 358 C 0\ns calJac1.Contig6394 10582 40 + 133105 ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG\ni calJac1.Contig6394 C 0 C 0\ns hg18.chr6 15874749 40 - 170899992 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16393315 40 - 173908612 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\nq panTro2.chr6 9999999999999999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16172967 40 - 174210431 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG\ni ponAbe2.chr6 C 0 C 0\ns canFam2.chr1 78071548 40 - 125616256 ATCTCAGTGAAGTCATTCTGACTCGCATGATTTAGGAATG\nq canFam2.chr1 9999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ns felCat3.scaffold_205680 73258 40 - 119354 ATCTCAGTGAAGTTATTCTGACTTGCATGATTTAGGTATG\nq felCat3.scaffold_205680 9999989999989988999997999979997996167779\ni felCat3.scaffold_205680 C 0 C 0\ns dasNov1.scaffold_56749 3116 40 - 10470 ACATCAGTGAAATCATTCCGACTCGTATGACTGAGCGATG\nq dasNov1.scaffold_56749 9759855999977756667495765475885678385647\ni dasNov1.scaffold_56749 N 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\ne cavPor2.scaffold_216473 9502 28 - 10026 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'C', 'C', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'C', 'G', 'C',\n 'C', 'A', 'C', 'T', 'G', 'G', 'A', 'T', 'T', 'T', 'T', 'G', 'T',\n 'A', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'A', 'T', 'A', 'C', 'T',\n 'G'],\n ['A', 'T', 'C', 'T', 'T', 'G', 'A', 'T', 'G', 'A', 'A', 'G', 'T',\n 'C', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'G',\n 'A', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'T'],\n ['A', 'T', 'C', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'T', 'T', 'T', 'A', 'T',\n 'G', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'T',\n 'G', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'C',\n 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'C',\n 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'C',\n 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'C', 'T', 'C', 'A', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'C', 'A', 'T', 'T', 'C', 'T', 'G', 'A', 'C', 'T', 'C', 'G', 'C',\n 'A', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T',\n 'G'],\n ['A', 'T', 'C', 'T', 'C', 'A', 'G', 'T', 'G', 'A', 'A', 'G', 'T',\n 'T', 'A', 'T', 'T', 'C', 'T', 'G', 'A', 'C', 'T', 'T', 'G', 'C',\n 'A', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'T', 'A', 'T',\n 'G'],\n ['A', 'C', 'A', 'T', 'C', 'A', 'G', 'T', 'G', 'A', 'A', 'A', 'T',\n 'C', 'A', 'T', 'T', 'C', 'C', 'G', 'A', 'C', 'T', 'C', 'G', 'T',\n 'A', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'G', 'C', 'G', 'A', 'T',\n 'G']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 115790)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021054 : 3021054 + 50],\n \"CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAGGACTTACATGCAG\",\n )\n self.assertEqual(\n alignment[0],\n \"CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAG--------------------GACTTACATGCAG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[458 : 458 + 38],\n \"TCACAAGTATTTATAGCAACTCTGAACTCCCAAATGAG\",\n )\n self.assertEqual(\n alignment[1],\n \"CTCATTTGGGAGTTCAGAGTT--------GCTATAAA--------------------TACTTGTGA----\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"78877766789884666566698766677876665669\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 28)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[4052 : 4052 + 69],\n \"ATACGTGTAATTAAGGAGGAAAAAAGAAGACTCCATTAGGCAGTTATAAAATGTAAGAGCCCAAATTAG\",\n )\n self.assertEqual(\n alignment[2],\n \"CTAATTTGGGCTCTTACATTTTATAACTGCCTAATGGAGTCTTCTTTTTTCCT-CCTTAATTACACGTAT\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"999999999999979997999999999999999999999997997999999979979999999495999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[3].seq), 359464)\n self.assertEqual(\n alignment.sequences[3].seq[171219 : 171219 + 69],\n \"GTACATAGAGTCTGGGGAAGGGACCAGTGGGCTCCATTAAGCCTTTATGAACCTGTGTCCCCAAGTTAG\",\n )\n self.assertEqual(\n alignment[3],\n \"CTAACTTGGGGACACAGG-TTCATAAAGGCTTAATGGAGCCCACTGGTCCCTTCCCCAGACTCTATGTAC\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"999999999999999999999999999999999999998999999689999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[4].seq), 133105)\n self.assertEqual(\n alignment.sequences[4].seq[10622 : 10622 + 70],\n \"CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGCCTATATGTAT\",\n )\n self.assertEqual(\n alignment[4],\n \"CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGCCTATATGTAT\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155025133 : 155025133 + 70],\n \"ATACATATAGTCTAGGGAAGGAAGGAGCAGACTTCATTAGGCAGTTAGGAAATGTAAATCCCCAAATTGT\",\n )\n self.assertEqual(\n alignment[5],\n \"ACAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCCTTCCTTCCCTAGACTATATGTAT\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[6].seq), 173908612)\n self.assertEqual(\n alignment.sequences[6].seq[157515187 : 157515187 + 70],\n \"ATACATATAGTCTAGGGAAGGAAAGAGCAGACTTCATTAGGCAGTTAGGAAATGTAAATCCCCAAATTGG\",\n )\n self.assertEqual(\n alignment[6],\n \"CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[7].seq), 174210431)\n self.assertEqual(\n alignment.sequences[7].seq[158037354 : 158037354 + 70],\n \"ATACATATAGTCTAGGGAAGGAAAGAGCAGACTTCATTAGGCAGTTAGGAAATGTAAATCCCCAAATTGG\",\n )\n self.assertEqual(\n alignment[7],\n \"CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[8].seq), 125616256)\n self.assertEqual(\n alignment.sequences[8].seq[47544598 : 47544598 + 70],\n \"ATACATATGGTGTAGGGAAGAAAACATCAGCTTTCATTAAGCAATTATGAAATTTGAGTCACCAAATTAG\",\n )\n self.assertEqual(\n alignment[8],\n \"CTAATTTGGTGACTCAAATTTCATAATTGCTTAATGAAAGCTGATGTTTTCTTCCCTACACCATATGTAT\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[9].seq), 119354)\n self.assertEqual(\n alignment.sequences[9].seq[45986 : 45986 + 70],\n \"ATGCATATAGTCTTGGGAAGGAAACAGCAGGCTTCCTTAAGCAATTATGAAATTCAAGTCACCAAATTAG\",\n )\n self.assertEqual(\n alignment[9],\n \"CTAATTTGGTGACTTGAATTTCATAATTGCTTAAGGAAGCCTGCTGTTTCCTTCCCAAGACTATATGCAT\",\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"9769999999975699868977669777966666596959759669595666758736585676666655\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[10].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[10].seq), 10470)\n self.assertEqual(\n alignment.sequences[10].seq[7244 : 7244 + 70],\n \"ATACTTATAGTCTAGAGAAGAAAACAGCAGGCTTCGGTTAGCAATTTTAAAATGTGAGTCCCCCAATTAG\",\n )\n self.assertEqual(\n alignment[10],\n \"CTAATTGGGGGACTCACATTTTAAAATTGCTAACCGAAGCCTGCTGTTTTCTTCTCTAGACTATAAGTAT\",\n )\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"],\n \"5556576999664654656985688667655565647767537567688856666555556565555656\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(record.seq), 100002)\n self.assertEqual(segment, (87661, 95225))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 11)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 3)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021054, 3021072, 3021073, 3021075, 3021083, 3021091,\n 3021091, 3021091, 3021091, 3021100, 3021104],\n [ 496, 478, 477, 475, 475, 467,\n 467, 467, 467, 458, 458],\n [ 4121, 4103, 4102, 4100, 4092, 4084,\n 4068, 4068, 4065, 4056, 4052],\n [ 171288, 171270, 171270, 171268, 171260, 171252,\n 171236, 171235, 171232, 171223, 171219],\n [ 10622, 10640, 10641, 10643, 10651, 10659,\n 10675, 10676, 10679, 10688, 10692],\n [155025203, 155025185, 155025184, 155025182, 155025174, 155025166,\n 155025150, 155025149, 155025146, 155025137, 155025133],\n [157515257, 157515239, 157515238, 157515236, 157515228, 157515220,\n 157515204, 157515203, 157515200, 157515191, 157515187],\n [158037424, 158037406, 158037405, 158037403, 158037395, 158037387,\n 158037371, 158037370, 158037367, 158037358, 158037354],\n [ 47544668, 47544650, 47544649, 47544647, 47544639, 47544631,\n 47544615, 47544614, 47544611, 47544602, 47544598],\n [ 46056, 46038, 46037, 46035, 46027, 46019,\n 46003, 46002, 45999, 45990, 45986],\n [ 7314, 7296, 7295, 7293, 7285, 7277,\n 7261, 7260, 7257, 7248, 7244],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021054 CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAG--------------------GAC\ncavPor2.s 496 CTCATTTGGGAGTTCAGAGTT--------GCTATAAA--------------------TAC\noryCun1.s 4121 CTAATTTGGGCTCTTACATTTTATAACTGCCTAATGGAGTCTTCTTTTTTCCT-CCTTAA\notoGar1.s 171288 CTAACTTGGGGACACAGG-TTCATAAAGGCTTAATGGAGCCCACTGGTCCCTTCCCCAGA\ncalJac1.C 10622 CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGC\nhg18.chr6 155025203 ACAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCCTTCCTTCCCTAGA\npanTro2.c 157515257 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGA\nponAbe2.c 158037424 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGA\ncanFam2.c 47544668 CTAATTTGGTGACTCAAATTTCATAATTGCTTAATGAAAGCTGATGTTTTCTTCCCTACA\nfelCat3.s 46056 CTAATTTGGTGACTTGAATTTCATAATTGCTTAAGGAAGCCTGCTGTTTCCTTCCCAAGA\ndasNov1.s 7314 CTAATTGGGGGACTCACATTTTAAAATTGCTAACCGAAGCCTGCTGTTTTCTTCTCTAGA\n\nmm9.chr10 3021094 TTACATGCAG 3021104\ncavPor2.s 464 TTGTGA---- 458\noryCun1.s 4062 TTACACGTAT 4052\notoGar1.s 171229 CTCTATGTAC 171219\ncalJac1.C 10682 CTATATGTAT 10692\nhg18.chr6 155025143 CTATATGTAT 155025133\npanTro2.c 157515197 CTATATGTAT 157515187\nponAbe2.c 158037364 CTATATGTAT 158037354\ncanFam2.c 47544608 CCATATGTAT 47544598\nfelCat3.s 45996 CTATATGCAT 45986\ndasNov1.s 7254 CTATAAGTAT 7244\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=115790.000000\ns mm9.chr10 3021054 50 + 129993255 CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAG--------------------GACTTACATGCAG\ns cavPor2.scaffold_216473 9530 38 - 10026 CTCATTTGGGAGTTCAGAGTT--------GCTATAAA--------------------TACTTGTGA----\nq cavPor2.scaffold_216473 788777667898846665666--------98766677--------------------876665669----\ni cavPor2.scaffold_216473 I 28 C 0\ns oryCun1.scaffold_156751 605 69 - 4726 CTAATTTGGGCTCTTACATTTTATAACTGCCTAATGGAGTCTTCTTTTTTCCT-CCTTAATTACACGTAT\nq oryCun1.scaffold_156751 99999999999997999799999999999999999999999799799999997-9979999999495999\ni oryCun1.scaffold_156751 C 0 C 0\ns otoGar1.scaffold_334.1-359464 188176 69 - 359464 CTAACTTGGGGACACAGG-TTCATAAAGGCTTAATGGAGCCCACTGGTCCCTTCCCCAGACTCTATGTAC\nq otoGar1.scaffold_334.1-359464 999999999999999999-999999999999999999998999999689999999999999999999999\ni otoGar1.scaffold_334.1-359464 C 0 C 0\ns calJac1.Contig6394 10622 70 + 133105 CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGCCTATATGTAT\ni calJac1.Contig6394 C 0 C 0\ns hg18.chr6 15874789 70 - 170899992 ACAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCCTTCCTTCCCTAGACTATATGTAT\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16393355 70 - 173908612 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT\nq panTro2.chr6 9999999999999999999999999999999999999999999999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16173007 70 - 174210431 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT\ni ponAbe2.chr6 C 0 C 0\ns canFam2.chr1 78071588 70 - 125616256 CTAATTTGGTGACTCAAATTTCATAATTGCTTAATGAAAGCTGATGTTTTCTTCCCTACACCATATGTAT\nq canFam2.chr1 9999999999999999999999999999999999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ns felCat3.scaffold_205680 73298 70 - 119354 CTAATTTGGTGACTTGAATTTCATAATTGCTTAAGGAAGCCTGCTGTTTCCTTCCCAAGACTATATGCAT\nq felCat3.scaffold_205680 9769999999975699868977669777966666596959759669595666758736585676666655\ni felCat3.scaffold_205680 C 0 C 0\ns dasNov1.scaffold_56749 3156 70 - 10470 CTAATTGGGGGACTCACATTTTAAAATTGCTAACCGAAGCCTGCTGTTTTCTTCTCTAGACTATAAGTAT\nq dasNov1.scaffold_56749 5556576999664654656985688667655565647767537567688856666555556565555656\ni dasNov1.scaffold_56749 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\ne echTel1.scaffold_288249 87661 7564 + 100002 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'T', 'C', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'A', 'A', 'C',\n 'T', 'T', 'A', 'C', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'C', 'A',\n 'A', 'A', 'G', 'G', 'C', 'T', 'T', 'C', 'C', 'A', 'G', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'G', 'A', 'C', 'T', 'T', 'A', 'C', 'A',\n 'T', 'G', 'C', 'A', 'G'],\n ['C', 'T', 'C', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'A', 'G', 'T',\n 'T', 'C', 'A', 'G', 'A', 'G', 'T', 'T', '-', '-', '-', '-', '-',\n '-', '-', '-', 'G', 'C', 'T', 'A', 'T', 'A', 'A', 'A', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', 'T', 'A', 'C', 'T', 'T', 'G', 'T', 'G',\n 'A', '-', '-', '-', '-'],\n ['C', 'T', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'C', 'T', 'C',\n 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'A',\n 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'G', 'A', 'G',\n 'T', 'C', 'T', 'T', 'C', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'C',\n 'T', '-', 'C', 'C', 'T', 'T', 'A', 'A', 'T', 'T', 'A', 'C', 'A',\n 'C', 'G', 'T', 'A', 'T'],\n ['C', 'T', 'A', 'A', 'C', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'C',\n 'A', 'C', 'A', 'G', 'G', '-', 'T', 'T', 'C', 'A', 'T', 'A', 'A',\n 'A', 'G', 'G', 'C', 'T', 'T', 'A', 'A', 'T', 'G', 'G', 'A', 'G',\n 'C', 'C', 'C', 'A', 'C', 'T', 'G', 'G', 'T', 'C', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'C', 'A', 'G', 'A', 'C', 'T', 'C', 'T', 'A',\n 'T', 'G', 'T', 'A', 'C'],\n ['C', 'C', 'A', 'G', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'C',\n 'T', 'T', 'A', 'G', 'A', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'A',\n 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G',\n 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'C', 'C', 'T', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'T'],\n ['A', 'C', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'T',\n 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G',\n 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'T'],\n ['C', 'C', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'T',\n 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G',\n 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'T'],\n ['C', 'C', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'T',\n 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'A',\n 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G',\n 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'T'],\n ['C', 'T', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'C',\n 'T', 'C', 'A', 'A', 'A', 'T', 'T', 'T', 'C', 'A', 'T', 'A', 'A',\n 'T', 'T', 'G', 'C', 'T', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'A',\n 'G', 'C', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'T', 'T', 'C', 'T',\n 'T', 'C', 'C', 'C', 'T', 'A', 'C', 'A', 'C', 'C', 'A', 'T', 'A',\n 'T', 'G', 'T', 'A', 'T'],\n ['C', 'T', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'C',\n 'T', 'T', 'G', 'A', 'A', 'T', 'T', 'T', 'C', 'A', 'T', 'A', 'A',\n 'T', 'T', 'G', 'C', 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'G',\n 'C', 'C', 'T', 'G', 'C', 'T', 'G', 'T', 'T', 'T', 'C', 'C', 'T',\n 'T', 'C', 'C', 'C', 'A', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A',\n 'T', 'G', 'C', 'A', 'T'],\n ['C', 'T', 'A', 'A', 'T', 'T', 'G', 'G', 'G', 'G', 'G', 'A', 'C',\n 'T', 'C', 'A', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'A', 'A', 'A',\n 'T', 'T', 'G', 'C', 'T', 'A', 'A', 'C', 'C', 'G', 'A', 'A', 'G',\n 'C', 'C', 'T', 'G', 'C', 'T', 'G', 'T', 'T', 'T', 'T', 'C', 'T',\n 'T', 'C', 'T', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A',\n 'A', 'G', 'T', 'A', 'T']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 44222)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021104 : 3021104 + 32],\n \"CTGTTAGTGCTGTTTTAATGTACCTCGCAGTA\",\n )\n self.assertEqual(alignment[0], \"CTGTTAGTGCTGTTTT---AATGTACCTCGCAGTA\")\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[431 : 431 + 27], \"TATAAAAATTTACATTAAGAAAGTAAT\"\n )\n self.assertEqual(alignment[1], \"-----ATTACTTTCTT---AATGTAAATTTTTATA\")\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"], \"554558687467957999989884575\"\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[4022 : 4022 + 30],\n \"TATAAAATATTACATTGAGAATACTAGCAA\",\n )\n self.assertEqual(alignment[2], \"TTGCTAGTA--TTCTC---AATGTAATATTTTATA\")\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"999979999966656999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[3].seq), 359464)\n self.assertEqual(\n alignment.sequences[3].seq[171187 : 171187 + 32],\n \"TATAAAACATTATATTAAGGGAACACCAGCAA\",\n )\n self.assertEqual(alignment[3], \"TTGCTGGTGTTCCCTT---AATATAATGTTTTATA\")\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"99999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[4].seq), 133105)\n self.assertEqual(\n alignment.sequences[4].seq[10692 : 10692 + 30],\n \"TTACTCGTGCCCTTAATATAGCATTTTATA\",\n )\n self.assertEqual(alignment[4], \"TTACTCGTG--CCCTT---AATATAGCATTTTATA\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155025103 : 155025103 + 30],\n \"TATAAAATGTGATATTAAGAGTACCAGCAA\",\n )\n self.assertEqual(alignment[5], \"TTGCTGGTA--CTCTT---AATATCACATTTTATA\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[6].seq), 173908612)\n self.assertEqual(\n alignment.sequences[6].seq[157515157 : 157515157 + 30],\n \"TATAAAATGTGATATTAAGAGTACCAGCAA\",\n )\n self.assertEqual(alignment[6], \"TTGCTGGTA--CTCTT---AATATCACATTTTATA\")\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[7].seq), 174210431)\n self.assertEqual(\n alignment.sequences[7].seq[158037324 : 158037324 + 30],\n \"TATAAAATGTTATATTAAGAGCACCAGCAA\",\n )\n self.assertEqual(alignment[7], \"TTGCTGGTG--CTCTT---AATATAACATTTTATA\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[8].seq), 125616256)\n self.assertEqual(\n alignment.sequences[8].seq[47544573 : 47544573 + 25],\n \"TGCTACATTTTGAGAGCACCAGCAA\",\n )\n self.assertEqual(alignment[8], \"TTGCTGGTGCTCTCAA---AATGTAGCA-------\")\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 196)\n self.assertEqual(alignment.sequences[9].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[9].seq), 119354)\n self.assertEqual(\n alignment.sequences[9].seq[45961 : 45961 + 25], \"TGTTATATTTTGAGAGCACCAGCAA\"\n )\n self.assertEqual(alignment[9], \"TTGCTGGTGCTCTCAA---AATATAACA-------\")\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"], \"8677668566555658876555655\"\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 6)\n self.assertEqual(alignment.sequences[10].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[10].seq), 10470)\n self.assertEqual(\n alignment.sequences[10].seq[7211 : 7211 + 33],\n \"CATAAAATGTTACATTAATCAGATCACCAGCAA\",\n )\n self.assertEqual(alignment[10], \"TTGCTGGTG--ATCTGATTAATGTAACATTTTATG\")\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"],\n \"856647736775356546747663745776545\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[11].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[11].seq), 100002)\n self.assertEqual(\n alignment.sequences[11].seq[95225 : 95225 + 21], \"CTGTTAATGCTCTGTTTTATG\"\n )\n self.assertEqual(alignment[11], \"CTGTTAATG--CTCTG------------TTTTATG\")\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"], \"999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 7564)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 12)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 2)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021104, 3021109, 3021113, 3021115, 3021120, 3021120,\n 3021129, 3021136],\n [ 458, 458, 454, 452, 447, 447,\n 438, 431],\n [ 4052, 4047, 4043, 4043, 4038, 4038,\n 4029, 4022],\n [ 171219, 171214, 171210, 171208, 171203, 171203,\n 171194, 171187],\n [ 10692, 10697, 10701, 10701, 10706, 10706,\n 10715, 10722],\n [155025133, 155025128, 155025124, 155025124, 155025119, 155025119,\n 155025110, 155025103],\n [157515187, 157515182, 157515178, 157515178, 157515173, 157515173,\n 157515164, 157515157],\n [158037354, 158037349, 158037345, 158037345, 158037340, 158037340,\n 158037331, 158037324],\n [ 47544598, 47544593, 47544589, 47544587, 47544582, 47544582,\n 47544573, 47544573],\n [ 45986, 45981, 45977, 45975, 45970, 45970,\n 45961, 45961],\n [ 7244, 7239, 7235, 7235, 7230, 7227,\n 7218, 7211],\n [ 95225, 95230, 95234, 95234, 95239, 95239,\n 95239, 95246],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021104 CTGTTAGTGCTGTTTT---AATGTACCTCGCAGTA 3021136\ncavPor2.s 458 -----ATTACTTTCTT---AATGTAAATTTTTATA 431\noryCun1.s 4052 TTGCTAGTA--TTCTC---AATGTAATATTTTATA 4022\notoGar1.s 171219 TTGCTGGTGTTCCCTT---AATATAATGTTTTATA 171187\ncalJac1.C 10692 TTACTCGTG--CCCTT---AATATAGCATTTTATA 10722\nhg18.chr6 155025133 TTGCTGGTA--CTCTT---AATATCACATTTTATA 155025103\npanTro2.c 157515187 TTGCTGGTA--CTCTT---AATATCACATTTTATA 157515157\nponAbe2.c 158037354 TTGCTGGTG--CTCTT---AATATAACATTTTATA 158037324\ncanFam2.c 47544598 TTGCTGGTGCTCTCAA---AATGTAGCA------- 47544573\nfelCat3.s 45986 TTGCTGGTGCTCTCAA---AATATAACA------- 45961\ndasNov1.s 7244 TTGCTGGTG--ATCTGATTAATGTAACATTTTATG 7211\nechTel1.s 95225 CTGTTAATG--CTCTG------------TTTTATG 95246\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=44222.000000\ns mm9.chr10 3021104 32 + 129993255 CTGTTAGTGCTGTTTT---AATGTACCTCGCAGTA\ns cavPor2.scaffold_216473 9568 27 - 10026 -----ATTACTTTCTT---AATGTAAATTTTTATA\nq cavPor2.scaffold_216473 -----55455868746---7957999989884575\ni cavPor2.scaffold_216473 C 0 C 0\ns oryCun1.scaffold_156751 674 30 - 4726 TTGCTAGTA--TTCTC---AATGTAATATTTTATA\nq oryCun1.scaffold_156751 999979999--96665---6999999999999999\ni oryCun1.scaffold_156751 C 0 C 0\ns otoGar1.scaffold_334.1-359464 188245 32 - 359464 TTGCTGGTGTTCCCTT---AATATAATGTTTTATA\nq otoGar1.scaffold_334.1-359464 9999999999999999---9999999999999999\ni otoGar1.scaffold_334.1-359464 C 0 C 0\ns calJac1.Contig6394 10692 30 + 133105 TTACTCGTG--CCCTT---AATATAGCATTTTATA\ni calJac1.Contig6394 C 0 C 0\ns hg18.chr6 15874859 30 - 170899992 TTGCTGGTA--CTCTT---AATATCACATTTTATA\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16393425 30 - 173908612 TTGCTGGTA--CTCTT---AATATCACATTTTATA\nq panTro2.chr6 999999999--99999---9999999999999999\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16173077 30 - 174210431 TTGCTGGTG--CTCTT---AATATAACATTTTATA\ni ponAbe2.chr6 C 0 C 0\ns canFam2.chr1 78071658 25 - 125616256 TTGCTGGTGCTCTCAA---AATGTAGCA-------\nq canFam2.chr1 9999999999999999---999999999-------\ni canFam2.chr1 C 0 I 196\ns felCat3.scaffold_205680 73368 25 - 119354 TTGCTGGTGCTCTCAA---AATATAACA-------\nq felCat3.scaffold_205680 8677668566555658---876555655-------\ni felCat3.scaffold_205680 C 0 I 6\ns dasNov1.scaffold_56749 3226 33 - 10470 TTGCTGGTG--ATCTGATTAATGTAACATTTTATG\nq dasNov1.scaffold_56749 856647736--775356546747663745776545\ni dasNov1.scaffold_56749 C 0 C 0\ns echTel1.scaffold_288249 95225 21 + 100002 CTGTTAATG--CTCTG------------TTTTATG\nq echTel1.scaffold_288249 999999999--99999------------9999999\ni echTel1.scaffold_288249 I 7564 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'T', 'G', 'T', 'T', 'A', 'G', 'T', 'G', 'C', 'T', 'G', 'T',\n 'T', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'C',\n 'C', 'T', 'C', 'G', 'C', 'A', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', 'A', 'T', 'T', 'A', 'C', 'T', 'T', 'T',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'A',\n 'A', 'T', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'A', 'G', 'T', 'A', '-', '-', 'T', 'T',\n 'C', 'T', 'C', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'A',\n 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', 'T', 'T', 'C', 'C',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'A',\n 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'A', 'C', 'T', 'C', 'G', 'T', 'G', '-', '-', 'C', 'C',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'G',\n 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'A', '-', '-', 'C', 'T',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'C', 'A',\n 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'A', '-', '-', 'C', 'T',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'C', 'A',\n 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', '-', '-', 'C', 'T',\n 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'A',\n 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', 'C', 'T', 'C', 'T',\n 'C', 'A', 'A', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'G',\n 'C', 'A', '-', '-', '-', '-', '-', '-', '-'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', 'C', 'T', 'C', 'T',\n 'C', 'A', 'A', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'A',\n 'C', 'A', '-', '-', '-', '-', '-', '-', '-'],\n ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', '-', '-', 'A', 'T',\n 'C', 'T', 'G', 'A', 'T', 'T', 'A', 'A', 'T', 'G', 'T', 'A', 'A',\n 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'G'],\n ['C', 'T', 'G', 'T', 'T', 'A', 'A', 'T', 'G', '-', '-', 'C', 'T',\n 'C', 'T', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'T', 'T', 'T', 'T', 'A', 'T', 'G']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 43757)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021136 : 3021136 + 44],\n \"AGGCAAATGAGGTGATAAGATTGTGTTTACTCCCTCTGTGCTTG\",\n )\n self.assertEqual(\n alignment[0],\n \"AGGCAAATGAGGTGATAAGA-------TTGTGTT-----TAC----TCCCTCTGTGC----------TTG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[388 : 388 + 43],\n \"catacacacagagaatgAATATATCACTGTTATCTCATCTGCT\",\n )\n self.assertEqual(\n alignment[1],\n \"AG-CAGATGAGATAACAGTG-------ATATATT-----cat----tctctgtgtgt----------atg\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"4996766988786798889867956675666896967579888\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[3980 : 3980 + 42],\n \"CACACAAATAAGAAATAGATGCCCTCATCACCTCATTTGCTT\",\n )\n self.assertEqual(\n alignment[2],\n \"AAGCAAATGAGGTGATGAGG---------GCATC-----TAT----TTCTTATTTGT----------GTG\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"999989999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[3].seq), 359464)\n self.assertEqual(\n alignment.sequences[3].seq[171142 : 171142 + 45],\n \"CACACGTGGGGGACAAGTACATATGTCCTGTGATCTCATTTGTTT\",\n )\n self.assertEqual(\n alignment[3],\n \"AAACAAATGAGATCACA-GG-------ACATATG-----TA--CTTGTCCCCCACGT----------GTG\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"999999999999999999999999999999939999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 15)\n self.assertEqual(alignment.sequences[4].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[4].seq), 133105)\n self.assertEqual(\n alignment.sequences[4].seq[10722 : 10722 + 45],\n \"AAGCAAATGAGATCACAGCACATGTATATTTTTTCTCCGTGTGTG\",\n )\n self.assertEqual(\n alignment[4],\n \"AAGCAAATGAGATCACA----------GCACATG-----TATATTTTTTCTCCGTGT----------GTG\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 15)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155025056 : 155025056 + 47],\n \"CACACACAGAGAAAAAAACATATATGCCCTTGTGATCTCATTTGTTT\",\n )\n self.assertEqual(\n alignment[5],\n \"AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 15)\n self.assertEqual(alignment.sequences[6].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[6].seq), 173908612)\n self.assertEqual(\n alignment.sequences[6].seq[157515110 : 157515110 + 47],\n \"CACACACAGAGAAAAAAACATATATGCCCTTGTGATCTCATTTGTTT\",\n )\n self.assertEqual(\n alignment[6],\n \"AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 15)\n self.assertEqual(alignment.sequences[7].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[7].seq), 174210431)\n self.assertEqual(\n alignment.sequences[7].seq[158037277 : 158037277 + 47],\n \"CACACACAGAGAAAAAAATACATATGCCCTTGTGATCTCATTTGTTT\",\n )\n self.assertEqual(\n alignment[7],\n \"AAACAAATGAGATCACAAGG-------GCATATG-----TAT-TTTTTTCTCTGTGT----------GTG\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 15)\n self.assertEqual(alignment.sequences[8].id, \"eriEur1.scaffold_266115\")\n self.assertEqual(len(alignment.sequences[8].seq), 4589)\n self.assertEqual(\n alignment.sequences[8].seq[358 : 358 + 65],\n \"taaataataagataagatgaaagCATAGCATGTATTTTCTtgccctctccttctctgtctctgtc\",\n )\n self.assertEqual(\n alignment[8],\n \"taaataataagataagatgaaagCATAGCATGTA-----TTTTCTtgccctctccttctctgtctctgtc\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[9].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[9].seq), 125616256)\n self.assertEqual(\n alignment.sequences[9].seq[47544326 : 47544326 + 51],\n \"CACAGACCCCACACAGAGAGAAAGCATATACACACGGTATCTCATTTTCTa\",\n )\n self.assertEqual(\n alignment[9],\n \"tAGAAAATGAGATACC-----------GTGTGTA-----TATGCTTTCTCTCTGTGT---GGGGTCTGTG\",\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 196)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[10].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[10].seq), 119354)\n self.assertEqual(\n alignment.sequences[10].seq[45904 : 45904 + 51],\n \"CACAGACACCACACAGAGAGGAAGAATACACGTGTCTTATCTCATTTGCTT\",\n )\n self.assertEqual(\n alignment[10],\n \"AAGCAAATGAGATAAG-----------ACACGTG-----TATTCTTCCTCTCTGTGT---GGTGTCTGTG\",\n )\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"],\n \"975559665645435353463242434515353544222333635339999\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 6)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[11].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[11].seq), 10470)\n self.assertEqual(\n alignment.sequences[11].seq[7165 : 7165 + 46],\n \"TACACAGAGAAAGAATATTTATTTGCCCTGGTCCTCTCACTTTCCT\",\n )\n self.assertEqual(\n alignment[11],\n \"AGGAAAGTGAGAGGACCAGG-------GCAAATA-----AATATTCTTTCTCTGTGT----------A--\",\n )\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"],\n \"5556976455665765856867685558586864578595356565\",\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[12].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[12].seq), 100002)\n self.assertEqual(\n alignment.sequences[12].seq[95246 : 95246 + 51],\n \"AAGAAGGTGAGATGACAAGGGTGTATAGATAGGATATTCTTGCTTTGGGTG\",\n )\n self.assertEqual(\n alignment[12],\n \"AAGAAGGTGAGATGACAAGG-------GTGTATAGATAGGATATTCTTGCTTTGGGT----------G--\",\n )\n self.assertEqual(\n alignment.sequences[12].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[12].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[12].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (324116, 323493))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 13)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 2)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021136, 3021138, 3021139, 3021152, 3021153, 3021154,\n 3021156, 3021156, 3021158, 3021163, 3021163, 3021165,\n 3021166, 3021166, 3021166, 3021177, 3021177, 3021177,\n 3021178, 3021180],\n [ 431, 429, 429, 416, 415, 414,\n 412, 412, 410, 405, 405, 403,\n 402, 402, 402, 391, 391, 391,\n 390, 388],\n [ 4022, 4020, 4019, 4006, 4005, 4004,\n 4002, 4002, 4002, 3997, 3997, 3995,\n 3994, 3994, 3994, 3983, 3983, 3983,\n 3982, 3980],\n [ 171187, 171185, 171184, 171171, 171170, 171170,\n 171168, 171168, 171166, 171161, 171161, 171159,\n 171159, 171159, 171156, 171145, 171145, 171145,\n 171144, 171142],\n [ 10722, 10724, 10725, 10738, 10739, 10739,\n 10739, 10739, 10741, 10746, 10746, 10748,\n 10749, 10750, 10753, 10764, 10764, 10764,\n 10765, 10767],\n [155025103, 155025101, 155025100, 155025087, 155025086, 155025085,\n 155025083, 155025083, 155025081, 155025076, 155025076, 155025074,\n 155025073, 155025073, 155025070, 155025059, 155025059, 155025059,\n 155025058, 155025056],\n [157515157, 157515155, 157515154, 157515141, 157515140, 157515139,\n 157515137, 157515137, 157515135, 157515130, 157515130, 157515128,\n 157515127, 157515127, 157515124, 157515113, 157515113, 157515113,\n 157515112, 157515110],\n [158037324, 158037322, 158037321, 158037308, 158037307, 158037306,\n 158037304, 158037304, 158037302, 158037297, 158037297, 158037295,\n 158037294, 158037294, 158037291, 158037280, 158037280, 158037280,\n 158037279, 158037277],\n [ 358, 360, 361, 374, 375, 376,\n 378, 385, 387, 392, 392, 394,\n 395, 396, 399, 410, 413, 420,\n 421, 423],\n [ 47544377, 47544375, 47544374, 47544361, 47544361, 47544361,\n 47544361, 47544361, 47544359, 47544354, 47544354, 47544352,\n 47544351, 47544350, 47544347, 47544336, 47544336, 47544329,\n 47544328, 47544326],\n [ 45955, 45953, 45952, 45939, 45939, 45939,\n 45939, 45939, 45937, 45932, 45932, 45930,\n 45929, 45928, 45925, 45914, 45914, 45907,\n 45906, 45904],\n [ 7211, 7209, 7208, 7195, 7194, 7193,\n 7191, 7191, 7189, 7184, 7184, 7182,\n 7181, 7180, 7177, 7166, 7166, 7166,\n 7165, 7165],\n [ 95246, 95248, 95249, 95262, 95263, 95264,\n 95266, 95266, 95268, 95273, 95278, 95280,\n 95281, 95282, 95285, 95296, 95296, 95296,\n 95297, 95297],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021136 AGGCAAATGAGGTGATAAGA-------TTGTGTT-----TAC----TCCCTCTGTGC---\ncavPor2.s 431 AG-CAGATGAGATAACAGTG-------ATATATT-----cat----tctctgtgtgt---\noryCun1.s 4022 AAGCAAATGAGGTGATGAGG---------GCATC-----TAT----TTCTTATTTGT---\notoGar1.s 171187 AAACAAATGAGATCACA-GG-------ACATATG-----TA--CTTGTCCCCCACGT---\ncalJac1.C 10722 AAGCAAATGAGATCACA----------GCACATG-----TATATTTTTTCTCCGTGT---\nhg18.chr6 155025103 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT---\npanTro2.c 157515157 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT---\nponAbe2.c 158037324 AAACAAATGAGATCACAAGG-------GCATATG-----TAT-TTTTTTCTCTGTGT---\neriEur1.s 358 taaataataagataagatgaaagCATAGCATGTA-----TTTTCTtgccctctccttctc\ncanFam2.c 47544377 tAGAAAATGAGATACC-----------GTGTGTA-----TATGCTTTCTCTCTGTGT---\nfelCat3.s 45955 AAGCAAATGAGATAAG-----------ACACGTG-----TATTCTTCCTCTCTGTGT---\ndasNov1.s 7211 AGGAAAGTGAGAGGACCAGG-------GCAAATA-----AATATTCTTTCTCTGTGT---\nechTel1.s 95246 AAGAAGGTGAGATGACAAGG-------GTGTATAGATAGGATATTCTTGCTTTGGGT---\n\nmm9.chr10 3021177 -------TTG 3021180\ncavPor2.s 391 -------atg 388\noryCun1.s 3983 -------GTG 3980\notoGar1.s 171145 -------GTG 171142\ncalJac1.C 10764 -------GTG 10767\nhg18.chr6 155025059 -------GTG 155025056\npanTro2.c 157515113 -------GTG 157515110\nponAbe2.c 158037280 -------GTG 158037277\neriEur1.s 413 tgtctctgtc 423\ncanFam2.c 47544336 GGGGTCTGTG 47544326\nfelCat3.s 45914 GGTGTCTGTG 45904\ndasNov1.s 7166 -------A-- 7165\nechTel1.s 95296 -------G-- 95297\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=43757.000000\ns mm9.chr10 3021136 44 + 129993255 AGGCAAATGAGGTGATAAGA-------TTGTGTT-----TAC----TCCCTCTGTGC----------TTG\ns cavPor2.scaffold_216473 9595 43 - 10026 AG-CAGATGAGATAACAGTG-------ATATATT-----cat----tctctgtgtgt----------atg\nq cavPor2.scaffold_216473 49-96766988786798889-------8679566-----756----66896967579----------888\ni cavPor2.scaffold_216473 C 0 C 0\ns oryCun1.scaffold_156751 704 42 - 4726 AAGCAAATGAGGTGATGAGG---------GCATC-----TAT----TTCTTATTTGT----------GTG\nq oryCun1.scaffold_156751 99998999999999999999---------99999-----999----99999999999----------999\ni oryCun1.scaffold_156751 C 0 C 0\ns otoGar1.scaffold_334.1-359464 188277 45 - 359464 AAACAAATGAGATCACA-GG-------ACATATG-----TA--CTTGTCCCCCACGT----------GTG\nq otoGar1.scaffold_334.1-359464 99999999999999999-99-------9999999-----99--99939999999999----------999\ni otoGar1.scaffold_334.1-359464 C 0 I 15\ns calJac1.Contig6394 10722 45 + 133105 AAGCAAATGAGATCACA----------GCACATG-----TATATTTTTTCTCCGTGT----------GTG\ni calJac1.Contig6394 C 0 I 15\ns hg18.chr6 15874889 47 - 170899992 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG\ni hg18.chr6 C 0 I 15\ns panTro2.chr6 16393455 47 - 173908612 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG\nq panTro2.chr6 99999999999999999999-------9999999-----999-99999999999999----------999\ni panTro2.chr6 C 0 I 15\ns ponAbe2.chr6 16173107 47 - 174210431 AAACAAATGAGATCACAAGG-------GCATATG-----TAT-TTTTTTCTCTGTGT----------GTG\ni ponAbe2.chr6 C 0 I 15\ns eriEur1.scaffold_266115 358 65 + 4589 taaataataagataagatgaaagCATAGCATGTA-----TTTTCTtgccctctccttctctgtctctgtc\nq eriEur1.scaffold_266115 9999999999999999999999999999999999-----9999999999999999999999999999999\ni eriEur1.scaffold_266115 N 0 I 9\ns canFam2.chr1 78071879 51 - 125616256 tAGAAAATGAGATACC-----------GTGTGTA-----TATGCTTTCTCTCTGTGT---GGGGTCTGTG\nq canFam2.chr1 9999999999999999-----------9999999-----999999999999999999---9999999999\ni canFam2.chr1 I 196 I 9\ns felCat3.scaffold_205680 73399 51 - 119354 AAGCAAATGAGATAAG-----------ACACGTG-----TATTCTTCCTCTCTGTGT---GGTGTCTGTG\nq felCat3.scaffold_205680 9755596656454353-----------5346324-----243451535354422233---3635339999\ni felCat3.scaffold_205680 I 6 I 9\ns dasNov1.scaffold_56749 3259 46 - 10470 AGGAAAGTGAGAGGACCAGG-------GCAAATA-----AATATTCTTTCTCTGTGT----------A--\nq dasNov1.scaffold_56749 55569764556657658568-------6768555-----858686457859535656----------5--\ni dasNov1.scaffold_56749 C 0 C 0\ns echTel1.scaffold_288249 95246 51 + 100002 AAGAAGGTGAGATGACAAGG-------GTGTATAGATAGGATATTCTTGCTTTGGGT----------G--\nq echTel1.scaffold_288249 99999999999999999999-------999999999999999999999999999999----------9--\ni echTel1.scaffold_288249 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\ne tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['A', 'G', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'G', 'T',\n 'G', 'A', 'T', 'A', 'A', 'G', 'A', '-', '-', '-', '-', '-', '-',\n '-', 'T', 'T', 'G', 'T', 'G', 'T', 'T', '-', '-', '-', '-', '-',\n 'T', 'A', 'C', '-', '-', '-', '-', 'T', 'C', 'C', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'C', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'T', 'T', 'G'],\n ['A', 'G', '-', 'C', 'A', 'G', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'A', 'A', 'C', 'A', 'G', 'T', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'A', 'T', 'A', 'T', 'A', 'T', 'T', '-', '-', '-', '-', '-',\n 'c', 'a', 't', '-', '-', '-', '-', 't', 'c', 't', 'c', 't', 'g',\n 't', 'g', 't', 'g', 't', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'a', 't', 'g'],\n ['A', 'A', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'G', 'T',\n 'G', 'A', 'T', 'G', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', 'G', 'C', 'A', 'T', 'C', '-', '-', '-', '-', '-',\n 'T', 'A', 'T', '-', '-', '-', '-', 'T', 'T', 'C', 'T', 'T', 'A',\n 'T', 'T', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'C', 'A', 'C', 'A', '-', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'A', 'C', 'A', 'T', 'A', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'A', '-', '-', 'C', 'T', 'T', 'G', 'T', 'C', 'C', 'C', 'C',\n 'C', 'A', 'C', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['A', 'A', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'C', 'A', 'C', 'A', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'C', 'A', 'C', 'A', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C',\n 'C', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'C', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'C', 'A', 'T', 'A', 'T', 'A', '-', '-', '-', '-', '-',\n 'T', 'G', 'T', '-', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'C', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'C', 'A', 'T', 'A', 'T', 'A', '-', '-', '-', '-', '-',\n 'T', 'G', 'T', '-', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'C', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'C', 'A', 'T', 'A', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'A', 'T', '-', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', 'T', 'G'],\n ['t', 'a', 'a', 'a', 't', 'a', 'a', 't', 'a', 'a', 'g', 'a', 't',\n 'a', 'a', 'g', 'a', 't', 'g', 'a', 'a', 'a', 'g', 'C', 'A', 'T',\n 'A', 'G', 'C', 'A', 'T', 'G', 'T', 'A', '-', '-', '-', '-', '-',\n 'T', 'T', 'T', 'T', 'C', 'T', 't', 'g', 'c', 'c', 'c', 't', 'c',\n 't', 'c', 'c', 't', 't', 'c', 't', 'c', 't', 'g', 't', 'c', 't',\n 'c', 't', 'g', 't', 'c'],\n ['t', 'A', 'G', 'A', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'A', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'T', 'G', 'T', 'G', 'T', 'A', '-', '-', '-', '-', '-',\n 'T', 'A', 'T', 'G', 'C', 'T', 'T', 'T', 'C', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', 'G', 'G', 'G', 'G', 'T',\n 'C', 'T', 'G', 'T', 'G'],\n ['A', 'A', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T',\n 'A', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', 'A', 'C', 'A', 'C', 'G', 'T', 'G', '-', '-', '-', '-', '-',\n 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', 'G', 'G', 'T', 'G', 'T',\n 'C', 'T', 'G', 'T', 'G'],\n ['A', 'G', 'G', 'A', 'A', 'A', 'G', 'T', 'G', 'A', 'G', 'A', 'G',\n 'G', 'A', 'C', 'C', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'C', 'A', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-',\n 'A', 'A', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'C', 'T', 'C',\n 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'A', '-', '-'],\n ['A', 'A', 'G', 'A', 'A', 'G', 'G', 'T', 'G', 'A', 'G', 'A', 'T',\n 'G', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-',\n '-', 'G', 'T', 'G', 'T', 'A', 'T', 'A', 'G', 'A', 'T', 'A', 'G',\n 'G', 'A', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'G', 'C', 'T', 'T',\n 'T', 'G', 'G', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', 'G', '-', '-']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 32886)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021180 : 3021180 + 24],\n \"TCCCAGAGAGTCTGATAGGAGGAG\",\n )\n self.assertEqual(\n alignment[0], \"-------------------TCCC-------AGAGAGTCTGA-TAGGAGGAG\"\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[356 : 356 + 32],\n \"TACTTTATACTCAGAGCCACTATACAAaggca\",\n )\n self.assertEqual(\n alignment[1], \"-------------------tgcctTTGTATAGTGGCTCTGAGTATAAAGTA\"\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"67576649966655666885655548785776\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[3953 : 3953 + 27], \"TATATTCAGAAATGCTATACACAGGCA\"\n )\n self.assertEqual(\n alignment[2], \"-------------------TGCCTGTGTATAGCATTTCTGAATATA-----\"\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"], \"999999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158037237 : 158037237 + 25],\n \"TACTTCATATTCATACACACTCAGA\",\n )\n self.assertEqual(\n alignment[3], \"-----------------------TCTG---AGTGTGTATGAATATGAAGTA\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 15)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 173908612)\n self.assertEqual(\n alignment.sequences[4].seq[157515070 : 157515070 + 25],\n \"TACTTCATATTCATACATACTCAGA\",\n )\n self.assertEqual(\n alignment[4], \"-----------------------TCTG---AGTATGTATGAATATGAAGTA\"\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 15)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155025016 : 155025016 + 25],\n \"TACTTCATATTCATACATACTCAGA\",\n )\n self.assertEqual(\n alignment[5], \"-----------------------TCTG---AGTATGTATGAATATGAAGTA\"\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 15)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[6].seq), 133105)\n self.assertEqual(\n alignment.sequences[6].seq[10782 : 10782 + 25], \"TCTGAGTATGTCTGAATATGAAGTG\"\n )\n self.assertEqual(\n alignment[6], \"-----------------------TCTG---AGTATGTCTGAATATGAAGTG\"\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 15)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[7].seq), 359464)\n self.assertEqual(\n alignment.sequences[7].seq[171102 : 171102 + 25],\n \"CACATCATGTTCAGACACACTTAGA\",\n )\n self.assertEqual(\n alignment[7], \"-----------------------TCTA---AGTGTGTCTGAACATGATGTG\"\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 15)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[8].seq), 498454)\n self.assertEqual(\n alignment.sequences[8].seq[323468 : 323468 + 25],\n \"TACCTCAAGTTCAGACACTCAGAGA\",\n )\n self.assertEqual(\n alignment[8], \"-----------------------TCTC---TGAGTGTCTGAACTTGAGGTA\"\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 623)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"eriEur1.scaffold_266115\")\n self.assertEqual(len(alignment.sequences[9].seq), 4589)\n self.assertEqual(\n alignment.sequences[9].seq[432 : 432 + 19], \"TCTCAGTGTGTCTGACCAG\"\n )\n self.assertEqual(\n alignment[9], \"-----------------------TCTC---AGTGTGTCTGACCAG------\"\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"], \"9999999999999999999\"\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[10].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[10].seq), 125616256)\n self.assertEqual(\n alignment.sequences[10].seq[47544292 : 47544292 + 25],\n \"TACCTCACATTCAGACACACTCAGA\",\n )\n self.assertEqual(\n alignment[10], \"-----------------------TCTG---AGTGTGTCTGAATGTGAGGTA\"\n )\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[11].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[11].seq), 119354)\n self.assertEqual(\n alignment.sequences[11].seq[45870 : 45870 + 25], \"CACCTCACATTCAGGAACACTCAGA\"\n )\n self.assertEqual(\n alignment[11], \"-----------------------TCTG---AGTGTTCCTGAATGTGAGGTG\"\n )\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"], \"9999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[12].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[12].seq), 10470)\n self.assertEqual(\n alignment.sequences[12].seq[7118 : 7118 + 47],\n \"TACCTCAAGTTCAGACACGCTCAGAAATGCTCCGCAAAGGCACACAA\",\n )\n self.assertEqual(\n alignment[12], \"T-TGTGTGCCTTTGCGGAGCATTTCTG---AGCGTGTCTGAACTTGAGGTA\"\n )\n self.assertEqual(\n alignment.sequences[12].annotations[\"quality\"],\n \"73659557766555777595699547965955937797755656587\",\n )\n self.assertEqual(alignment.sequences[12].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[12].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[13].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[13].seq), 100002)\n self.assertEqual(\n alignment.sequences[13].seq[95297 : 95297 + 48],\n \"TGCCCAGGACTGCGCATGGTATTTCTTGGTGTGTCTGAAGGTGAGATA\",\n )\n self.assertEqual(\n alignment[13], \"TGCCCAGGACTGCGCATGGTATTTCTT---GGTGTGTCTGAAGGTGAGATA\"\n )\n self.assertEqual(\n alignment.sequences[13].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[13].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[13].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 14)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021180, 3021180, 3021180, 3021180, 3021184, 3021184,\n 3021184, 3021195, 3021195, 3021198, 3021199, 3021204],\n [ 388, 388, 388, 388, 384, 380,\n 377, 366, 365, 362, 361, 356],\n [ 3980, 3980, 3980, 3980, 3976, 3972,\n 3969, 3958, 3957, 3954, 3953, 3953],\n [158037262, 158037262, 158037262, 158037262, 158037262, 158037258,\n 158037258, 158037247, 158037246, 158037243, 158037242, 158037237],\n [157515095, 157515095, 157515095, 157515095, 157515095, 157515091,\n 157515091, 157515080, 157515079, 157515076, 157515075, 157515070],\n [155025041, 155025041, 155025041, 155025041, 155025041, 155025037,\n 155025037, 155025026, 155025025, 155025022, 155025021, 155025016],\n [ 10782, 10782, 10782, 10782, 10782, 10786,\n 10786, 10797, 10798, 10801, 10802, 10807],\n [ 171127, 171127, 171127, 171127, 171127, 171123,\n 171123, 171112, 171111, 171108, 171107, 171102],\n [ 323493, 323493, 323493, 323493, 323493, 323489,\n 323489, 323478, 323477, 323474, 323473, 323468],\n [ 432, 432, 432, 432, 432, 436,\n 436, 447, 448, 451, 451, 451],\n [ 47544317, 47544317, 47544317, 47544317, 47544317, 47544313,\n 47544313, 47544302, 47544301, 47544298, 47544297, 47544292],\n [ 45895, 45895, 45895, 45895, 45895, 45891,\n 45891, 45880, 45879, 45876, 45875, 45870],\n [ 7165, 7164, 7164, 7147, 7143, 7139,\n 7139, 7128, 7127, 7124, 7123, 7118],\n [ 95297, 95298, 95299, 95316, 95320, 95324,\n 95324, 95335, 95336, 95339, 95340, 95345],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021180 -------------------TCCC-------AGAGAGTCTGA-TAGGAGGAG\ncavPor2.s 388 -------------------tgcctTTGTATAGTGGCTCTGAGTATAAAGTA\noryCun1.s 3980 -------------------TGCCTGTGTATAGCATTTCTGAATATA-----\nponAbe2.c 158037262 -----------------------TCTG---AGTGTGTATGAATATGAAGTA\npanTro2.c 157515095 -----------------------TCTG---AGTATGTATGAATATGAAGTA\nhg18.chr6 155025041 -----------------------TCTG---AGTATGTATGAATATGAAGTA\ncalJac1.C 10782 -----------------------TCTG---AGTATGTCTGAATATGAAGTG\notoGar1.s 171127 -----------------------TCTA---AGTGTGTCTGAACATGATGTG\ntupBel1.s 323493 -----------------------TCTC---TGAGTGTCTGAACTTGAGGTA\neriEur1.s 432 -----------------------TCTC---AGTGTGTCTGACCAG------\ncanFam2.c 47544317 -----------------------TCTG---AGTGTGTCTGAATGTGAGGTA\nfelCat3.s 45895 -----------------------TCTG---AGTGTTCCTGAATGTGAGGTG\ndasNov1.s 7165 T-TGTGTGCCTTTGCGGAGCATTTCTG---AGCGTGTCTGAACTTGAGGTA\nechTel1.s 95297 TGCCCAGGACTGCGCATGGTATTTCTT---GGTGTGTCTGAAGGTGAGATA\n\nmm9.chr10 3021204\ncavPor2.s 356\noryCun1.s 3953\nponAbe2.c 158037237\npanTro2.c 157515070\nhg18.chr6 155025016\ncalJac1.C 10807\notoGar1.s 171102\ntupBel1.s 323468\neriEur1.s 451\ncanFam2.c 47544292\nfelCat3.s 45870\ndasNov1.s 7118\nechTel1.s 95345\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=32886.000000\ns mm9.chr10 3021180 24 + 129993255 -------------------TCCC-------AGAGAGTCTGA-TAGGAGGAG\ns cavPor2.scaffold_216473 9638 32 - 10026 -------------------tgcctTTGTATAGTGGCTCTGAGTATAAAGTA\nq cavPor2.scaffold_216473 -------------------67576649966655666885655548785776\ni cavPor2.scaffold_216473 C 0 C 0\ns oryCun1.scaffold_156751 746 27 - 4726 -------------------TGCCTGTGTATAGCATTTCTGAATATA-----\nq oryCun1.scaffold_156751 -------------------999999999999999999999999999-----\ni oryCun1.scaffold_156751 C 0 C 0\ns ponAbe2.chr6 16173169 25 - 174210431 -----------------------TCTG---AGTGTGTATGAATATGAAGTA\ni ponAbe2.chr6 I 15 C 0\ns panTro2.chr6 16393517 25 - 173908612 -----------------------TCTG---AGTATGTATGAATATGAAGTA\nq panTro2.chr6 -----------------------9999---999999999999999999999\ni panTro2.chr6 I 15 C 0\ns hg18.chr6 15874951 25 - 170899992 -----------------------TCTG---AGTATGTATGAATATGAAGTA\ni hg18.chr6 I 15 C 0\ns calJac1.Contig6394 10782 25 + 133105 -----------------------TCTG---AGTATGTCTGAATATGAAGTG\ni calJac1.Contig6394 I 15 C 0\ns otoGar1.scaffold_334.1-359464 188337 25 - 359464 -----------------------TCTA---AGTGTGTCTGAACATGATGTG\nq otoGar1.scaffold_334.1-359464 -----------------------9999---999999999999999999999\ni otoGar1.scaffold_334.1-359464 I 15 C 0\ns tupBel1.scaffold_114895.1-498454 174961 25 - 498454 -----------------------TCTC---TGAGTGTCTGAACTTGAGGTA\nq tupBel1.scaffold_114895.1-498454 -----------------------9999---999999999999999999999\ni tupBel1.scaffold_114895.1-498454 I 623 C 0\ns eriEur1.scaffold_266115 432 19 + 4589 -----------------------TCTC---AGTGTGTCTGACCAG------\nq eriEur1.scaffold_266115 -----------------------9999---999999999999999------\ni eriEur1.scaffold_266115 I 9 C 0\ns canFam2.chr1 78071939 25 - 125616256 -----------------------TCTG---AGTGTGTCTGAATGTGAGGTA\nq canFam2.chr1 -----------------------9999---999999999999999999999\ni canFam2.chr1 I 9 C 0\ns felCat3.scaffold_205680 73459 25 - 119354 -----------------------TCTG---AGTGTTCCTGAATGTGAGGTG\nq felCat3.scaffold_205680 -----------------------9999---999999999999999999999\ni felCat3.scaffold_205680 I 9 C 0\ns dasNov1.scaffold_56749 3305 47 - 10470 T-TGTGTGCCTTTGCGGAGCATTTCTG---AGCGTGTCTGAACTTGAGGTA\nq dasNov1.scaffold_56749 7-3659557766555777595699547---965955937797755656587\ni dasNov1.scaffold_56749 C 0 C 0\ns echTel1.scaffold_288249 95297 48 + 100002 TGCCCAGGACTGCGCATGGTATTTCTT---GGTGTGTCTGAAGGTGAGATA\nq echTel1.scaffold_288249 999999999999999999999999999---999999999999999999999\ni echTel1.scaffold_288249 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', 'T', 'C', 'C', 'C', '-', '-', '-',\n '-', '-', '-', '-', 'A', 'G', 'A', 'G', 'A', 'G', 'T', 'C', 'T',\n 'G', 'A', '-', 'T', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'G'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', 't', 'g', 'c', 'c', 't', 'T', 'T',\n 'G', 'T', 'A', 'T', 'A', 'G', 'T', 'G', 'G', 'C', 'T', 'C', 'T',\n 'G', 'A', 'G', 'T', 'A', 'T', 'A', 'A', 'A', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', 'T', 'G', 'C', 'C', 'T', 'G', 'T',\n 'G', 'T', 'A', 'T', 'A', 'G', 'C', 'A', 'T', 'T', 'T', 'C', 'T',\n 'G', 'A', 'A', 'T', 'A', 'T', 'A', '-', '-', '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'A', 'T',\n 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'A', 'T', 'G', 'T', 'A', 'T',\n 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'A', 'T', 'G', 'T', 'A', 'T',\n 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'A', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'G'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'A', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'C', 'A', 'T', 'G', 'A', 'T', 'G', 'T', 'G'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'C', '-', '-', '-', 'T', 'G', 'A', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'C', 'T', 'T', 'G', 'A', 'G', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'C', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'C', 'C', 'A', 'G', '-', '-', '-', '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'T', 'G', 'T', 'G', 'A', 'G', 'G', 'T', 'A'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'T', 'C', 'C', 'T',\n 'G', 'A', 'A', 'T', 'G', 'T', 'G', 'A', 'G', 'G', 'T', 'G'],\n ['T', '-', 'T', 'G', 'T', 'G', 'T', 'G', 'C', 'C', 'T', 'T', 'T',\n 'G', 'C', 'G', 'G', 'A', 'G', 'C', 'A', 'T', 'T', 'T', 'C', 'T',\n 'G', '-', '-', '-', 'A', 'G', 'C', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'C', 'T', 'T', 'G', 'A', 'G', 'G', 'T', 'A'],\n ['T', 'G', 'C', 'C', 'C', 'A', 'G', 'G', 'A', 'C', 'T', 'G', 'C',\n 'G', 'C', 'A', 'T', 'G', 'G', 'T', 'A', 'T', 'T', 'T', 'C', 'T',\n 'T', '-', '-', '-', 'G', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T',\n 'G', 'A', 'A', 'G', 'G', 'T', 'G', 'A', 'G', 'A', 'T', 'A']],\n dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 309116)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021204 : 3021204 + 71],\n \"TGCACTGGTTTTCCTGCAGTGGTTCTCAGTAATAGGAAGACAACAGAATTTGAAGTATCCGGCTTTGGCCA\",\n )\n self.assertEqual(\n alignment[0],\n \"TGCACTGGTTTTCC-TGCAGTGGTTCTCAGTAATAGGAAGACA-ACAGAATTTGAAGTATCCGGCTTTGGCCA\",\n )\n self.assertEqual(alignment.sequences[1].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[1].seq), 100002)\n self.assertEqual(\n alignment.sequences[1].seq[95345 : 95345 + 73],\n \"GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAAATATTCTTGGCTA\",\n )\n self.assertEqual(\n alignment[1],\n \"GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAAATATTCTTGGCTA\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[2].seq), 10470)\n self.assertEqual(\n alignment.sequences[2].seq[7048 : 7048 + 70],\n \"TAGCCAAGAGCATTTATTATAAATTCAAAATGCTCTCTTAGTGTGATTTCCCTCACTGAAAATCAATGCA\",\n )\n self.assertEqual(\n alignment[2],\n \"TGCATTGATTTTCAGTGAGGGAAATCACAC---TAAGAGAGCATTTTGAATTTATAATAAATGCTCTTGGCTA\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"5796635799979575966667835948658458696597898258979678997999677999997699\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[3].seq), 119354)\n self.assertEqual(\n alignment.sequences[3].seq[45798 : 45798 + 72],\n \"CAGCCAAAAACATTTGCTATAATTTCAAAATGCATTCCTATTCATGTGAATCAATGCATGAAAATCAATGCA\",\n )\n self.assertEqual(\n alignment[3],\n \"TGCATTGATTTTCA-TGCATTGATTCACATGAATAGGAATGCATTTTGAAATTATAGCAAATGTTTTTGGCTG\",\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[4].seq), 125616256)\n self.assertEqual(\n alignment.sequences[4].seq[47544221 : 47544221 + 71],\n \"CAGCCAAAAGCATTTCCTATAAATTCAAATGTATTCCTATTCATGTGAATCAACGCATGAAAATTAATGCA\",\n )\n self.assertEqual(\n alignment[4],\n \"TGCATTAATTTTCA-TGCGTTGATTCACATGAATAGGAATACA-TTTGAATTTATAGGAAATGCTTTTGGCTG\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"eriEur1.scaffold_266115\")\n self.assertEqual(len(alignment.sequences[5].seq), 4589)\n self.assertEqual(\n alignment.sequences[5].seq[451 : 451 + 70],\n \"GCACTGATTCTCGAGGGTTGATTCCCAGTAAGAGGAAACTGCGTGAGTTTACAGTACATGGGCTTGGCTG\",\n )\n self.assertEqual(\n alignment[5],\n \"-GCACTGATTCTCG-AGGGTTGATTCCCAGTAAGAGGAAACTG-CGTGAGTTTACAGTACATGGGCTTGGCTG\",\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999799\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"sorAra1.scaffold_2476\")\n self.assertEqual(len(alignment.sequences[6].seq), 4997)\n self.assertEqual(\n alignment.sequences[6].seq[1615 : 1615 + 70],\n \"TGGCCAAATCATTTATCATAAATTGAAGTGCTTTCCTTTTCATGTGAATCAATACTTAAAAATCAATGCA\",\n )\n self.assertEqual(\n alignment[6],\n \"TGCATTGATTTTTA-AGTATTGATTCACATGAAAAGGAAAGCA-CTTCAATTTATGATAAAT-GATTTGGCCA\",\n )\n self.assertEqual(\n alignment.sequences[6].annotations[\"quality\"],\n \"8999999999998999999999999999999999999999999999999997999999999999999999\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"N\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[7].seq), 498454)\n self.assertEqual(\n alignment.sequences[7].seq[323397 : 323397 + 71],\n \"TGGTCAGAAGCATTTCCTATCAATTAGAATCGTTTCCTATTAATGTGACATAACACATGGAATTCAATGCA\",\n )\n self.assertEqual(\n alignment[7],\n \"TGCATTGAATTCCA-TGTGTTATGTCACATTAATAGGAAACGA-TTCTAATTGATAGGAAATGCTTCTGACCA\",\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"],\n \"99999899899999999999999999999999999999999999999999999999999999999999997\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(alignment.sequences[8].seq), 359464)\n self.assertEqual(\n alignment.sequences[8].seq[171035 : 171035 + 67],\n \"TGGCCAAATGCCTTTCCTACAAATTCACATGTTTTCCCGTTAAGGTGAATCAATGTGTAAAAATCCA\",\n )\n self.assertEqual(\n alignment[8],\n \"TG----GATTTTTA-CACATTGATTCACCTTAACGGGAAAACA-TGTGAATTTGTAGGAAAGGCATTTGGCCA\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"8899999999989999989994384888899999999966359999569699999923799351281\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 6280)\n self.assertEqual(alignment.sequences[9].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[9].seq), 133105)\n self.assertEqual(\n alignment.sequences[9].seq[10807 : 10807 + 71],\n \"TGCATTGGTTTTTATGCCTTGATTCACATGAATAGGAAAACGTTTGAATTTATAGGAAATGGTTTTGGCCA\",\n )\n self.assertEqual(\n alignment[9],\n \"TGCATTGGTTTTTA-TGCCTTGATTCACATGAATAGGAAAACG-TTTGAATTTATAGGAAATGGTTTTGGCCA\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[10].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[10].seq), 170899992)\n self.assertEqual(\n alignment.sequences[10].seq[155024945 : 155024945 + 71],\n \"TGGCCAAAACCATTTACTATAAATTCAAACATTTTCCTATTCATGTAAATCAATGCATAAAAATCAAAGCA\",\n )\n self.assertEqual(\n alignment[10],\n \"TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAATG-TTTGAATTTATAGTAAATGGTTTTGGCCA\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[11].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[11].seq), 173908612)\n self.assertEqual(\n alignment.sequences[11].seq[157514999 : 157514999 + 71],\n \"TGGCCAAAACCATTTACTATAAATTCAAATGTTTTCCTATTCATGTAAATCAATGCATAAAAATCAAAGCA\",\n )\n self.assertEqual(\n alignment[11],\n \"TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAACA-TTTGAATTTATAGTAAATGGTTTTGGCCA\",\n )\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[12].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[12].seq), 174210431)\n self.assertEqual(\n alignment.sequences[12].seq[158037166 : 158037166 + 71],\n \"TGGCCAAAACCATTTACTATAAATTCAAACGTTTTCCTATCCATGTAAATCAATGCATAAAAATCAAAGCA\",\n )\n self.assertEqual(\n alignment[12],\n \"TGCTTTGATTTTTA-TGCATTGATTTACATGGATAGGAAAACG-TTTGAATTTATAGTAAATGGTTTTGGCCA\",\n )\n self.assertEqual(alignment.sequences[12].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[12].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[13].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[13].seq), 4726)\n self.assertEqual(\n alignment.sequences[13].seq[3888 : 3888 + 65],\n \"TGACCAAAAGCCATTGCTATAAATGCAAATGTTTTCCCGTCGATGTAAATCAAAGTATGTAAAGA\",\n )\n self.assertEqual(\n alignment[13],\n \"------TCTTTACA-TACTTTGATTTACATCGACGGGAAAACA-TTTGCATTTATAGCAATGGCTTTTGGTCA\",\n )\n self.assertEqual(\n alignment.sequences[13].annotations[\"quality\"],\n \"99999994999999999999989999999999999999999999999999899999999999999\",\n )\n self.assertEqual(alignment.sequences[13].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[13].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[14].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[14].seq), 10026)\n self.assertEqual(\n alignment.sequences[14].seq[285 : 285 + 71],\n \"TGGCCAAAACCATTTACTATAAATTGGACTGTTTTCCTATTAATGTGAATTAATGCATGGAAATCAATGCC\",\n )\n self.assertEqual(\n alignment[14],\n \"GGCATTGATTTCCA-TGCATTAATTCACATTAATAGGAAAACA-GTCCAATTTATAGTAAATGGTTTTGGCCA\",\n )\n self.assertEqual(\n alignment.sequences[14].annotations[\"quality\"],\n \"77888768786695388675879644655668865666547868687676669688688666687574686\",\n )\n self.assertEqual(alignment.sequences[14].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[14].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[14].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[14].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"ornAna1.chr2\")\n self.assertEqual(len(record.seq), 54797317)\n self.assertEqual(segment, (40046122, 40040432))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 15)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021204, 3021205, 3021206, 3021210, 3021218, 3021218,\n 3021233, 3021236, 3021246, 3021246, 3021264, 3021265,\n 3021275],\n [ 95345, 95346, 95347, 95351, 95359, 95360,\n 95375, 95378, 95388, 95389, 95407, 95408,\n 95418],\n [ 7118, 7117, 7116, 7112, 7104, 7103,\n 7088, 7088, 7078, 7077, 7059, 7058,\n 7048],\n [ 45870, 45869, 45868, 45864, 45856, 45856,\n 45841, 45838, 45828, 45827, 45809, 45808,\n 45798],\n [ 47544292, 47544291, 47544290, 47544286, 47544278, 47544278,\n 47544263, 47544260, 47544250, 47544250, 47544232, 47544231,\n 47544221],\n [ 451, 451, 452, 456, 464, 464,\n 479, 482, 492, 492, 510, 511,\n 521],\n [ 1685, 1684, 1683, 1679, 1671, 1671,\n 1656, 1653, 1643, 1643, 1625, 1625,\n 1615],\n [ 323468, 323467, 323466, 323462, 323454, 323454,\n 323439, 323436, 323426, 323426, 323408, 323407,\n 323397],\n [ 171102, 171101, 171100, 171100, 171092, 171092,\n 171077, 171074, 171064, 171064, 171046, 171045,\n 171035],\n [ 10807, 10808, 10809, 10813, 10821, 10821,\n 10836, 10839, 10849, 10849, 10867, 10868,\n 10878],\n [155025016, 155025015, 155025014, 155025010, 155025002, 155025002,\n 155024987, 155024984, 155024974, 155024974, 155024956, 155024955,\n 155024945],\n [157515070, 157515069, 157515068, 157515064, 157515056, 157515056,\n 157515041, 157515038, 157515028, 157515028, 157515010, 157515009,\n 157514999],\n [158037237, 158037236, 158037235, 158037231, 158037223, 158037223,\n 158037208, 158037205, 158037195, 158037195, 158037177, 158037176,\n 158037166],\n [ 3953, 3953, 3953, 3953, 3945, 3945,\n 3930, 3927, 3917, 3917, 3899, 3898,\n 3888],\n [ 356, 355, 354, 350, 342, 342,\n 327, 324, 314, 314, 296, 295,\n 285],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021204 TGCACTGGTTTTCC-TGCAGTGGTTCTCAGTAATAGGAAGACA-ACAGAATTTGAAGTAT\nechTel1.s 95345 GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAA\ndasNov1.s 7118 TGCATTGATTTTCAGTGAGGGAAATCACAC---TAAGAGAGCATTTTGAATTTATAATAA\nfelCat3.s 45870 TGCATTGATTTTCA-TGCATTGATTCACATGAATAGGAATGCATTTTGAAATTATAGCAA\ncanFam2.c 47544292 TGCATTAATTTTCA-TGCGTTGATTCACATGAATAGGAATACA-TTTGAATTTATAGGAA\neriEur1.s 451 -GCACTGATTCTCG-AGGGTTGATTCCCAGTAAGAGGAAACTG-CGTGAGTTTACAGTAC\nsorAra1.s 1685 TGCATTGATTTTTA-AGTATTGATTCACATGAAAAGGAAAGCA-CTTCAATTTATGATAA\ntupBel1.s 323468 TGCATTGAATTCCA-TGTGTTATGTCACATTAATAGGAAACGA-TTCTAATTGATAGGAA\notoGar1.s 171102 TG----GATTTTTA-CACATTGATTCACCTTAACGGGAAAACA-TGTGAATTTGTAGGAA\ncalJac1.C 10807 TGCATTGGTTTTTA-TGCCTTGATTCACATGAATAGGAAAACG-TTTGAATTTATAGGAA\nhg18.chr6 155025016 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAATG-TTTGAATTTATAGTAA\npanTro2.c 157515070 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAACA-TTTGAATTTATAGTAA\nponAbe2.c 158037237 TGCTTTGATTTTTA-TGCATTGATTTACATGGATAGGAAAACG-TTTGAATTTATAGTAA\noryCun1.s 3953 ------TCTTTACA-TACTTTGATTTACATCGACGGGAAAACA-TTTGCATTTATAGCAA\ncavPor2.s 356 GGCATTGATTTCCA-TGCATTAATTCACATTAATAGGAAAACA-GTCCAATTTATAGTAA\n\nmm9.chr10 3021262 CCGGCTTTGGCCA 3021275\nechTel1.s 95405 ATATTCTTGGCTA 95418\ndasNov1.s 7061 ATGCTCTTGGCTA 7048\nfelCat3.s 45811 ATGTTTTTGGCTG 45798\ncanFam2.c 47544234 ATGCTTTTGGCTG 47544221\neriEur1.s 508 ATGGGCTTGGCTG 521\nsorAra1.s 1627 AT-GATTTGGCCA 1615\ntupBel1.s 323410 ATGCTTCTGACCA 323397\notoGar1.s 171048 AGGCATTTGGCCA 171035\ncalJac1.C 10865 ATGGTTTTGGCCA 10878\nhg18.chr6 155024958 ATGGTTTTGGCCA 155024945\npanTro2.c 157515012 ATGGTTTTGGCCA 157514999\nponAbe2.c 158037179 ATGGTTTTGGCCA 158037166\noryCun1.s 3901 TGGCTTTTGGTCA 3888\ncavPor2.s 298 ATGGTTTTGGCCA 285\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=309116.000000\ns mm9.chr10 3021204 71 + 129993255 TGCACTGGTTTTCC-TGCAGTGGTTCTCAGTAATAGGAAGACA-ACAGAATTTGAAGTATCCGGCTTTGGCCA\ns echTel1.scaffold_288249 95345 73 + 100002 GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAAATATTCTTGGCTA\nq echTel1.scaffold_288249 9999999999999999999999999999999999999999999999999999999999999999999999999\ni echTel1.scaffold_288249 C 0 C 0\ns dasNov1.scaffold_56749 3352 70 - 10470 TGCATTGATTTTCAGTGAGGGAAATCACAC---TAAGAGAGCATTTTGAATTTATAATAAATGCTCTTGGCTA\nq dasNov1.scaffold_56749 579663579997957596666783594865---8458696597898258979678997999677999997699\ni dasNov1.scaffold_56749 C 0 C 0\ns felCat3.scaffold_205680 73484 72 - 119354 TGCATTGATTTTCA-TGCATTGATTCACATGAATAGGAATGCATTTTGAAATTATAGCAAATGTTTTTGGCTG\nq felCat3.scaffold_205680 99999999999999-9999999999999999999999999999999999999999999999999999999999\ni felCat3.scaffold_205680 C 0 C 0\ns canFam2.chr1 78071964 71 - 125616256 TGCATTAATTTTCA-TGCGTTGATTCACATGAATAGGAATACA-TTTGAATTTATAGGAAATGCTTTTGGCTG\nq canFam2.chr1 99999999999999-9999999999999999999999999999-99999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ns eriEur1.scaffold_266115 451 70 + 4589 -GCACTGATTCTCG-AGGGTTGATTCCCAGTAAGAGGAAACTG-CGTGAGTTTACAGTACATGGGCTTGGCTG\nq eriEur1.scaffold_266115 -9999999999999-9999999999999999999999999999-99999999999999999999999999799\ni eriEur1.scaffold_266115 C 0 C 0\ns sorAra1.scaffold_2476 3312 70 - 4997 TGCATTGATTTTTA-AGTATTGATTCACATGAAAAGGAAAGCA-CTTCAATTTATGATAAAT-GATTTGGCCA\nq sorAra1.scaffold_2476 89999999999989-9999999999999999999999999999-999999999799999999-9999999999\ni sorAra1.scaffold_2476 N 0 C 0\ns tupBel1.scaffold_114895.1-498454 174986 71 - 498454 TGCATTGAATTCCA-TGTGTTATGTCACATTAATAGGAAACGA-TTCTAATTGATAGGAAATGCTTCTGACCA\nq tupBel1.scaffold_114895.1-498454 99999899899999-9999999999999999999999999999-99999999999999999999999999997\ni tupBel1.scaffold_114895.1-498454 C 0 C 0\ns otoGar1.scaffold_334.1-359464 188362 67 - 359464 TG----GATTTTTA-CACATTGATTCACCTTAACGGGAAAACA-TGTGAATTTGTAGGAAAGGCATTTGGCCA\nq otoGar1.scaffold_334.1-359464 88----99999999-9899999899943848888999999999-66359999569699999923799351281\ni otoGar1.scaffold_334.1-359464 C 0 I 6280\ns calJac1.Contig6394 10807 71 + 133105 TGCATTGGTTTTTA-TGCCTTGATTCACATGAATAGGAAAACG-TTTGAATTTATAGGAAATGGTTTTGGCCA\ni calJac1.Contig6394 C 0 C 0\ns hg18.chr6 15874976 71 - 170899992 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAATG-TTTGAATTTATAGTAAATGGTTTTGGCCA\ni hg18.chr6 C 0 C 0\ns panTro2.chr6 16393542 71 - 173908612 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAACA-TTTGAATTTATAGTAAATGGTTTTGGCCA\nq panTro2.chr6 99999999999999-9999999999999999999999999999-99999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns ponAbe2.chr6 16173194 71 - 174210431 TGCTTTGATTTTTA-TGCATTGATTTACATGGATAGGAAAACG-TTTGAATTTATAGTAAATGGTTTTGGCCA\ni ponAbe2.chr6 C 0 C 0\ns oryCun1.scaffold_156751 773 65 - 4726 ------TCTTTACA-TACTTTGATTTACATCGACGGGAAAACA-TTTGCATTTATAGCAATGGCTTTTGGTCA\nq oryCun1.scaffold_156751 ------99999994-9999999999999899999999999999-99999999999999899999999999999\ni oryCun1.scaffold_156751 C 0 C 0\ns cavPor2.scaffold_216473 9670 71 - 10026 GGCATTGATTTCCA-TGCATTAATTCACATTAATAGGAAAACA-GTCCAATTTATAGTAAATGGTTTTGGCCA\nq cavPor2.scaffold_216473 77888768786695-3886758796446556688656665478-68687676669688688666687574686\ni cavPor2.scaffold_216473 C 0 C 0\ne ornAna1.chr2 14751195 5690 - 54797317 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 891219)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021275 : 3021275 + 146],\n \"CTTTCTCTGACATTACTGTAACTGAAGTAGCTCAGAAGCACAAAAGGTCACATCATGCATCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGCCACGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG\",\n )\n self.assertEqual(\n alignment[0],\n \"CTTTCTCTGACATTACTGTAACTGAAGTAGCTC-AGAAGCACAAAAGGTCACATCATGCATCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGC-----------------------CACGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[116 : 116 + 169],\n \"TTGAAATATGGAAGGAAATGATGGCGTGACTGGATTTCCTGCGAGACACATGAACTAAGTAATAAAATGCGAGGTGCCTTTATGAACGGAACTAGTAAATTTTGCATAAATGCCTGACATGACCTTTTGTGCTTTTCAGCTAGTTCGCTTACAGTAACATCAGCAAAGG\",\n )\n self.assertEqual(\n alignment[1],\n \"CCTTTGCTGATGTTACTGTAAGCGAACTAGCTG-AAAAGCACAAAAGGTCATGTCAGGCATTTATGCAAAATTTACTAGTTCCGTTCATAAAGGCACCTCGCATTTTATTACTTAGTTCATGTGTCTCGCAGGAAATCCAGTCACGCCATCATTTCCTTCCATATTTCAA\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"6685365455476645398666666666666688787886799997788875886655536666688786768476688854689668876558688874778656675665668746666788474786888875667457786687996867886548798845555\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[3730 : 3730 + 158],\n \"TTGAAATGTGGAAGGAAATCGCGGCGTGACTGGATTTCCTGAACAAAGTAATACAACACAAGGTGCTGTTATAAACAGTGCTAGTACATTTGACATAAATGCCTGCCATGGCCTTTTGTGCTTTGGAGCGCTTTCAGCTAGAGTAACATCAGAGACGA\",\n )\n self.assertEqual(\n alignment[2],\n \"TCGTCTCTGATGTTACTCTAGCTGAAAGCGCTC-CAAAGCACAAAAGGCCATGGCAGGCATTTATGTCAAATGTACTAGCACTGTTTATAACAGCACCTTGTGTTGTATTACTTTGTTCA-----------GGAAATCCAGTCACGCCGCGATTTCCTTCCACATTTCAA\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"99999987999999999999999999999799999999799999999898999999988999999988999999989996999999999988897996999999999999979999987899998987999799998998999999999777999899\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158036997 : 158036997 + 169],\n \"ATGAAATATGGAAGGAAATGATGGCGTGACTGAATTTCCTGAAAGATACATTAACAAAGTAATAAAACACAAGGTACCCTTATAAACAGCACTAGTAAGTTTTACATGAATGCCTCCCATGACCTTTTGTGCTTTTGAGCTATTTCAGTTACAGTAACATCAGAGAAGG\",\n )\n self.assertEqual(\n alignment[3],\n \"CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTCATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTATCTTTCAGGAAATTCAGTCACGCCATCATTTCCTTCCATATTTCAT\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[4].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 173908612)\n self.assertEqual(\n alignment.sequences[4].seq[157514830 : 157514830 + 169],\n \"ATGAAATATGGAAGGAAATGATGGCATGACTGGATTTCCTGAAAGGTACATTAACAAAGTAATAAAACACAAGGTACCCTTATAAACAGCACTAGTAAGTTTTACATAAATGCCTCCCATGACCTTTTGTGCTTTTGAGCTATTTCAGTTACAGTAACATCAGAGAAGG\",\n )\n self.assertEqual(\n alignment[4],\n \"CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155024776 : 155024776 + 169],\n \"ATGAAATATGGAAGGAAATGATGGCATGACTGGATTTCCTGAAAGGTACATTAACAAAGTAATAAAACACAAGATACCCTTATAAACAGCACTAGTAAGTTTTACATAAATGCCTCCCATGACCTTTTGTGCTTTTGAGCTATTTCAGTTACAGTAACATCAGAGAAGG\",\n )\n self.assertEqual(\n alignment[5],\n \"CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTATCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[6].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[6].seq), 133105)\n self.assertEqual(\n alignment.sequences[6].seq[10878 : 10878 + 169],\n \"CCTTCTCTGATATTACTGTAACTGAAATAGCTCAAAAGCACAAAAGGTCATGGCAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\",\n )\n self.assertEqual(\n alignment[6],\n \"CCTTCTCTGATATTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGCAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[7].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[7].seq), 498454)\n self.assertEqual(\n alignment.sequences[7].seq[323241 : 323241 + 156],\n \"CTGAGATATGGAAGGAAATGATGGCCCGACTGGATTTCCTGTAAGGCACATGAACAAAGTAATAAAACACGAGATGCCTTCAGAAACTTTACATCAATGCCTGGCATGACCTTTTGTGCTTCTGAGCTACTTTGGTTACAGGAACATCTGAGAGGA\",\n )\n self.assertEqual(\n alignment[7],\n \"TCCTCTCAGATGTTCCTGTAACCAAAGTAGCTC-AGAAGCACAAAAGGTCATGCCAGGCATTGATGTAAA-------------GTTTCTGAAGGCATCTCGTGTTTTATTACTTTGTTCATGTGCCTTACAGGAAATCCAGTCGGGCCATCATTTCCTTCCATATCTCAG\",\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[8].id, \"sorAra1.scaffold_2476\")\n self.assertEqual(len(alignment.sequences[8].seq), 4997)\n self.assertEqual(\n alignment.sequences[8].seq[1445 : 1445 + 170],\n \"CTGGAATATGGGAGGAAATGATGAGATTACAGGATTTCCGGAAAAGTTCATGATCAACAACATTATATGCAAGGGGTCTTTATAAACAGCACTGGTATATTTTACATCAATGCCTGACATGACCTTTTGTGCTTTTTGAGCTACCTCAGTTACAGTAACATCAGAGAAGG\",\n )\n self.assertEqual(\n alignment[8],\n \"CCTTCTCTGATGTTACTGTAACTGAGGTAGCTCAAAAAGCACAAAAGGTCATGTCAGGCATTGATGTAAAATATACCAGTGCTGTTTATAAAGACCCCTTGCATATAATGTTGTTGATCATGAACTTTTCCGGAAATCCTGTAATCTCATCATTTCCTCCCATATTCCAG\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"99999999999999997999999999999999999999999999999999999999999999999999999999999979999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"eriEur1.scaffold_266115\")\n self.assertEqual(len(alignment.sequences[9].seq), 4589)\n self.assertEqual(\n alignment.sequences[9].seq[521 : 521 + 156],\n \"CCTTCTCTGATCTGACTGTAACCGAAGTCTCTCGAAAGCACAAAAGCTCACGGCAGGCCTTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgcagatgtctctcacgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCCTTCCTG\",\n )\n self.assertEqual(\n alignment[9],\n \"CCTTCTCTGATCTGACTGTAACCGAAGTCTCTC-GAAAGCACAAAAGCTCACGGCAGGCCTTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgca------gatgtctctcacgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCC-------TTCCTG\",\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999799999999999999999999998987999899999999999999999999999999999999999999999999999999999999999998999989\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[10].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[10].seq), 125616256)\n self.assertEqual(\n alignment.sequences[10].seq[47544053 : 47544053 + 168],\n \"TTGAAATATGGAAGGAAGTAACAGGATGACAGGATTTCCTGTAAAGTACATGAACAAAGCAATATTACACGAGGTGCCTTTATAAACAGCTCTAGTAAATTTTACATAAAGCCTGACATGACCTTTTGTGCTTTTGAGCTACTTCAGTTACAGTAACATCAGAGACAG\",\n )\n self.assertEqual(\n alignment[10],\n \"CTGTCTCTGATGTTACTGTAACTGAAGTAGCTC-AAAAGCACAAAAGGTCATGTCAGGC-TTTATGTAAAATTTACTAGAGCTGTTTATAAAGGCACCTCGTGTAATATTGCTTTGTTCATGTACTTTACAGGAAATCCTGTCATCCTGTTACTTCCTTCCATATTTCAA\",\n )\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[11].id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(alignment.sequences[11].seq), 119354)\n self.assertEqual(\n alignment.sequences[11].seq[45629 : 45629 + 169],\n \"CTGAACTATGGAAGGAAATGACAGGATGACAGGATTTCCTATAAAGTGCATGAACAAAGCAATAATACACAAGGTACCTTTATAAACAGCACTAGTAAATTTTACATAAATGCCTGACATCACCTTTTGTGCTTTTGAACTATTTCAGTTACAGTAACATCAGAGACAG\",\n )\n self.assertEqual(\n alignment[11],\n \"CTGTCTCTGATGTTACTGTAACTGAAATAGTTC-AAAAGCACAAAAGGTGATGTCAGGCATTTATGTAAAATTTACTAGTGCTGTTTATAAAGGTACCTTGTGTATTATTGCTTTGTTCATGCACTTTATAGGAAATCCTGTCATCCTGTCATTTCCTTCCATAGTTCAG\",\n )\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 34165)\n self.assertEqual(alignment.sequences[12].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[12].seq), 10470)\n self.assertEqual(\n alignment.sequences[12].seq[6880 : 6880 + 168],\n \"GTGACTTATGGAAGGAAATGATGGTATGACAGGATTTCCTGTAAGGGGGATAGAAAAAGTAATAGAACACAAGGTCCTTTATAAACAGCACTAGTAAATTTTACATCAATGCCCGACATGACCTTTTGTGCTTTTGAGCCTCTTCAGTTACAGTAACATCAGAGAAGG\",\n )\n self.assertEqual(\n alignment[12],\n \"CCTTCTCTGATGTTACTGTAACTGAAGAGGCTC-AAAAGCACAAAAGGTCATGTCGGGCATTGATGTAAAATTTACTAGTGCTG-TTTATAAAGGACCTTGTGTTCTATTACTTTTTCTATCCCCCTTACAGGAAATCCTGTCATACCATCATTTCCTTCCATAAGTCAC\",\n )\n self.assertEqual(\n alignment.sequences[12].annotations[\"quality\"],\n \"989999999999999937699999999999999799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[12].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[12].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[13].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[13].seq), 100002)\n self.assertEqual(\n alignment.sequences[13].seq[95418 : 95418 + 169],\n \"CCATCTCTGATATTACTGTAATGGAATTACTTTGAAAGCACAAAAGGTCAGGACAAGCGTGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCATTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG\",\n )\n self.assertEqual(\n alignment[13],\n \"CCATCTCTGATATTACTGTAATGGAATTACTTT-GAAAGCACAAAAGGTCAGGACAAGCGTGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCATTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG\",\n )\n self.assertEqual(\n alignment.sequences[13].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[13].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[13].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[14].id, \"ornAna1.chr2\")\n self.assertEqual(len(alignment.sequences[14].seq), 54797317)\n self.assertEqual(\n alignment.sequences[14].seq[40040263 : 40040263 + 169],\n \"TGAAGATATGGAAGGAAATGATGGCTTGACAGGATTTCCCCTAAGGTGAATGAATAGCCTCATAAAACACAAAGCAGCTTTATGAACAGGGCTATTAAGTTGCACATGATTGGCTGATATGACCTTTCCTATCTTCTGGGTAGCTGAGTTACAGTGATATCAGAGGTGG\",\n )\n self.assertEqual(\n alignment[14],\n \"CCACCTCTGATATCACTGTAACTCAGCTACCCA-GAAGATAGGAAAGGTCATATCAGCCAATCATGTGCAACTTAATAGCCCTGTTCATAAAGCTGCTTTGTGTTTTATGAGGCTATTCATTCACCTTAGGGGAAATCCTGTCAAGCCATCATTTCCTTCCATATCTTCA\",\n )\n self.assertEqual(alignment.sequences[14].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[14].annotations[\"leftCount\"], 5690)\n self.assertEqual(alignment.sequences[14].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[14].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171035, 164755))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 15)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 1)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021275, 3021308, 3021308, 3021333, 3021334, 3021344,\n 3021357, 3021358, 3021359, 3021369, 3021369, 3021369,\n 3021369, 3021371, 3021382, 3021408, 3021415, 3021421],\n [ 285, 252, 252, 227, 226, 216,\n 203, 202, 201, 191, 183, 177,\n 168, 166, 155, 129, 122, 116],\n [ 3888, 3855, 3855, 3830, 3829, 3819,\n 3806, 3805, 3804, 3794, 3786, 3780,\n 3771, 3769, 3769, 3743, 3736, 3730],\n [158037166, 158037133, 158037133, 158037108, 158037107, 158037097,\n 158037084, 158037083, 158037082, 158037072, 158037064, 158037058,\n 158037049, 158037047, 158037036, 158037010, 158037003, 158036997],\n [157514999, 157514966, 157514966, 157514941, 157514940, 157514930,\n 157514917, 157514916, 157514915, 157514905, 157514897, 157514891,\n 157514882, 157514880, 157514869, 157514843, 157514836, 157514830],\n [155024945, 155024912, 155024912, 155024887, 155024886, 155024876,\n 155024863, 155024862, 155024861, 155024851, 155024843, 155024837,\n 155024828, 155024826, 155024815, 155024789, 155024782, 155024776],\n [ 10878, 10911, 10911, 10936, 10937, 10947,\n 10960, 10961, 10962, 10972, 10980, 10986,\n 10995, 10997, 11008, 11034, 11041, 11047],\n [ 323397, 323364, 323364, 323339, 323338, 323328,\n 323328, 323327, 323326, 323316, 323308, 323302,\n 323293, 323291, 323280, 323254, 323247, 323241],\n [ 1615, 1582, 1581, 1556, 1555, 1545,\n 1532, 1531, 1530, 1520, 1512, 1506,\n 1497, 1495, 1484, 1458, 1451, 1445],\n [ 521, 554, 554, 579, 580, 590,\n 603, 604, 605, 615, 623, 623,\n 632, 634, 645, 671, 671, 677],\n [ 47544221, 47544188, 47544188, 47544163, 47544163, 47544153,\n 47544140, 47544139, 47544138, 47544128, 47544120, 47544114,\n 47544105, 47544103, 47544092, 47544066, 47544059, 47544053],\n [ 45798, 45765, 45765, 45740, 45739, 45729,\n 45716, 45715, 45714, 45704, 45696, 45690,\n 45681, 45679, 45668, 45642, 45635, 45629],\n [ 7048, 7015, 7015, 6990, 6989, 6979,\n 6966, 6965, 6965, 6955, 6947, 6941,\n 6932, 6930, 6919, 6893, 6886, 6880],\n [ 95418, 95451, 95451, 95476, 95477, 95487,\n 95500, 95501, 95502, 95512, 95520, 95526,\n 95535, 95537, 95548, 95574, 95581, 95587],\n [ 40040432, 40040399, 40040399, 40040374, 40040373, 40040363,\n 40040350, 40040349, 40040348, 40040338, 40040330, 40040324,\n 40040315, 40040313, 40040302, 40040276, 40040269, 40040263],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021275 CTTTCTCTGACATTACTGTAACTGAAGTAGCTC-AGAAGCACAAAAGGTCACATCATGCA\ncavPor2.s 285 CCTTTGCTGATGTTACTGTAAGCGAACTAGCTG-AAAAGCACAAAAGGTCATGTCAGGCA\noryCun1.s 3888 TCGTCTCTGATGTTACTCTAGCTGAAAGCGCTC-CAAAGCACAAAAGGCCATGGCAGGCA\nponAbe2.c 158037166 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCA\npanTro2.c 157514999 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCA\nhg18.chr6 155024945 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCA\ncalJac1.C 10878 CCTTCTCTGATATTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGCAGGCA\ntupBel1.s 323397 TCCTCTCAGATGTTCCTGTAACCAAAGTAGCTC-AGAAGCACAAAAGGTCATGCCAGGCA\nsorAra1.s 1615 CCTTCTCTGATGTTACTGTAACTGAGGTAGCTCAAAAAGCACAAAAGGTCATGTCAGGCA\neriEur1.s 521 CCTTCTCTGATCTGACTGTAACCGAAGTCTCTC-GAAAGCACAAAAGCTCACGGCAGGCC\ncanFam2.c 47544221 CTGTCTCTGATGTTACTGTAACTGAAGTAGCTC-AAAAGCACAAAAGGTCATGTCAGGC-\nfelCat3.s 45798 CTGTCTCTGATGTTACTGTAACTGAAATAGTTC-AAAAGCACAAAAGGTGATGTCAGGCA\ndasNov1.s 7048 CCTTCTCTGATGTTACTGTAACTGAAGAGGCTC-AAAAGCACAAAAGGTCATGTCGGGCA\nechTel1.s 95418 CCATCTCTGATATTACTGTAATGGAATTACTTT-GAAAGCACAAAAGGTCAGGACAAGCG\nornAna1.c 40040432 CCACCTCTGATATCACTGTAACTCAGCTACCCA-GAAGATAGGAAAGGTCATATCAGCCA\n\nmm9.chr10 3021334 TCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGC-----------------------CA\ncavPor2.s 226 TTTATGCAAAATTTACTAGTTCCGTTCATAAAGGCACCTCGCATTTTATTACTTAGTTCA\noryCun1.s 3829 TTTATGTCAAATGTACTAGCACTGTTTATAACAGCACCTTGTGTTGTATTACTTTGTTCA\nponAbe2.c 158037107 TTCATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAA\npanTro2.c 157514940 TTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAA\nhg18.chr6 155024886 TTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTATCTTGTGTTTTATTACTTTGTTAA\ncalJac1.C 10937 TTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAA\ntupBel1.s 323338 TTGATGTAAA-------------GTTTCTGAAGGCATCTCGTGTTTTATTACTTTGTTCA\nsorAra1.s 1555 TTGATGTAAAATATACCAGTGCTGTTTATAAAGACCCCTTGCATATAATGTTGTTGATCA\neriEur1.s 580 TTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgca------gatgtctctca\ncanFam2.c 47544163 TTTATGTAAAATTTACTAGAGCTGTTTATAAAGGCACCTCGTGTAATATTGCTTTGTTCA\nfelCat3.s 45739 TTTATGTAAAATTTACTAGTGCTGTTTATAAAGGTACCTTGTGTATTATTGCTTTGTTCA\ndasNov1.s 6989 TTGATGTAAAATTTACTAGTGCTG-TTTATAAAGGACCTTGTGTTCTATTACTTTTTCTA\nechTel1.s 95477 TGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCA\nornAna1.c 40040373 ATCATGTGCAACTTAATAGCCCTGTTCATAAAGCTGCTTTGTGTTTTATGAGGCTATTCA\n\nmm9.chr10 3021371 CGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG 3021421\ncavPor2.s 166 TGTGTCTCGCAGGAAATCCAGTCACGCCATCATTTCCTTCCATATTTCAA 116\noryCun1.s 3769 -----------GGAAATCCAGTCACGCCGCGATTTCCTTCCACATTTCAA 3730\nponAbe2.c 158037047 TGTATCTTTCAGGAAATTCAGTCACGCCATCATTTCCTTCCATATTTCAT 158036997\npanTro2.c 157514880 TGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT 157514830\nhg18.chr6 155024826 TGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT 155024776\ncalJac1.C 10997 TGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT 11047\ntupBel1.s 323291 TGTGCCTTACAGGAAATCCAGTCGGGCCATCATTTCCTTCCATATCTCAG 323241\nsorAra1.s 1495 TGAACTTTTCCGGAAATCCTGTAATCTCATCATTTCCTCCCATATTCCAG 1445\neriEur1.s 634 cgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCC-------TTCCTG 677\ncanFam2.c 47544103 TGTACTTTACAGGAAATCCTGTCATCCTGTTACTTCCTTCCATATTTCAA 47544053\nfelCat3.s 45679 TGCACTTTATAGGAAATCCTGTCATCCTGTCATTTCCTTCCATAGTTCAG 45629\ndasNov1.s 6930 TCCCCCTTACAGGAAATCCTGTCATACCATCATTTCCTTCCATAAGTCAC 6880\nechTel1.s 95537 TTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG 95587\nornAna1.c 40040313 TTCACCTTAGGGGAAATCCTGTCAAGCCATCATTTCCTTCCATATCTTCA 40040263\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=891219.000000\ns mm9.chr10 3021275 146 + 129993255 CTTTCTCTGACATTACTGTAACTGAAGTAGCTC-AGAAGCACAAAAGGTCACATCATGCATCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGC-----------------------CACGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG\ns cavPor2.scaffold_216473 9741 169 - 10026 CCTTTGCTGATGTTACTGTAAGCGAACTAGCTG-AAAAGCACAAAAGGTCATGTCAGGCATTTATGCAAAATTTACTAGTTCCGTTCATAAAGGCACCTCGCATTTTATTACTTAGTTCATGTGTCTCGCAGGAAATCCAGTCACGCCATCATTTCCTTCCATATTTCAA\nq cavPor2.scaffold_216473 668536545547664539866666666666668-8787886799997788875886655536666688786768476688854689668876558688874778656675665668746666788474786888875667457786687996867886548798845555\ni cavPor2.scaffold_216473 C 0 C 0\ns oryCun1.scaffold_156751 838 158 - 4726 TCGTCTCTGATGTTACTCTAGCTGAAAGCGCTC-CAAAGCACAAAAGGCCATGGCAGGCATTTATGTCAAATGTACTAGCACTGTTTATAACAGCACCTTGTGTTGTATTACTTTGTTCA-----------GGAAATCCAGTCACGCCGCGATTTCCTTCCACATTTCAA\nq oryCun1.scaffold_156751 999999879999999999999999999997999-99999799999999898999999988999999988999999989996999999999988897996999999999999979999987-----------899998987999799998998999999999777999899\ni oryCun1.scaffold_156751 C 0 C 0\ns ponAbe2.chr6 16173265 169 - 174210431 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTCATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTATCTTTCAGGAAATTCAGTCACGCCATCATTTCCTTCCATATTTCAT\ni ponAbe2.chr6 C 0 C 0\ns panTro2.chr6 16393613 169 - 173908612 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\nq panTro2.chr6 999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni panTro2.chr6 C 0 C 0\ns hg18.chr6 15875047 169 - 170899992 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTATCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\ni hg18.chr6 C 0 C 0\ns calJac1.Contig6394 10878 169 + 133105 CCTTCTCTGATATTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGCAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT\ni calJac1.Contig6394 C 0 C 0\ns tupBel1.scaffold_114895.1-498454 175057 156 - 498454 TCCTCTCAGATGTTCCTGTAACCAAAGTAGCTC-AGAAGCACAAAAGGTCATGCCAGGCATTGATGTAAA-------------GTTTCTGAAGGCATCTCGTGTTTTATTACTTTGTTCATGTGCCTTACAGGAAATCCAGTCGGGCCATCATTTCCTTCCATATCTCAG\nq tupBel1.scaffold_114895.1-498454 999999999999999999999999999999999-999999999999999999999999999999999999-------------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni tupBel1.scaffold_114895.1-498454 C 0 C 0\ns sorAra1.scaffold_2476 3382 170 - 4997 CCTTCTCTGATGTTACTGTAACTGAGGTAGCTCAAAAAGCACAAAAGGTCATGTCAGGCATTGATGTAAAATATACCAGTGCTGTTTATAAAGACCCCTTGCATATAATGTTGTTGATCATGAACTTTTCCGGAAATCCTGTAATCTCATCATTTCCTCCCATATTCCAG\nq sorAra1.scaffold_2476 99999999999999997999999999999999999999999999999999999999999999999999999999999979999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni sorAra1.scaffold_2476 C 0 C 0\ns eriEur1.scaffold_266115 521 156 + 4589 CCTTCTCTGATCTGACTGTAACCGAAGTCTCTC-GAAAGCACAAAAGCTCACGGCAGGCCTTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgca------gatgtctctcacgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCC-------TTCCTG\nq eriEur1.scaffold_266115 999999999999999999999999999999999-999999999999999999999999799999999999999999999998987999899999999999999------999999999999999999999999999999999999999999999998-------999989\ni eriEur1.scaffold_266115 C 0 C 0\ns canFam2.chr1 78072035 168 - 125616256 CTGTCTCTGATGTTACTGTAACTGAAGTAGCTC-AAAAGCACAAAAGGTCATGTCAGGC-TTTATGTAAAATTTACTAGAGCTGTTTATAAAGGCACCTCGTGTAATATTGCTTTGTTCATGTACTTTACAGGAAATCCTGTCATCCTGTTACTTCCTTCCATATTTCAA\nq canFam2.chr1 999999999999999999999999999999999-9999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni canFam2.chr1 C 0 C 0\ns felCat3.scaffold_205680 73556 169 - 119354 CTGTCTCTGATGTTACTGTAACTGAAATAGTTC-AAAAGCACAAAAGGTGATGTCAGGCATTTATGTAAAATTTACTAGTGCTGTTTATAAAGGTACCTTGTGTATTATTGCTTTGTTCATGCACTTTATAGGAAATCCTGTCATCCTGTCATTTCCTTCCATAGTTCAG\nq felCat3.scaffold_205680 999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni felCat3.scaffold_205680 C 0 I 34165\ns dasNov1.scaffold_56749 3422 168 - 10470 CCTTCTCTGATGTTACTGTAACTGAAGAGGCTC-AAAAGCACAAAAGGTCATGTCGGGCATTGATGTAAAATTTACTAGTGCTG-TTTATAAAGGACCTTGTGTTCTATTACTTTTTCTATCCCCCTTACAGGAAATCCTGTCATACCATCATTTCCTTCCATAAGTCAC\nq dasNov1.scaffold_56749 989999999999999937699999999999999-79999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni dasNov1.scaffold_56749 C 0 C 0\ns echTel1.scaffold_288249 95418 169 + 100002 CCATCTCTGATATTACTGTAATGGAATTACTTT-GAAAGCACAAAAGGTCAGGACAAGCGTGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCATTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG\nq echTel1.scaffold_288249 999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999\ni echTel1.scaffold_288249 C 0 C 0\ns ornAna1.chr2 14756885 169 - 54797317 CCACCTCTGATATCACTGTAACTCAGCTACCCA-GAAGATAGGAAAGGTCATATCAGCCAATCATGTGCAACTTAATAGCCCTGTTCATAAAGCTGCTTTGTGTTTTATGAGGCTATTCATTCACCTTAGGGGAAATCCTGTCAAGCCATCATTTCCTTCCATATCTTCA\ni ornAna1.chr2 I 5690 C 0\ne otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 30254)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021421 : 3021421 + 44],\n \"ACGTTGCTCATTGTAATTGAAGCATTTATTACCAATGCCTTCCC\",\n )\n self.assertEqual(\n alignment[0],\n \"-ACGTTGCTCATTGT-----AATTGAAGCATTTATTACCAA--------TG--------------CCTTCCC\",\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[69 : 69 + 47],\n \"CAGAGGGGCCGTCAGCAAAACATACTTTTATTTGTAACAAGGAACAG\",\n )\n self.assertEqual(\n alignment[1],\n \"-CTGTTCCTTGTTACA----AATAAAAGTATGTTTTGCTGA--------CG-------G-----CCCCTCTG\",\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"47675464566778886867867744466523545576436669356\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(alignment.sequences[2].seq), 4726)\n self.assertEqual(\n alignment.sequences[2].seq[3693 : 3693 + 37],\n \"ATTAGCAGTGAATGCTTTAATCCATAATGAGGAACCA\",\n )\n self.assertEqual(\n alignment[2],\n \"-TGGTTCCTCATTATG----GATTAAAGCATTCACTGCTAA--------T----------------------\",\n )\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999998999998879999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 2345)\n self.assertEqual(alignment.sequences[3].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 174210431)\n self.assertEqual(\n alignment.sequences[3].seq[158036952 : 158036952 + 45],\n \"GAGAAAGCATTAGCAATAAACACTTTTATTTATAATGAGCAACAG\",\n )\n self.assertEqual(\n alignment[3],\n \"-CTGTTGCTCATTATA----AATAAAAGTGTTTATTGCTAA--------T--------------GCTTTCTC\",\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 4)\n self.assertEqual(alignment.sequences[4].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 173908612)\n self.assertEqual(\n alignment.sequences[4].seq[157514785 : 157514785 + 45],\n \"GAGAAAGCGTTAGCAATAAACACTTTTATTTATAATGAGGAACAG\",\n )\n self.assertEqual(\n alignment[4],\n \"-CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC\",\n )\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 4)\n self.assertEqual(alignment.sequences[5].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[5].seq), 170899992)\n self.assertEqual(\n alignment.sequences[5].seq[155024731 : 155024731 + 45],\n \"GAGAAAGCGTTAGCAATAAACACTTTTATTTATAATGAGGAACAG\",\n )\n self.assertEqual(\n alignment[5],\n \"-CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 4)\n self.assertEqual(alignment.sequences[6].id, \"calJac1.Contig6394\")\n self.assertEqual(len(alignment.sequences[6].seq), 133105)\n self.assertEqual(\n alignment.sequences[6].seq[11047 : 11047 + 43],\n \"CTGTTTCTCATTATAAATAAGTGTTTATTGCTAACGCTTTCTC\",\n )\n self.assertEqual(\n alignment[6],\n \"-CTGTTTCTCATTATA----AAT--AAGTGTTTATTGCTAA--------C--------------GCTTTCTC\",\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 701)\n self.assertEqual(alignment.sequences[7].id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(alignment.sequences[7].seq), 498454)\n self.assertEqual(\n alignment.sequences[7].seq[323206 : 323206 + 35],\n \"TTAGCAACAAACGCTATATTTATCATGAGGAGCAG\",\n )\n self.assertEqual(\n alignment[7],\n \"-CTGCTCCTCATGATA----AAT-ATAGCGTTTGTTGCTAA-------------------------------\",\n )\n self.assertEqual(\n alignment.sequences[7].annotations[\"quality\"],\n \"99999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[7].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[7].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[7].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[7].annotations[\"rightCount\"], 10695)\n self.assertEqual(alignment.sequences[8].id, \"sorAra1.scaffold_2476\")\n self.assertEqual(len(alignment.sequences[8].seq), 4997)\n self.assertEqual(\n alignment.sequences[8].seq[1397 : 1397 + 48],\n \"GGAACCTGCTGGTCATAAACGCTCtttttttAATCTAAGAAGGAACAG\",\n )\n self.assertEqual(\n alignment[8],\n \"-CTGTTCCTTCTTAGATTaaaaaaaGAGCGTTTATGACCAG--------CA-------GGTTCC--------\",\n )\n self.assertEqual(\n alignment.sequences[8].annotations[\"quality\"],\n \"999999999999999999999999999999999766975599999999\",\n )\n self.assertEqual(alignment.sequences[8].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[8].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[8].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[8].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[9].id, \"eriEur1.scaffold_266115\")\n self.assertEqual(len(alignment.sequences[9].seq), 4589)\n self.assertEqual(\n alignment.sequences[9].seq[677 : 677 + 35],\n \"CTCCTTGTTCTTGAAGCCGTTTTTTATTGTCAGTG\",\n )\n self.assertEqual(\n alignment[9],\n \"-CTCCTTGTTCTTGAAGC----------CGTTTTTTATTGT--------CA-------GTG-----------\",\n )\n self.assertEqual(\n alignment.sequences[9].annotations[\"quality\"],\n \"98959997997999999999999999999989999\",\n )\n self.assertEqual(alignment.sequences[9].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[9].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[9].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[9].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[10].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[10].seq), 125616256)\n self.assertEqual(\n alignment.sequences[10].seq[47544013 : 47544013 + 40],\n \"GACATTAGCAATAAATGCTTTTATTTATAATGAGAAACAG\",\n )\n self.assertEqual(\n alignment[10],\n \"-CTGTTTCTCATTATA----AATAAAAGCATTTATTGCTAA--------TG-------T------------C\",\n )\n self.assertEqual(\n alignment.sequences[10].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[10].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[10].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[10].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[11].id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(alignment.sequences[11].seq), 10470)\n self.assertEqual(\n alignment.sequences[11].seq[6836 : 6836 + 44],\n \"GAGGAGCCGTTAGCAGTAAATGCTTTTATTATAAAGAGGAACAG\",\n )\n self.assertEqual(\n alignment[11],\n \"-CTGTTCCTCTTTAT-----AATAAAAGCATTTACTGCTAA--------CGGCTCCTC--------------\",\n )\n self.assertEqual(\n alignment.sequences[11].annotations[\"quality\"],\n \"99999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[11].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[11].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[11].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[11].annotations[\"rightCount\"], 904)\n self.assertEqual(alignment.sequences[12].id, \"echTel1.scaffold_288249\")\n self.assertEqual(len(alignment.sequences[12].seq), 100002)\n self.assertEqual(\n alignment.sequences[12].seq[95587 : 95587 + 38],\n \"CTGATCCTCATTATAAATAAAAGTGTTTGTTACTAATG\",\n )\n self.assertEqual(\n alignment[12],\n \"-CTGATCCTCATTATA----AATAAAAGTGTTTGTTACTAA--------TG---------------------\",\n )\n self.assertEqual(\n alignment.sequences[12].annotations[\"quality\"],\n \"99999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[12].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[12].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[12].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[12].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[13].id, \"ornAna1.chr2\")\n self.assertEqual(len(alignment.sequences[13].seq), 54797317)\n self.assertEqual(\n alignment.sequences[13].seq[40040218 : 40040218 + 45],\n \"GGGGGATCTTTAGTAATAAAAGAGTCCCTGTACAATGAGGACAGT\",\n )\n self.assertEqual(\n alignment[13],\n \"ACTG-TCCTCATTGTA----CAGGGACTCTTTTATTACTAAAGATCCCCC----------------------\",\n )\n self.assertEqual(alignment.sequences[13].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[13].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[13].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (45629, 11464))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171035, 164755))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 14)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 2)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021421, 3021421, 3021424, 3021425, 3021435, 3021435,\n 3021435, 3021435, 3021438, 3021439, 3021440, 3021443,\n 3021456, 3021456, 3021457, 3021458, 3021458, 3021458,\n 3021458, 3021458, 3021458, 3021464, 3021465],\n [ 116, 116, 113, 112, 102, 101,\n 101, 101, 98, 97, 96, 93,\n 80, 80, 79, 78, 78, 77,\n 77, 77, 76, 70, 69],\n [ 3730, 3730, 3727, 3726, 3716, 3715,\n 3715, 3715, 3712, 3711, 3710, 3707,\n 3694, 3694, 3693, 3693, 3693, 3693,\n 3693, 3693, 3693, 3693, 3693],\n [158036997, 158036997, 158036994, 158036993, 158036983, 158036982,\n 158036982, 158036982, 158036979, 158036978, 158036977, 158036974,\n 158036961, 158036961, 158036960, 158036960, 158036960, 158036960,\n 158036960, 158036960, 158036959, 158036953, 158036952],\n [157514830, 157514830, 157514827, 157514826, 157514816, 157514815,\n 157514815, 157514815, 157514812, 157514811, 157514810, 157514807,\n 157514794, 157514794, 157514793, 157514793, 157514793, 157514793,\n 157514793, 157514793, 157514792, 157514786, 157514785],\n [155024776, 155024776, 155024773, 155024772, 155024762, 155024761,\n 155024761, 155024761, 155024758, 155024757, 155024756, 155024753,\n 155024740, 155024740, 155024739, 155024739, 155024739, 155024739,\n 155024739, 155024739, 155024738, 155024732, 155024731],\n [ 11047, 11047, 11050, 11051, 11061, 11062,\n 11062, 11062, 11065, 11065, 11065, 11068,\n 11081, 11081, 11082, 11082, 11082, 11082,\n 11082, 11082, 11083, 11089, 11090],\n [ 323241, 323241, 323238, 323237, 323227, 323226,\n 323226, 323226, 323223, 323223, 323222, 323219,\n 323206, 323206, 323206, 323206, 323206, 323206,\n 323206, 323206, 323206, 323206, 323206],\n [ 1445, 1445, 1442, 1441, 1431, 1430,\n 1428, 1426, 1423, 1422, 1421, 1418,\n 1405, 1405, 1404, 1403, 1403, 1402,\n 1400, 1397, 1397, 1397, 1397],\n [ 677, 677, 680, 681, 691, 692,\n 694, 694, 694, 694, 694, 694,\n 707, 707, 708, 709, 709, 710,\n 712, 712, 712, 712, 712],\n [ 47544053, 47544053, 47544050, 47544049, 47544039, 47544038,\n 47544038, 47544038, 47544035, 47544034, 47544033, 47544030,\n 47544017, 47544017, 47544016, 47544015, 47544015, 47544014,\n 47544014, 47544014, 47544014, 47544014, 47544013],\n [ 6880, 6880, 6877, 6876, 6866, 6866,\n 6866, 6866, 6863, 6862, 6861, 6858,\n 6845, 6845, 6844, 6843, 6836, 6836,\n 6836, 6836, 6836, 6836, 6836],\n [ 95587, 95587, 95590, 95591, 95601, 95602,\n 95602, 95602, 95605, 95606, 95607, 95610,\n 95623, 95623, 95624, 95625, 95625, 95625,\n 95625, 95625, 95625, 95625, 95625],\n [ 40040263, 40040262, 40040259, 40040259, 40040249, 40040248,\n 40040248, 40040248, 40040245, 40040244, 40040243, 40040240,\n 40040227, 40040219, 40040218, 40040218, 40040218, 40040218,\n 40040218, 40040218, 40040218, 40040218, 40040218],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021421 -ACGTTGCTCATTGT-----AATTGAAGCATTTATTACCAA--------TG---------\ncavPor2.s 116 -CTGTTCCTTGTTACA----AATAAAAGTATGTTTTGCTGA--------CG-------G-\noryCun1.s 3730 -TGGTTCCTCATTATG----GATTAAAGCATTCACTGCTAA--------T----------\nponAbe2.c 158036997 -CTGTTGCTCATTATA----AATAAAAGTGTTTATTGCTAA--------T----------\npanTro2.c 157514830 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C----------\nhg18.chr6 155024776 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C----------\ncalJac1.C 11047 -CTGTTTCTCATTATA----AAT--AAGTGTTTATTGCTAA--------C----------\ntupBel1.s 323241 -CTGCTCCTCATGATA----AAT-ATAGCGTTTGTTGCTAA-------------------\nsorAra1.s 1445 -CTGTTCCTTCTTAGATTaaaaaaaGAGCGTTTATGACCAG--------CA-------GG\neriEur1.s 677 -CTCCTTGTTCTTGAAGC----------CGTTTTTTATTGT--------CA-------GT\ncanFam2.c 47544053 -CTGTTTCTCATTATA----AATAAAAGCATTTATTGCTAA--------TG-------T-\ndasNov1.s 6880 -CTGTTCCTCTTTAT-----AATAAAAGCATTTACTGCTAA--------CGGCTCCTC--\nechTel1.s 95587 -CTGATCCTCATTATA----AATAAAAGTGTTTGTTACTAA--------TG---------\nornAna1.c 40040263 ACTG-TCCTCATTGTA----CAGGGACTCTTTTATTACTAAAGATCCCCC----------\n\nmm9.chr10 3021458 -----CCTTCCC 3021465\ncavPor2.s 77 ----CCCCTCTG 69\noryCun1.s 3693 ------------ 3693\nponAbe2.c 158036960 ----GCTTTCTC 158036952\npanTro2.c 157514793 ----GCTTTCTC 157514785\nhg18.chr6 155024739 ----GCTTTCTC 155024731\ncalJac1.C 11082 ----GCTTTCTC 11090\ntupBel1.s 323206 ------------ 323206\nsorAra1.s 1401 TTCC-------- 1397\neriEur1.s 711 G----------- 712\ncanFam2.c 47544014 -----------C 47544013\ndasNov1.s 6836 ------------ 6836\nechTel1.s 95625 ------------ 95625\nornAna1.c 40040218 ------------ 40040218\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=30254.000000\ns mm9.chr10 3021421 44 + 129993255 -ACGTTGCTCATTGT-----AATTGAAGCATTTATTACCAA--------TG--------------CCTTCCC\ns cavPor2.scaffold_216473 9910 47 - 10026 -CTGTTCCTTGTTACA----AATAAAAGTATGTTTTGCTGA--------CG-------G-----CCCCTCTG\nq cavPor2.scaffold_216473 -476754645667788----868678677444665235455--------76-------4-----36669356\ni cavPor2.scaffold_216473 C 0 C 0\ns oryCun1.scaffold_156751 996 37 - 4726 -TGGTTCCTCATTATG----GATTAAAGCATTCACTGCTAA--------T----------------------\nq oryCun1.scaffold_156751 -999999999899999----887999999999999999999--------9----------------------\ni oryCun1.scaffold_156751 C 0 I 2345\ns ponAbe2.chr6 16173434 45 - 174210431 -CTGTTGCTCATTATA----AATAAAAGTGTTTATTGCTAA--------T--------------GCTTTCTC\ni ponAbe2.chr6 C 0 I 4\ns panTro2.chr6 16393782 45 - 173908612 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC\nq panTro2.chr6 -999999999999999----999999999999999999999--------9--------------99999999\ni panTro2.chr6 C 0 I 4\ns hg18.chr6 15875216 45 - 170899992 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC\ni hg18.chr6 C 0 I 4\ns calJac1.Contig6394 11047 43 + 133105 -CTGTTTCTCATTATA----AAT--AAGTGTTTATTGCTAA--------C--------------GCTTTCTC\ni calJac1.Contig6394 C 0 I 701\ns tupBel1.scaffold_114895.1-498454 175213 35 - 498454 -CTGCTCCTCATGATA----AAT-ATAGCGTTTGTTGCTAA-------------------------------\nq tupBel1.scaffold_114895.1-498454 -999999999999999----999-99999999999999999-------------------------------\ni tupBel1.scaffold_114895.1-498454 C 0 I 10695\ns sorAra1.scaffold_2476 3552 48 - 4997 -CTGTTCCTTCTTAGATTaaaaaaaGAGCGTTTATGACCAG--------CA-------GGTTCC--------\nq sorAra1.scaffold_2476 -9999999999999999999999999999999997669755--------99-------999999--------\ni sorAra1.scaffold_2476 C 0 N 0\ns eriEur1.scaffold_266115 677 35 + 4589 -CTCCTTGTTCTTGAAGC----------CGTTTTTTATTGT--------CA-------GTG-----------\nq eriEur1.scaffold_266115 -98959997997999999----------9999999999999--------89-------999-----------\ni eriEur1.scaffold_266115 C 0 N 0\ns canFam2.chr1 78072203 40 - 125616256 -CTGTTTCTCATTATA----AATAAAAGCATTTATTGCTAA--------TG-------T------------C\nq canFam2.chr1 -999999999999999----999999999999999999999--------99-------9------------9\ni canFam2.chr1 C 0 C 0\ns dasNov1.scaffold_56749 3590 44 - 10470 -CTGTTCCTCTTTAT-----AATAAAAGCATTTACTGCTAA--------CGGCTCCTC--------------\nq dasNov1.scaffold_56749 -99999999999999-----999999999999999999999--------999999999--------------\ni dasNov1.scaffold_56749 C 0 I 904\ns echTel1.scaffold_288249 95587 38 + 100002 -CTGATCCTCATTATA----AATAAAAGTGTTTGTTACTAA--------TG---------------------\nq echTel1.scaffold_288249 -999999999999999----999999999999999999999--------99---------------------\ni echTel1.scaffold_288249 C 0 N 0\ns ornAna1.chr2 14757054 45 - 54797317 ACTG-TCCTCATTGTA----CAGGGACTCTTTTATTACTAAAGATCCCCC----------------------\ni ornAna1.chr2 C 0 C 0\ne felCat3.scaffold_205680 73725 34165 - 119354 I\ne otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I\n\n\"\"\",\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, -9167)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021465 : 3021465 + 29],\n \"CCCTACACTGTCAAGTGGGAGGAGACAGT\",\n )\n self.assertEqual(\n alignment[0], \"CCCT--ACACTGTC----AAGTGGGAGGAGACAGT--------------------\"\n )\n self.assertEqual(alignment.sequences[1].id, \"cavPor2.scaffold_216473\")\n self.assertEqual(len(alignment.sequences[1].seq), 10026)\n self.assertEqual(\n alignment.sequences[1].seq[41 : 41 + 28], \"accatcccaccccacccccagtgtGGCT\"\n )\n self.assertEqual(\n alignment[1], \"AGCC--acactgg-----gggtggggtgggatggt--------------------\"\n )\n self.assertEqual(\n alignment.sequences[1].annotations[\"quality\"],\n \"7667687856666544895554554677\",\n )\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"N\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 0)\n self.assertEqual(alignment.sequences[2].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 174210431)\n self.assertEqual(\n alignment.sequences[2].seq[158036924 : 158036924 + 24],\n \"GCTGCTCCTATCGCCCCCACAGGG\",\n )\n self.assertEqual(\n alignment[2], \"-------CCCTGTG----GGGGCGATAGGAGCAGC--------------------\"\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 4)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[3].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 173908612)\n self.assertEqual(\n alignment.sequences[3].seq[157514757 : 157514757 + 24],\n \"GCTGCCCCTATCGCCCCCACATGG\",\n )\n self.assertEqual(\n alignment[3], \"-------CCATGTG----GGGGCGATAGGGGCAGC--------------------\"\n )\n self.assertEqual(\n alignment.sequences[3].annotations[\"quality\"], \"999999999999999999999999\"\n )\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 4)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[4].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[4].seq), 170899992)\n self.assertEqual(\n alignment.sequences[4].seq[155024703 : 155024703 + 24],\n \"GCTGCCCCTATCGCCCCCACATGG\",\n )\n self.assertEqual(\n alignment[4], \"-------CCATGTG----GGGGCGATAGGGGCAGC--------------------\"\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 4)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 9)\n self.assertEqual(alignment.sequences[5].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[5].seq), 125616256)\n self.assertEqual(\n alignment.sequences[5].seq[47543982 : 47543982 + 31],\n \"CACACACACACACCCCCCATGTGGTTCAGGG\",\n )\n self.assertEqual(\n alignment[5], \"CCCTGAACCACATG----GGGGGTGTGTGTGTGTG--------------------\"\n )\n self.assertEqual(\n alignment.sequences[5].annotations[\"quality\"],\n \"9999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 13)\n self.assertEqual(alignment.sequences[6].id, \"ornAna1.chr2\")\n self.assertEqual(len(alignment.sequences[6].seq), 54797317)\n self.assertEqual(\n alignment.sequences[6].seq[40040173 : 40040173 + 45],\n \"GCCAGCAAAGATGAAAGAGGGCTACATCCAAACTCCTATGACACA\",\n )\n self.assertEqual(\n alignment[6], \"----------TGTGTCATAGGAGTTTGGATGTAGCCCTCTTTCATCTTTGCTGGC\"\n )\n self.assertEqual(alignment.sequences[6].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[6].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[6].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(record.seq), 10470)\n self.assertEqual(segment, (6836, 5932))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (45629, 11464))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (11090, 11791))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (323206, 312511))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171035, 164755))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(record.seq), 4726)\n self.assertEqual(segment, (3693, 1348))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 7)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021465, 3021469, 3021469, 3021470, 3021473, 3021476,\n 3021477, 3021477, 3021494, 3021494],\n [ 69, 65, 65, 64, 61, 58,\n 58, 58, 41, 41],\n [158036948, 158036948, 158036948, 158036948, 158036945, 158036942,\n 158036941, 158036941, 158036924, 158036924],\n [157514781, 157514781, 157514781, 157514781, 157514778, 157514775,\n 157514774, 157514774, 157514757, 157514757],\n [155024727, 155024727, 155024727, 155024727, 155024724, 155024721,\n 155024720, 155024720, 155024703, 155024703],\n [ 47544013, 47544009, 47544007, 47544006, 47544003, 47544000,\n 47543999, 47543999, 47543982, 47543982],\n [ 40040218, 40040218, 40040218, 40040218, 40040218, 40040215,\n 40040214, 40040210, 40040193, 40040173],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021465 CCCT--ACACTGTC----AAGTGGGAGGAGACAGT--------------------\ncavPor2.s 69 AGCC--acactgg-----gggtggggtgggatggt--------------------\nponAbe2.c 158036948 -------CCCTGTG----GGGGCGATAGGAGCAGC--------------------\npanTro2.c 157514781 -------CCATGTG----GGGGCGATAGGGGCAGC--------------------\nhg18.chr6 155024727 -------CCATGTG----GGGGCGATAGGGGCAGC--------------------\ncanFam2.c 47544013 CCCTGAACCACATG----GGGGGTGTGTGTGTGTG--------------------\nornAna1.c 40040218 ----------TGTGTCATAGGAGTTTGGATGTAGCCCTCTTTCATCTTTGCTGGC\n\nmm9.chr10 3021494\ncavPor2.s 41\nponAbe2.c 158036924\npanTro2.c 157514757\nhg18.chr6 155024703\ncanFam2.c 47543982\nornAna1.c 40040173\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=-9167.000000\ns mm9.chr10 3021465 29 + 129993255 CCCT--ACACTGTC----AAGTGGGAGGAGACAGT--------------------\ns cavPor2.scaffold_216473 9957 28 - 10026 AGCC--acactgg-----gggtggggtgggatggt--------------------\nq cavPor2.scaffold_216473 7667--6878566-----66544895554554677--------------------\ni cavPor2.scaffold_216473 C 0 N 0\ns ponAbe2.chr6 16173483 24 - 174210431 -------CCCTGTG----GGGGCGATAGGAGCAGC--------------------\ni ponAbe2.chr6 I 4 I 9\ns panTro2.chr6 16393831 24 - 173908612 -------CCATGTG----GGGGCGATAGGGGCAGC--------------------\nq panTro2.chr6 -------9999999----99999999999999999--------------------\ni panTro2.chr6 I 4 I 9\ns hg18.chr6 15875265 24 - 170899992 -------CCATGTG----GGGGCGATAGGGGCAGC--------------------\ni hg18.chr6 I 4 I 9\ns canFam2.chr1 78072243 31 - 125616256 CCCTGAACCACATG----GGGGGTGTGTGTGTGTG--------------------\nq canFam2.chr1 99999999999999----99999999999999999--------------------\ni canFam2.chr1 C 0 I 13\ns ornAna1.chr2 14757099 45 - 54797317 ----------TGTGTCATAGGAGTTTGGATGTAGCCCTCTTTCATCTTTGCTGGC\ni ornAna1.chr2 C 0 C 0\ne dasNov1.scaffold_56749 3634 904 - 10470 I\ne felCat3.scaffold_205680 73725 34165 - 119354 I\ne calJac1.Contig6394 11090 701 + 133105 I\ne tupBel1.scaffold_114895.1-498454 175248 10695 - 498454 I\ne otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I\ne oryCun1.scaffold_156751 1033 2345 - 4726 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['C', 'C', 'C', 'T', '-', '-', 'A', 'C', 'A', 'C', 'T', 'G', 'T',\n 'C', '-', '-', '-', '-', 'A', 'A', 'G', 'T', 'G', 'G', 'G', 'A',\n 'G', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'T', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['A', 'G', 'C', 'C', '-', '-', 'a', 'c', 'a', 'c', 't', 'g', 'g',\n '-', '-', '-', '-', '-', 'g', 'g', 'g', 't', 'g', 'g', 'g', 'g',\n 't', 'g', 'g', 'g', 'a', 't', 'g', 'g', 't', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'C', 'T', 'G', 'T',\n 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'C', 'G', 'A', 'T',\n 'A', 'G', 'G', 'A', 'G', 'C', 'A', 'G', 'C', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'A', 'T', 'G', 'T',\n 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'C', 'G', 'A', 'T',\n 'A', 'G', 'G', 'G', 'G', 'C', 'A', 'G', 'C', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'A', 'T', 'G', 'T',\n 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'C', 'G', 'A', 'T',\n 'A', 'G', 'G', 'G', 'G', 'C', 'A', 'G', 'C', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['C', 'C', 'C', 'T', 'G', 'A', 'A', 'C', 'C', 'A', 'C', 'A', 'T',\n 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'G', 'T', 'G', 'T',\n 'G', 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'G', '-', '-', '-', '-',\n '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',\n '-', '-', '-'],\n ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'G', 'T',\n 'G', 'T', 'C', 'A', 'T', 'A', 'G', 'G', 'A', 'G', 'T', 'T', 'T',\n 'G', 'G', 'A', 'T', 'G', 'T', 'A', 'G', 'C', 'C', 'C', 'T', 'C',\n 'T', 'T', 'T', 'C', 'A', 'T', 'C', 'T', 'T', 'T', 'G', 'C', 'T',\n 'G', 'G', 'C']], dtype='U')\n # fmt: on\n )\n )\n alignment = next(alignments)\n self.assertEqual(alignment.score, 15763)\n self.assertEqual(alignment.sequences[0].id, \"mm9.chr10\")\n self.assertEqual(len(alignment.sequences[0].seq), 129993255)\n self.assertEqual(\n alignment.sequences[0].seq[3021494 : 3021494 + 42],\n \"TGTTTAGTACCATGCTTAGGAATGATAAACTCACTTAGTGtt\",\n )\n self.assertEqual(alignment[0], \"TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt\")\n self.assertEqual(alignment.sequences[1].id, \"ponAbe2.chr6\")\n self.assertEqual(len(alignment.sequences[1].seq), 174210431)\n self.assertEqual(\n alignment.sequences[1].seq[158036869 : 158036869 + 46],\n \"AAGATTGGGTGAGCCTATCACGCCAAAGAATAAAGGACATGCAACA\",\n )\n self.assertEqual(alignment[1], \"TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[1].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[1].annotations[\"rightCount\"], 943)\n self.assertEqual(alignment.sequences[2].id, \"panTro2.chr6\")\n self.assertEqual(len(alignment.sequences[2].seq), 173908612)\n self.assertEqual(\n alignment.sequences[2].seq[157514702 : 157514702 + 46],\n \"AAGATTGGGTGAGCCTATCACGCCAAAGAATAAAGGATATGCAACA\",\n )\n self.assertEqual(alignment[2], \"TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\")\n self.assertEqual(\n alignment.sequences[2].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[2].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[2].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[2].annotations[\"rightCount\"], 10)\n self.assertEqual(alignment.sequences[3].id, \"hg18.chr6\")\n self.assertEqual(len(alignment.sequences[3].seq), 170899992)\n self.assertEqual(\n alignment.sequences[3].seq[155024648 : 155024648 + 46],\n \"AAGATTGGGTGAGCCTATCACGCCAAAGAATAAACGACATGCAACA\",\n )\n self.assertEqual(alignment[3], \"TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"leftCount\"], 9)\n self.assertEqual(alignment.sequences[3].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[3].annotations[\"rightCount\"], 931)\n self.assertEqual(alignment.sequences[4].id, \"canFam2.chr1\")\n self.assertEqual(len(alignment.sequences[4].seq), 125616256)\n self.assertEqual(\n alignment.sequences[4].seq[47543923 : 47543923 + 46],\n \"ATGATGGAGTGAAGCTATCACTTTGAACAGCAAGTGAGACTTAACA\",\n )\n self.assertEqual(alignment[4], \"TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT\")\n self.assertEqual(\n alignment.sequences[4].annotations[\"quality\"],\n \"9999999999999999999999999999999999999999999999\",\n )\n self.assertEqual(alignment.sequences[4].annotations[\"leftStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"leftCount\"], 13)\n self.assertEqual(alignment.sequences[4].annotations[\"rightStatus\"], \"I\")\n self.assertEqual(alignment.sequences[4].annotations[\"rightCount\"], 1)\n self.assertEqual(alignment.sequences[5].id, \"ornAna1.chr2\")\n self.assertEqual(len(alignment.sequences[5].seq), 54797317)\n self.assertEqual(\n alignment.sequences[5].seq[40040137 : 40040137 + 36],\n \"TCCAGTGAGTAGAAGTTCTAGCAATCATTTTAAACA\",\n )\n self.assertEqual(alignment[5], \"TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"leftCount\"], 0)\n self.assertEqual(alignment.sequences[5].annotations[\"rightStatus\"], \"C\")\n self.assertEqual(alignment.sequences[5].annotations[\"rightCount\"], 0)\n empty = alignment.annotations[\"empty\"][0]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"dasNov1.scaffold_56749\")\n self.assertEqual(len(record.seq), 10470)\n self.assertEqual(segment, (6836, 5932))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][1]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"felCat3.scaffold_205680\")\n self.assertEqual(len(record.seq), 119354)\n self.assertEqual(segment, (45629, 11464))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][2]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"calJac1.Contig6394\")\n self.assertEqual(len(record.seq), 133105)\n self.assertEqual(segment, (11090, 11791))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][3]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"tupBel1.scaffold_114895.1-498454\")\n self.assertEqual(len(record.seq), 498454)\n self.assertEqual(segment, (323206, 312511))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][4]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"otoGar1.scaffold_334.1-359464\")\n self.assertEqual(len(record.seq), 359464)\n self.assertEqual(segment, (171035, 164755))\n self.assertEqual(status, \"I\")\n empty = alignment.annotations[\"empty\"][5]\n (record, segment, status) = empty\n self.assertEqual(record.id, \"oryCun1.scaffold_156751\")\n self.assertEqual(len(record.seq), 4726)\n self.assertEqual(segment, (3693, 1348))\n self.assertEqual(status, \"I\")\n self.assertEqual(len(alignment.sequences), 6)\n self.assertEqual(len(alignment.annotations[\"empty\"]), 6)\n self.assertTrue(\n np.array_equal(\n alignment.coordinates,\n np.array(\n # fmt: off\n [[ 3021494, 3021505, 3021505, 3021521, 3021523, 3021532,\n 3021536],\n [158036915, 158036904, 158036900, 158036884, 158036882, 158036873,\n 158036869],\n [157514748, 157514737, 157514733, 157514717, 157514715, 157514706,\n 157514702],\n [155024694, 155024683, 155024679, 155024663, 155024661, 155024652,\n 155024648],\n [ 47543969, 47543958, 47543954, 47543938, 47543936, 47543927,\n 47543923],\n [ 40040173, 40040162, 40040162, 40040146, 40040146, 40040137,\n 40040137],\n ]\n # fmt: on\n ),\n )\n )\n self.assertEqual(\n str(alignment),\n \"\"\"\\\nmm9.chr10 3021494 TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt 3021536\nponAbe2.c 158036915 TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT 158036869\npanTro2.c 157514748 TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT 157514702\nhg18.chr6 155024694 TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT 155024648\ncanFam2.c 47543969 TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT 47543923\nornAna1.c 40040173 TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA---- 40040137\n\"\"\",\n )\n self.assertEqual(\n format(alignment, \"maf\"),\n \"\"\"\\\na score=15763.000000\ns mm9.chr10 3021494 42 + 129993255 TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt\ns ponAbe2.chr6 16173516 46 - 174210431 TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\ni ponAbe2.chr6 I 9 I 943\ns panTro2.chr6 16393864 46 - 173908612 TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\nq panTro2.chr6 9999999999999999999999999999999999999999999999\ni panTro2.chr6 I 9 I 10\ns hg18.chr6 15875298 46 - 170899992 TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT\ni hg18.chr6 I 9 I 931\ns canFam2.chr1 78072287 46 - 125616256 TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT\nq canFam2.chr1 9999999999999999999999999999999999999999999999\ni canFam2.chr1 I 13 I 1\ns ornAna1.chr2 14757144 36 - 54797317 TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----\ni ornAna1.chr2 C 0 C 0\ne dasNov1.scaffold_56749 3634 904 - 10470 I\ne felCat3.scaffold_205680 73725 34165 - 119354 I\ne calJac1.Contig6394 11090 701 + 133105 I\ne tupBel1.scaffold_114895.1-498454 175248 10695 - 498454 I\ne otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I\ne oryCun1.scaffold_156751 1033 2345 - 4726 I\n\n\"\"\",\n )\n self.assertTrue(\n np.array_equal(\n np.array(alignment, \"U\"),\n # fmt: off\n# flake8: noqa\nnp.array([['T', 'G', 'T', 'T', 'T', 'A', 'G', 'T', 'A', 'C', 'C', '-', '-',\n '-', '-', 'A', 'T', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A',\n 'T', 'G', 'A', 'T', 'A', 'A', 'A', 'C', 'T', 'C', 'A', 'C', 'T',\n 'T', 'A', 'G', 'T', 'G', 't', 't'],\n ['T', 'G', 'T', 'T', 'G', 'C', 'A', 'T', 'G', 'T', 'C', 'C', 'T',\n 'T', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'G', 'G', 'C', 'G',\n 'T', 'G', 'A', 'T', 'A', 'G', 'G', 'C', 'T', 'C', 'A', 'C', 'C',\n 'C', 'A', 'A', 'T', 'C', 'T', 'T'],\n ['T', 'G', 'T', 'T', 'G', 'C', 'A', 'T', 'A', 'T', 'C', 'C', 'T',\n 'T', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'G', 'G', 'C', 'G',\n 'T', 'G', 'A', 'T', 'A', 'G', 'G', 'C', 'T', 'C', 'A', 'C', 'C',\n 'C', 'A', 'A', 'T', 'C', 'T', 'T'],\n ['T', 'G', 'T', 'T', 'G', 'C', 'A', 'T', 'G', 'T', 'C', 'G', 'T',\n 'T', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'G', 'G', 'C', 'G',\n 'T', 'G', 'A', 'T', 'A', 'G', 'G', 'C', 'T', 'C', 'A', 'C', 'C',\n 'C', 'A', 'A', 'T', 'C', 'T', 'T'],\n ['T', 'G', 'T', 'T', 'A', 'A', 'G', 'T', 'C', 'T', 'C', 'A', 'C',\n 'T', 'T', 'G', 'C', 'T', 'G', 'T', 'T', 'C', 'A', 'A', 'A', 'G',\n 'T', 'G', 'A', 'T', 'A', 'G', 'C', 'T', 'T', 'C', 'A', 'C', 'T',\n 'C', 'C', 'A', 'T', 'C', 'A', 'T'],\n ['T', 'G', 'T', 'T', 'T', 'A', 'A', 'A', 'A', 'T', 'G', '-', '-',\n '-', '-', 'A', 'T', 'T', 'G', 'C', 'T', 'A', 'G', 'A', 'A', 'C',\n 'T', 'T', 'C', 'T', 'A', '-', '-', 'C', 'T', 'C', 'A', 'C', 'T',\n 'G', 'G', 'A', '-', '-', '-', '-']], dtype='U')\n # fmt: on\n )\n )\n self.assertRaises(StopIteration, next, alignments)",
"def test_load_random_map(self, map_name):\n m = maps.get(map_name)\n run_config = run_configs.get()\n\n with run_config.start() as controller:\n logging.info(\"Loading map: %s\", m.name)\n create = sc_pb.RequestCreateGame(local_map=sc_pb.LocalMap(\n map_path=m.path, map_data=m.data(run_config)))\n create.player_setup.add(type=sc_pb.Participant)\n create.player_setup.add(type=sc_pb.Computer, race=sc_common.Random,\n difficulty=sc_pb.VeryEasy)\n join = sc_pb.RequestJoinGame(race=sc_common.Random,\n options=sc_pb.InterfaceOptions(raw=True))\n\n controller.create_game(create)\n controller.join_game(join)\n\n # Verify it has the right mods and isn't running into licensing issues.\n info = controller.game_info()\n logging.info(\"Mods for %s: %s\", m.name, info.mod_names)\n self.assertIn(\"Mods/Void.SC2Mod\", info.mod_names)\n self.assertIn(\"Mods/VoidMulti.SC2Mod\", info.mod_names)\n\n # Verify it can be played without making actions.\n for _ in range(3):\n controller.step()\n controller.observe()",
"def test_reading_ucsc_mm9_chr10_bad(self):\n path = \"MAF/ucsc_mm9_chr10_bad.maf\"\n alignments = Align.parse(path, \"maf\")\n self.assertEqual(alignments.metadata[\"MAF Version\"], \"1\")\n self.assertEqual(alignments.metadata[\"Scoring\"], \"autoMZ.v1\")\n next(alignments)\n next(alignments)\n next(alignments)\n next(alignments)\n next(alignments)\n next(alignments)\n with self.assertRaises(ValueError) as cm:\n next(alignments)\n self.assertEqual(\n str(cm.exception), \"sequence size is incorrect (found 219, expected 319)\"\n )",
"def test_readData(self):\n\t\tpath = \"sdada\"\n\t\tairbnb_file_name = \"wrong_name1\"\n\t\trestaurant_data_file_name = \"wrong_name2\"\n\t\ttry:\n\t\t\tmm.read_data(path, airbnb_file_name, restaurant_data_file_name)\n\t\texcept IOError:\n\t\t\tself.assertTrue(True)",
"def test_read(self):\n # check against a correct input file\n renamer = bioformats.seqname.BaseSeqRenamer()\n renamer.read_renaming_dict(self.__correct)\n # check against an incorrect input file\n with self.assertRaises(IncorrectDictError):\n renamer.read_renaming_dict(self.__incorrect)",
"def load_map(maps):\n with open(maps,\"r\") as read_file:\n map_data = json.load(read_file)\n if map_data != '': # You should probably raise an exception here. Not return ''\n return map_data, True\n else:\n return '', False"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Attempt to load and validate the sections of each map in the directory
|
def test_load_all_R6_maps(self):
settings = load_settings(TEST_SETTINGS_FILE)
discovered_files = gather_files_in_path(".MAP", settings["gamePath_R6_EW"])
for map_filepath in discovered_files:
if map_filepath.endswith("obstacletest.map") or map_filepath.endswith("mansion.map") or map_filepath.endswith("m8.map") or map_filepath.endswith("m14.map"):
#TODO: remove all of these maps, except obstacletest.map from this skip, once the last data structure is deciphered
#I believe this is an early test map that was shipped by accident.
# It's data structures are not consistent with the rest of the map files
# and it is not used anywhere so it is safe to skip
continue
loadedFile = MAPLevelReader.MAPLevelFile()
readSucessfullyToEOF = loadedFile.read_file(map_filepath)
self.assertTrue(readSucessfullyToEOF, f'Failed to read whole file: {map_filepath}')
self.check_section_strings(loadedFile)
|
[
"def test_R6_MAP_Structure(self):\n settings = load_settings(TEST_SETTINGS_FILE)\n\n map_filepath = path.join(settings[\"gamePath_R6_EW\"], \"data\", \"map\", \"m01\", \"M01.map\")\n\n loadedFile = MAPLevelReader.MAPLevelFile()\n readSucessfullyToEOF = loadedFile.read_file(map_filepath)\n\n self.assertTrue(readSucessfullyToEOF, \"Failed to read whole file\")\n\n self.check_section_strings(loadedFile)\n\n self.assertEqual(loadedFile.materialListHeader.numMaterials, 263, \"Unexpected number of materials\")\n\n self.assertEqual(loadedFile.geometryListHeader.count, 57, \"Unexpected number of geometry objects\")\n\n self.assertEqual(loadedFile.portalList.portalCount, 65, \"Unexpected number of portals\")\n\n self.assertEqual(loadedFile.lightList.lightCount, 162, \"Unexpected number of lights\")\n\n self.assertEqual(loadedFile.objectList.objectCount, 38, \"Unexpected number of objects\")\n\n self.assertEqual(loadedFile.roomList.roomCount, 47, \"Unexpected number of rooms\")\n\n self.assertEqual(loadedFile.planningLevelList.planningLevelCount, 4, \"Unexpected number of planning levels\")",
"def test_load_map(self):\r\n test = Maps()\r\n test.load_map(path_to_map)\r\n self.assertIn(\"facile\", test.names)\r\n self.assertNotIn(\"empty\", test.names)\r\n self.assertEqual(len(test.drawings), 1)",
"def load_fieldmaps(astra_input, search_paths=[], fieldmap_dict={}, sections=['cavity', 'solenoid'], verbose=False, strip_path=False):\n fmap = {}\n for sec in sections:\n \n if sec not in astra_input: \n continue\n \n ixlist = find_fieldmap_ixlist(astra_input, sec) \n for ix in ixlist:\n k = file_(section=sec, index=ix)\n file = astra_input[sec][k]\n\n # Skip 3D fieldmaps. These are symlinked\n if os.path.split(file)[1].lower().startswith('3d_'):\n continue\n \n if file not in fmap:\n # Look inside dict\n if file in fieldmap_dict:\n if verbose:\n print(f'Fieldmap inside dict: {file}')\n fmap[file] = fieldmap_dict[file]\n continue\n \n if verbose:\n print(f'Loading fieldmap file {file}') \n \n # Look in search path\n if not os.path.exists(file):\n if verbose:\n print(f'{file} not found, searching:')\n for path in search_paths:\n _, file = os.path.split(file)\n tryfile = os.path.join(path, file)\n \n if os.path.exists(tryfile):\n if verbose:\n print('Found:', tryfile)\n file = tryfile\n break\n \n \n # Set input\n astra_input[sec][k] = file\n \n fmap[file] = parse_fieldmap(file)\n \n # Loop again\n if strip_path:\n # Make a secondary dict with the shorter names. \n # Protect against /path1/dat1, /path2/dat1 overwriting\n fmap2 = {}\n translate = {}\n for k in fmap:\n _, k2 = os.path.split(k)\n i=0 # Check for uniqueness\n while k2 in fmap2:\n i+=1\n k2 = f'{k2}_{i}'\n # Collect translation\n translate[k] = k2\n fmap2[k2] = fmap[k] \n\n for sec in sections:\n ixlist = find_fieldmap_ixlist(astra_input, sec) \n for ix in ixlist:\n k = file_(section=sec, index=ix)\n file = astra_input[sec][k]\n astra_input[sec][k] = translate[file]\n\n return fmap2\n \n else:\n return fmap",
"def dumpAllMaps(self, path, outPath):\n errors = {} # map name => Exception\n def isMap(name):\n return os.path.isfile(os.path.join(path, name, 'MODELS.bin'))\n maps = list(filter(isMap, os.listdir(path)))\n for i, name in enumerate(maps):\n try:\n printf(\"Extracting %3d/%3d: %s... \", i+1, len(maps), name)\n self.dumpMap(os.path.join(path, name),\n os.path.join(outPath, name))\n print(\"OK\")\n except Exception as ex:\n errors[name] = ex\n print(\"Failed\")\n for name, ex in errors.items():\n print(\"Failed extracting:\", name, ex)",
"def check_maps(self):\n if self.is_spatial:\n Landscape.check_maps(self)\n if (\n self.grid.file_name == \"set\"\n and self.sample_map.x_offset + self.grid.x_size > self.sample_map.x_size\n or self.sample_map.y_offset + self.grid.y_size > self.sample_map.y_size\n ):\n raise ValueError(\"Grid is not within the sample map - please check offsets of sample map.\")\n self.check_dispersal_map()\n self.check_reproduction_map()\n self.check_death_map()",
"def _read_maps(self):\n try:\n f = open(self._procpath('%d/maps' % self.pid))\n except IOError as e:\n # ignore killed process\n if e.errno != errno.ENOENT:\n raise\n return\n for line in f:\n try:\n so = line.split()[5].strip()\n self.mapped.append(so)\n except IndexError:\n pass",
"def test_parse_map_file(self):\n\n correct_map = [0,1.,1.]\n parsed_map = fizzy.parse_map_file(self.map_file_handle, \"Class\", [u'ID0',u'ID1',u'ID2'])\n self.assertEqual(parsed_map, correct_map)",
"def validate_maps(self):\n self._log.info(\"validating maps ...\")\n\n maps_url = \"%s/maps/\" % self._fastdl_url\n pattern = r'href=[\\'\"]?([^\\'\" >]+)'\n response = None\n\n try:\n response = urllib2.urlopen(maps_url).read()\n except urllib2.URLError:\n self._log.error(\n \"fastdl server '%s' unreachable\" % self._fastdl_url\n )\n return False\n\n # get all present maps from fastdl_url\n maps_present = []\n for map_url in re.findall(pattern, response):\n if 'bz2' in map_url:\n map_name = map_url.split(\".\")[0]\n maps_present.append(map_name)\n\n for _map in self._maps:\n if _map not in maps_present:\n self._log.error(\n \"map '%s' not available on fastdl server\" % _map\n )\n return False\n self._log.info(\"map '%s' found on fastdl server\" % _map)",
"def load_splits(self, folder):\n split_paths = [f\"{folder}/{self.prefix}_{name}.txt\" for name in self.sets]\n if all(os.path.exists(path) for path in split_paths):\n file_lists = [get_lines(path) for path in split_paths]\n labeled_sets = self.convert_splits(file_lists)\n for name, split_set in zip(self.sets, labeled_sets):\n setattr(self, name, split_set)\n return True\n return False",
"def load_map(self, cell_anns, map_path):\n def load_plane(plane_string):\n temp = plane_string.split(\"\\n\")\n plane_cell_data = [i.split(\",\") for i in temp]\n return plane_cell_data\n\n with open(map_path) as f:\n total = f.read().strip()\n planes = total.split(\"\\n\\n\")\n cell_data = [load_plane(plane) for plane in planes]\n logging.debug((cell_anns, cell_data))\n return self.load_cells(cell_anns, cell_data)",
"def Load_Map(self, map_name):\n\n self.current_map.clear()\n\n config = configparser.ConfigParser()\n config.read(self.available_maps[map_name]) # reads .map file\n\n self.map_information = config['information']\n if not self.Verify_Map(self.map_information, config.get('layout', 'design')): # pass parameters -> [information] section and the map design\n raise SyntaxError(\"[ERROR] - Invalid map configuration on map \\\"%s\\\"\" % map_name)\n\n map_lines = [i for i in config.get('layout', 'design').splitlines() if i] # Checks for valid map lines / strips white spaces.\n\n for y, map_row in enumerate(map_lines): # run through each row in the map, give it an index with enumerate.\n row = []\n map_tile = map_row.split(\"|\") # Get each tile in the given row.\n map_tile = [t for t in map_tile if t] # removes unnecessary white spaces, adds to list.\n for x, map_tile in enumerate(map_tile):\n tile_type = self.tile_types[map_tile]\n\n if tile_type == StartTile:\n self.start_tile_location = x, y\n\n row.append(tile_type(x, y) if tile_type else None)\n self.current_map.append(row)",
"def load(self, load_dir=\"faiss\"):\n self.index = faiss.read_index(os.path.join(load_dir, \"faiss.index\"))\n self.id_map = load_json_file(\n os.path.join(load_dir, \"faiss.map\"))",
"def load_sections(self):\n pass",
"def test_list_all_maps(self, map_name):\n run_config = run_configs.get()\n map_inst = maps.get(map_name)\n logging.info(\"map: %s\", map_inst.name)\n self.assertTrue(map_inst.data(run_config), msg=\"Failed on %s\" % map_inst)",
"def analyzeMapDump(self, path):\n files = self._analyzeMapDump(path, path)\n names = list(sorted(files.keys()))\n for name in names:\n hashes = files[name]\n if len(hashes) > 1:\n print(name)\n for hash, path in hashes.items():\n print('', path)",
"def load_maps(self):\n maps = {}\n maps_file = Path(\"resources/data/maps.yml\")\n if maps_file.is_file():\n with open(maps_file, 'r') as stream:\n try:\n maps_dict = yaml.safe_load(stream)\n if maps_dict is not None:\n for map_name, map_values in maps_dict.items():\n maps[map_name] = Map(map_name, self.bioms[map_values['biom']],\n map_values['height_map_path'],\n map_values['texture_map_path'],\n map_values['height_conversion'],\n map_values['max_soil_depth'],\n map_values['pixel_size'])\n except yaml.YAMLError as exc:\n print(exc)\n self.maps = maps",
"def test_map_dir(self):\n prefix = \"/eos/uscms/store/user/cmsdas/\"\n directory = \"test\"\n output = RecursiveFileList.map_dir(prefix, directory)\n assert len(output[directory][0]['testing'][0]['2017'][0]['facilitators']) == 33",
"def load_valid(self):\n images, labels = self.load(os.path.join('mnist', 'valid', 'images'),\n os.path.join('mnist', 'valid', 'labels'))\n self.valid_data = zip(images, labels)",
"def test_read_input_groups(file_groups):\n config = MapcheteConfig(file_groups.path)\n input_files = config.params_at_zoom(0)[\"input\"]\n assert \"file1\" in input_files[\"group1\"]\n assert \"file2\" in input_files[\"group1\"]\n assert \"file1\" in input_files[\"group2\"]\n assert \"file2\" in input_files[\"group2\"]\n assert \"nested_group\" in input_files\n assert \"group1\" in input_files[\"nested_group\"]\n assert \"file1\" in input_files[\"nested_group\"][\"group1\"]\n assert \"file2\" in input_files[\"nested_group\"][\"group1\"]\n assert \"file1\" in input_files[\"nested_group\"][\"group2\"]\n assert \"file2\" in input_files[\"nested_group\"][\"group2\"]\n assert config.area_at_zoom()"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Get metrics from training log file.
|
def get_metrics_from_log(fn: str) -> List[Dict[str, List[float]]]:
# Create a list for each trained model
ensemble = []
# Open the log file
with open(fn) as f:
# Read lines into a list
lines = f.readlines()
# Iterate
for line in lines:
# Add a new item when read a "Model" header in the log file
if line[0:5] == "Model":
# The new item is a dictionary with metrics as keys
ensemble.append(
{
"training_losses": [],
"validation_losses": [],
"balanced_accuracy": [],
}
)
# Read loss in training log
if line[0] == "T":
c = line.split()
ensemble[-1]["training_losses"].append(float(c[4].strip(",")))
# Read loss and bacc in validation log
elif line[0] == "V":
c = line.split()
ensemble[-1]["validation_losses"].append(float(c[4].strip(",")))
ensemble[-1]["balanced_accuracy"].append(float(c[8].strip(",")))
return ensemble
|
[
"def load_metrics(path) -> None:\n logger.info(f\"Loading metrics from '{path}'\")\n state_dict = torch.load(path, map_location=device)\n return state_dict['train_loss_list'], state_dict['valid_loss_list'], state_dict['global_steps_list']",
"def get_val_losses(log_file : str):\n losses = []\n ctr = 0 \n epoch_re = r\"Validation mae = (\\d+\\.\\d+) *\\nEpoch (\\d+)\"\n lines = open(log_file, \"r\").readlines()\n for index, line in enumerate(lines[:-1]): \n ctr += 1\n search_str = \"\".join([line,lines[index+1]])\n examples = re.findall(epoch_re, search_str)\n if len(examples) > 0: \n loss, epoch = examples[0]\n losses.append(float(loss))\n return losses",
"def get_M_from_log(filepath):\n M_list = []\n with open(filepath, \"r\") as f:\n for line in f:\n line_split = line.split(sep=\", \")\n if \"Finished trial\" in line_split[0]: # indicator that this is a log written by benchmark_logger\n M_part = line_split[5]\n M_val = float(M_part.split(\"=\")[-1])\n if M_val not in M_list:\n M_list.append(M_val)\n\n return M_list",
"def read_log(filename):\n data = {}\n expnumber = 0\n epochoffset = 0\n modeoffset = 0\n for line in open(filename):\n line = line[:-1]\n if line.startswith('Experiment'):\n print line\n p1,description = line.split(': ')\n expnumber = int(p1.split(' ')[-1])\n data[expnumber] = {'description':description,\n 'layersizes':[],\n 'layerdata':[]}\n epochoffset = 0\n modeoffset = 0\n elif line.startswith('created dA'):\n sizestr = line.split(' ')[-1]\n sizel1,sizel2 = map(int,sizestr.split('x'))\n data[expnumber]['layersizes'].append(sizel2)\n data[expnumber]['layerdata'].append([{'indices':[],\n 'values':[]},\n {'indices':[],\n 'values':[]}])\n elif line.startswith('Pre-training'):\n # Pre-training layer 0, epoch 0, cost 175.97775\n pts = line.split()\n layer = int(pts[2][:-1]) #remove comma\n epoch = int(pts[4][:-1]) + epochoffset\n cost = float(pts[-1])\n normcost = cost / data[expnumber]['layersizes'][layer] / 2\n data[expnumber]['layerdata'][layer][modeoffset]['indices'].append(epoch)\n data[expnumber]['layerdata'][layer][modeoffset]['values'].append(normcost)\n elif line.startswith('finished'):\n epochoffset = int(line.split()[1])\n modeoffset += 1\n return data",
"def read_logs(self, parameters, measure_name = 'Err'):\n\n\t\tpath_to_run = self.params['path_to_run']['value']\n\t\tif not path_to_run.endswith('/'):\n\t\t\tpath_to_run = path_to_run + '/'\n\t\t\n\t\tif not os.path.isfile(path_to_run + 'run.sh'):\n\t\t\tprint(\"path_to_run variable has been set wrongly. No run.sh found in: \", path_to_run)\n\t\t\tsys.exit()\n\n\t\tpath_to_run = path_to_run.split('/')\n\t\t# following [-3] because path always like egs/\"benchmark\"/asr1/, hence always 3rd from end\n\t\tbenchmark_path = '../log/' + path_to_run[-3]\n\t\tif not os.path.isdir(benchmark_path):\n\t\t\tprint(\"The folder \" + benchmark_path + \" could not be found. Do .log files of this benchmark exist?\")\n\t\t\tsys.exit()\n\n\t\td = [os.path.join(benchmark_path, o) for o in os.listdir(benchmark_path) if os.path.isdir(os.path.join(benchmark_path,o))]\n\t\texpdir = get_expdir(self)\n\t\tX = None\n\t\tY = None\n\t\tfor dir in d:\n\t\t\tif not dir.endswith('/'):\n\t\t\t\tdir = dir + '/'\n\n\t\t\t# construct Y\n\t\t\tif not os.path.isfile(dir + 'result.txt'):\n\t\t\t\tcontinue\n\t\t\tnew_y = self.parse_result(dir, measure_name)\n\t\t\tprint(\"dir: \", dir)\n\t\t\tprint(\"new_y: \", new_y)\n\t\t\tif new_y is None: \n\t\t\t\t# this case will happen if something went wrong in the espnet training. there will be a result.txt file in the folder, however, it is empty and hence cannot be used but leads to an error later in conditioning out gaussian function. we omit this case\n\t\t\t\tcontinue\n\n\t\t\tif Y is None:\n\t\t\t\tY = np.array([new_y])\n\t\t\telse:\n\t\t\t\tY = np.vstack((Y, new_y))\n\t\t\t\n\t\t\t# construct X\n\t\t\tself.read_ini(dir + 'parameters.log') # overwrites self.params\n\t\t\trow = np.array(self.retrieve_params(parameters))\n\t\t\tif X is None:\n\t\t\t\tX = row\n\t\t\telif row.tolist() in X.tolist(): # to make sure we use each point only once, avoids potential conflicts in setting up the function due to noise\n\t\t\t\tY = np.delete(Y, -1, 0) # delete the last row of Y\n\t\t\t\tcontinue\n\t\t\telse:\n\t\t\t\tX = np.vstack((X, row))\n\n\t\treturn X, Y",
"def train_metrics(self):\n return self._train_metrics",
"def analyse_log():\n y_test = []\n y_predict = []\n for row in open(\"log/pred_true_log.csv\"):\n row = row.split(\",\")\n y_test.append(int(row[0]))\n y_predict.append(int(row[1]))\n n = len(y_test)\n label_names = get_label(DatasetEnum.MNIST_AZ)\n print(classification_report(y_test, y_predict, target_names=label_names))\n cm = confusion_matrix(y_test, y_predict)\n np.savetxt(\"log/confusion_matrix_log.csv\", cm, delimiter=\",\", fmt='%d')",
"def get_metrics_from_train_tfevent(logdir, every_n: int = None):\n INVALID_PUNC = '''!\"#$%&'()*+, :;<=>?@[\\]^`{|}~'''\n IGNORE_TAGS = ['train_input_images', 'steps_per_sec']\n DEFAULT_SIZE_GUIDANCE = {\n \"compressedHistograms\": 1,\n \"images\": 1,\n \"scalars\": 0, # 0 means load all\n \"histograms\": 1,\n \"tensors\":0\n }\n # get data from tfevent file\n path = sorted(glob.glob(os.path.join(logdir, \"event*\")))[0]\n event_acc = EventAccumulator(path, DEFAULT_SIZE_GUIDANCE)\n event_acc.Reload()\n tags = [x for x in event_acc.Tags()['tensors'] if x not in IGNORE_TAGS]\n all_step = len(event_acc.Tensors(tags[0]))\n if every_n is None:\n return_dict = {i:dict() for i in range(all_step)}\n for tag in tags:\n metric_name = 'train_' + tag.translate(str.maketrans(INVALID_PUNC, '_'*len(INVALID_PUNC)))\n tensor_list = event_acc.Tensors(tag)\n for i, (_, _, tensor_content_value) in enumerate(tensor_list):\n scalar_value = tf.make_ndarray(tensor_content_value)\n return_dict[i].update({metric_name:scalar_value.item()})\n return return_dict\n else:\n every_n_step = np.arange(0, all_step + 1, every_n)\n return_dict = {i:dict() for i in every_n_step}\n for tag in tags:\n metric_name = 'train_' + tag.translate(str.maketrans(INVALID_PUNC, '_'*len(INVALID_PUNC)))\n tensor_list = event_acc.Tensors(tag)\n for i, (_, _, tensor_content_value) in enumerate(tensor_list):\n if i in every_n_step:\n scalar_value = tf.make_ndarray(tensor_content_value)\n return_dict[i].update({metric_name:scalar_value.item()})\n return return_dict",
"def get_model_training_logs(self, name):\n core_api = kubernetes.client.CoreV1Api(_build_client())\n\n return core_api.read_namespaced_pod_log(f'{name}-training-pod', self._namespace, container='builder')",
"def getydata(filename):\n train_error_list = []\n with open(filename, 'rt') as f:\n for line in f:\n if line.startswith('[dev'):\n data_substr = line.split(\",\")\n train_acc1 = data_substr[0].split(\" \")\n train_error_list.append(float(train_acc1[-1]))\n return train_error_list",
"def read_gnina_log(log_file: str) -> np.ndarray:\n\n scores = []\n lines = open(log_file).readlines()\n mode_start = np.inf\n for idx, line in enumerate(lines):\n if line[:6] == '-----+':\n mode_start = idx\n if idx > mode_start:\n mode = line.split()\n score = [float(x) for x in mode[1:]]\n scores.append(score)\n\n return np.array(scores)",
"def loadModelMetrics(self, file_path: str):\n print('INFO: Loading model metrics from: ' + file_path)\n with open(file_path, \"r\") as read_file:\n metrics_data = json.load(read_file) \n # Update the metrics containers\n self.test_metrics_accuracy = metrics_data['test']['accuracy']\n self.test_metrics_loss = metrics_data['test']['loss']\n self.training_metrics_accuracy = metrics_data['training']['accuracy']\n self.training_metrics_loss = metrics_data['training']['loss']",
"def get_training_outputs_from_logs(logs, print_training_accuracy):\n outputs = []\n for log in logs:\n if 'images/sec' in log and '+/-' in log:\n parts = log.split()\n if print_training_accuracy:\n # Example log with training accuracy:\n # 10 images/sec: 0.2 +/- 0.0 (jitter = 0.0) 6.908 0.500 1.000\n assert len(parts) == 11\n top_1_acc = float(parts[9])\n top_5_acc = float(parts[10])\n else:\n # Example log without training accuracy:\n # 10 images/sec: 0.2 +/- 0.0 (jitter = 0.0) 6.908\n assert len(parts) == 9\n top_1_acc = -1\n top_5_acc = -1\n loss = float(parts[8])\n outputs.append(TrainingOutput(loss=loss, top_1_accuracy=top_1_acc,\n top_5_accuracy=top_5_acc))\n assert len(outputs) >= 1\n return outputs",
"def get_evaluation_outputs_from_logs(logs):\n eval_outputs = []\n for log in logs:\n if 'Accuracy @ ' in log:\n # Example log:\n # Accuracy @ 1 = 0.5000 Accuracy @ 5 = 1.0000 [80 examples]\n parts = log.split()\n assert len(parts) == 12\n top_1_accuracy = float(parts[4])\n top_5_accuracy = float(parts[9])\n eval_outputs.append(EvalOutput(top_1_accuracy, top_5_accuracy))\n assert eval_outputs\n return eval_outputs",
"def analyse_log(log_file):\r\n \r\n summary = {'successful':False}\r\n lf = open(log_file, 'r')\r\n lines = lf.readlines() \r\n for line_number, line in enumerate(lines):\r\n if line.find('Integration terminated successfully at T =') > -1:\r\n summary['successful'] = True\r\n elif line.find('CPU time for integration') > -1 or \\\r\n line.find('CPU-time for integration') > -1:\r\n summary['cpu_time'] = line.split(' ')[-2]\r\n elif line.find('Number of (successful) steps') > -1:\r\n summary['successful_steps'] = line.split(' ')[-1]\r\n elif line.find('Number of (model) time events') > -1:\r\n summary['time_events_model'] = line.split(' ')[-1]\r\n elif line.find('Number of (U) time events') > -1:\r\n summary['time_events_U'] = line.split(' ')[-1]\r\n elif line.find('Number of state events') > -1:\r\n summary['state_events'] = line.split(' ')[-1]\r\n elif line.find('Number of step events') > -1:\r\n summary['step_events'] = line.split(' ')[-1]\r\n elif line.find('Minimum integration stepsize') > -1:\r\n summary['step_size_min'] = line.split(' ')[-1]\r\n elif line.find('Maximum integration stepsize') > -1:\r\n summary['step_size_max'] = line.split(' ')[-1]\r\n elif line.find('Maximum integration order') > -1:\r\n summary['int_order_max'] = line.split(' ')[-1]\r\n elif line.find('Number of rejected steps') > -1:\r\n summary['steps_nok'] = line.split(' ')[-1]\r\n elif line.find('Number of Jacobian-evaluations') > -1:\r\n summary['jacobians'] = line.split(' ')[-1].strip('\\n')\r\n elif line.find('Integration started at 0 using integration method:') > -1:\r\n summary['algorithm'] = lines[line_number + 1].strip('\\n')\r\n elif line.find('Integration started at T = 0 using integration method') > -1:\r\n summary['algorithm'] = line.split(' ')[-1].strip('\\n')\r\n elif line.find('This simulation timed out and was killed') > -1:\r\n summary['successful'] = False\r\n summary['timed_out'] = True\r\n elif line.find('Corresponding result file') > -1:\r\n summary['result file'] = line.split(' ')[-1].strip('\\n')\r\n lf.close()\r\n if summary.has_key('steps_nok'): \r\n summary['perc_wrong'] = 100. * float(summary['steps_nok']) / \\\r\n float(summary['steps_ok'])\r\n else:\r\n summary['perc_wrong'] = 0\r\n return summary",
"def read_callback(self):\n if self.config.logdir:\n gc_logs = sorted([os.path.join(self.config.logdir, log) for log in os.listdir(self.config.logdir) if log.startswith(self.config.log_prefix)], key=os.path.getmtime)\n if gc_logs:\n new_metrics = self.read_recent_data_from_log(LogHandle(gc_logs[-1]))\n if new_metrics:\n self.dispatch_metrics(self.update_metrics(new_metrics))\n else:\n self.collectd.warning('g1gc plugin: skipping because no log directory (\"LogDir\") has been configured')",
"def load_json_log(json_log):\n log_dict = dict(train=[], val=[])\n with open(json_log, 'r') as log_file:\n for line in log_file:\n log = json.loads(line.strip())\n # A hack trick to determine whether the line is training log.\n mode = 'train' if 'lr' in log else 'val'\n log_dict[mode].append(log)\n\n return log_dict",
"def calc_log_stats(args, datastore):\n with open(args.logfile) as f:\n analyze(cleaner(f, datastore), datastore, args.charm_filter)",
"def get_training_logits(self):\n _verif(self._training_logits, \"training_logits\")\n return self._training_logits"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Calculate mean, min5 and max95 for each ensemble metric.
|
def calculate_stats(
ensemble: List[Dict[str, List[float]]]
) -> Tuple[Dict[str, np.ndarray], Dict[str, np.ndarray], Dict[str, np.ndarray]]:
# Create empty dictionaries
mean = {"training_losses": [], "validation_losses": [], "balanced_accuracy": []}
min5 = {"training_losses": [], "validation_losses": [], "balanced_accuracy": []}
max95 = {"training_losses": [], "validation_losses": [], "balanced_accuracy": []}
# Calculate mean, min5 and max95 for each metric
for i in range(len(ensemble[0]["training_losses"])):
for k in ensemble[0].keys():
mean[k].append(np.mean([e[k][i] for e in ensemble]))
# is there a better way to use limit this 90% interval?
min5[k].append(np.percentile([e[k][i] for e in ensemble], 5))
max95[k].append(np.percentile([e[k][i] for e in ensemble], 95))
# Convert each key from list to numpy.ndarray
for k in mean.keys():
mean[k] = np.asarray(mean[k])
min5[k] = np.asarray(min5[k])
max95[k] = np.asarray(max95[k])
return mean, min5, max95
|
[
"def ml_mean(values):\n\n # return the equation for mean\n return sum(values)/len(values)",
"def get_mean_basin_performance(metrics: dict, model: str) -> Dict:\n seeds = [k for k in metrics[model].keys() if k != \"ensemble\"]\n metric = defaultdict(list)\n for seed in seeds:\n for basin, nse in metrics[model][seed].items():\n metric[basin].append(nse)\n return {basin: np.mean(values) for basin, values in metric.items()}",
"def estimated_mean(self):\n estimands=scipy.array(list(itertools.chain(*self.estimands)))\n return sum(estimands)/float(len(estimands))",
"def traj_ensemble_stats(traj_set):\n all_values = [traj.values for traj in traj_set]\n\n mean_values = scipy.mean(all_values, 0)\n std_values = scipy.std(all_values, 0)\n\n mean_traj = copy.deepcopy(traj_set[0])\n mean_traj.values = mean_values\n\n std_traj = copy.deepcopy(traj_set[0])\n std_traj.values = std_values\n\n return mean_traj, std_traj",
"def vpd_means(self):\n for source in [\"target\", \"percentile\", \"projected\"]:\n folder = self.__getattribute__(f\"{source}_folder\")\n minsrc = os.path.join(folder, \"vpdmin.nc\")\n maxsrc = os.path.join(folder, \"vpdmax.nc\")\n dst = os.path.join(folder, \"vpdmean.nc\")\n meanNC(minsrc, maxsrc, dst)",
"def mean_score(self):\n pass",
"def aggregate_data(self):\n oa_ma = [(x - y) for x, y in zip(self.oat_values, self.mat_values)]\n ra_ma = [(x - y) for x, y in zip(self.rat_values, self.mat_values)]\n ma_oa = [(y - x) for x, y in zip(self.oat_values, self.mat_values)]\n ma_ra = [(y - x) for x, y in zip(self.rat_values, self.mat_values)]\n avg_oa_ma = mean(oa_ma)\n avg_ra_ma = mean(ra_ma)\n avg_ma_oa = mean(ma_oa)\n avg_ma_ra = mean(ma_ra)\n return avg_oa_ma, avg_ra_ma, avg_ma_oa, avg_ma_ra",
"def load_5mavg_alerter(self, alert_threshold):\n try:\n # spliting list into multiple list based on services\n list_split_result = collections.defaultdict(list)\n for metric in self.metric_data:\n list_split_result[metric['service']].append(metric)\n result_list = list(list_split_result.values())\n\n for result in result_list:\n activeServerResultList = [d for d in result if d['active'] and d['component'].lower() == \"Load5mAvg\".lower()]\n half = len(activeServerResultList) / 2\n thresholdMetActiveValueList = [d for d in activeServerResultList if d['value'] > alert_threshold]\n if (len(thresholdMetActiveValueList) > half):\n for entry in thresholdMetActiveValueList:\n self.alert_list.append({'clusterd_service': True, 'timestamp': entry['timestamp'], 'component': entry['component'], 'value': alert_threshold, 'service': entry['service'] })\n except Exception as error:\n self.logger.error(\"Error while getting load average alert. Please review error: %s\" % error)",
"def _calc_basic_statistics(self):\n self.mean = stats.mean(self._data_samples)\n self.geom_mean = stats.geomean(self._data_samples)\n self.median = stats.median(self._data_samples)\n self.std_dev = stats.stddev(self._data_samples)\n\n self.min = min(self._data_samples)\n self.max = max(self._data_samples)",
"def avg_Ao(self):\n ...",
"def calculate_mean(self):\n\t\t\t\t\t\n avg = 1.0 * sum(self.data) / len(self.data)\n\t\t\n self.mean = avg\n \n return self.mean",
"def compute_averages(self):\n self.energy_average = self.cumulative_energy / self.N\n self.energy_squared_average = self.cumulative_squared_energy / self.N\n self.wave_function_derivative_average = self.cumulative_wave_function_derivative / self.N\n self.wave_function_energy_average = self.cumulative_wave_function_energy / self.N",
"def mean(self):\n\t\treturn 0.8",
"def get_average(self):\n # compute the mean\n self.average_fit = statistics.mean([self.fitness_dict[key] for key in self.fitness_dict])\n self.average_age = statistics.mean([self.age_dict[key] for key in self.age_dict])\n\n # Add average fitness at each time step to the collector\n self.average_fit_list.append(self.average_fit)\n self.average_age_list.append(self.average_age)",
"def MuonMeanInelasticity_CC_Avg(E,neutype,datapath = global_datapath):\n \n if E >= 100.0 or E < 1.0:\n\treturn ymuCC(E,neutype)\n else : \n\texistfile = False \n\tfor ff in os.listdir(datapath):\n\t if ff == \"y_avg_neutrino.dat\" and neutype == 0:\n\t existfile = True\n\t elif ff == \"y_avg_antineutrino.dat\" and neutype == 1:\n\t existfile = True\n\n\tif not existfile : \n\t QE_xsec_file = \"xsections_QE.dat\"\n\t RES_xsec_file = \"xsections_RES.dat\"\n\t DIS_xsec_file = \"xsections_DIS.dat\"\n\t \n\t file_QE \t= open(datapath+QE_xsec_file,'r')\n\t file_RES \t= open(datapath+RES_xsec_file,'r')\n\t file_DIS \t= open(datapath+DIS_xsec_file,'r')\n\t \n\t h,QE = gt.hreadfilev2(file_QE)\n\t h,RES = gt.hreadfilev2(file_RES)\n\t h,DIS = gt.hreadfilev2(file_DIS)\n\t \n\t QE_inter = interpolate.interp1d(np.array(QE)[:,0],np.array(QE)[:,1])\n\t RES_inter = interpolate.interp1d(np.array(RES)[:,0],np.array(RES)[:,1])\n\t DIS_inter = interpolate.interp1d(np.array(DIS)[:,0],np.array(DIS)[:,1])\n\t \n\t Enu = np.arange(1.0,100.0,0.1) # [GeV]\n\t ratio_DIS = map(lambda EE : DIS_inter(EE)/(DIS_inter(EE)+QE_inter(EE)+RES_inter(EE)), Enu)\n\t ratio_QE_RES = map(lambda EE : (RES_inter(EE)+QE_inter(EE))/(DIS_inter(EE)+QE_inter(EE)+RES_inter(EE)), Enu)\n\t \n\t avg_y = []\n\t avg_y_list =[]\n\t for i,EE in enumerate(Enu):\n\t avg_y.append(ymuCC(EE,neutype)*ratio_DIS[i]+0.0*ratio_QE_RES[i])\n\t avg_y_list.append([EE,ymuCC(EE,neutype)*ratio_DIS[i]+0.0*ratio_QE_RES[i]])\n\t \n\t if neutype == 0:\n\t file = open(datapath+\"y_avg_neutrino.dat\", 'w')\n\t elif neutype == 1:\n\t file = open(datapath+\"y_avg_antineutrino.dat\", 'w')\n\t gt.quickprint(file,avg_y_list)\n\telse :\n\t if neutype == 0:\n\t file = open(datapath+\"y_avg_neutrino.dat\", 'r')\n\t elif neutype == 1:\n\t file = open(datapath+\"y_avg_antineutrino.dat\", 'r')\n\t h,dat = gt.hreadfilev2(file)\n\t \n\t dat = np.array(dat)\n\t Enu = dat[:,0]\n\t avg_y = dat[:,1]\n\tif E > Enu[-1]:\n\t return ymuCC(E,neutype)\n\telse :\n\t inter_y_avg = interpolate.interp1d(Enu,avg_y)\n\t return inter_y_avg(E)",
"def _mean(self):\n mat = self._factorize(self.matrix, self.xdef)\n mat = self._rdc_x(mat, self.xdef)\n ysects = self._by_ysect(mat, self.ydef)\n return np.expand_dims([np.nansum(ymat[:, 0] /\n np.nansum(ymat[:, -1]))\n for ymat in ysects], 1).T",
"def five_number_stats(numberlist):\n minval = numpy.min(numberlist)\n maxval = numpy.max(numberlist)\n avg = numpy.mean(numberlist)\n median = numpy.median(numberlist)\n std = numpy.std(numberlist)\n return (minval, maxval, avg, median, std)",
"def poolMean(inObj):\n\n inObj.gs()",
"def model_mean_and_variance(binned_data):\n\n emp_values = [] # tuple(major_allele, mean, var, gmean, gvar, lmean, lvar)\n for major_allele, data in binned_data.iteritems():\n N_tot = sum(freq for _, freq in data.iteritems())\n mean_tot = sum(freq*float(allele) for allele, freq in data.items()) / N_tot\n var_tot = sum(freq*(float(allele) - mean_tot)**2 for allele, freq in data.items()) / (N_tot - 1)\n\n gains = [ (allele, freq) for allele, freq in data.items() if allele > 0 ]\n N_gain = sum(freq for _, freq in gains)\n if N_gain > 1:\n mean_gain = sum(freq*float(allele) for allele, freq in gains) / N_gain\n var_gain = sum(freq*(float(allele) - mean_gain)**2 for allele, freq in gains) / (N_gain - 1)\n else:\n mean_gain = None\n var_gain = None\n\n losses = [ (allele, freq) for allele, freq in data.items() if allele < 0 ]\n N_loss = sum(freq for _, freq in losses)\n if N_loss > 1:\n mean_loss = sum(freq*float(allele) for allele, freq in losses) / N_loss\n var_loss = sum(freq*(float(allele) - mean_loss)**2 for allele, freq in losses) / (N_loss - 1)\n else:\n mean_loss = None\n var_loss = None\n\n emp_values.append((int(major_allele), mean_tot, var_tot, mean_gain, var_gain, mean_loss, var_loss))\n\n # These are just for getting plot boundaries\n all_means = sum([ [ tup[1], tup[3], tup[5] ] for tup in emp_values ], [])\n all_means = [ x for x in all_means if x ] # drop Nones\n all_vars = sum([ [ tup[2], tup[4], tup[6] ] for tup in emp_values ], [])\n all_vars = [ x for x in all_vars if x ] # drop Nones\n\n rpy.r.layout(rpy.r.matrix([1,2], ncol=1))\n # Plots for visual inspection, move elsewhere\n ylim_mean = [ min(all_means), max(all_means) ]\n x_axis = [ tup[0] for tup in emp_values ]\n # Total mean\n rpy.r.plot([ na(tup[1]) for tup in emp_values ],\n x=x_axis, ylim=ylim_mean,\n main=\"Empirical mean error vs. major allele length\",\n xlab=\"Major allele length (units)\",\n ylab=\"Empirical mean error\")\n # Mean for gain alleles\n rpy.r.lines([ na(tup[3]) for tup in emp_values ], x=x_axis, col=\"green\")\n # Mean for loss alleles\n rpy.r.lines([ na(tup[5]) for tup in emp_values ], x=x_axis, col=\"red\")\n rpy.r.legend(\"bottomleft\", horiz=True, legend=[\"Total\", \"Gain\", \"Loss\"],\n fill=[\"black\", \"green\", \"red\"])\n\n # Total variance\n ylim_var = [ min(all_vars), max(all_vars) ]\n rpy.r.plot([ na(tup[2]) for tup in emp_values ],\n x=x_axis, ylim=ylim_var, log=\"y\",\n main=\"Empirical variance of error vs. major allele length\",\n xlab=\"Major allele length (units)\",\n ylab=\"Empirical variance of error\")\n # Gain variance\n rpy.r.lines([ na(tup[4]) for tup in emp_values ], x=x_axis, col=\"green\")\n # Loss variance\n rpy.r.lines([ na(tup[6]) for tup in emp_values ], x=x_axis, col=\"red\")\n rpy.r.legend(\"topleft\", horiz=True, legend=[\"Total\", \"Gain\", \"Loss\"],\n fill=[\"black\", \"green\", \"red\"])\n\n # Linear regression on mean. What sort of function should be used?\n # CAREFUL: might expect to use linear function since mean of each distn\n # should be roughly the major allele len, but these data are all\n # normalized to the major allele already--that is, 0=major allele len\n # and +/-(1,2,..) refer to deviations from the major allele. So we're\n # modeling the error, not the mean."
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Removes all characters from string 'nickname', that are not alphanumeric or '_' or '.'
|
def make_valid_nickname(nickname):
return re.sub('[^a-zA-Z0-9_\.]', '', nickname)
|
[
"def clean_usernames(text):\n return re.sub(\"@[^\\s]+\", \"\", str(text))",
"def clean_name(name):\n return name.strip()",
"def normalize_username(name):\n underscores = re.sub(r'\\s', '_', name)\n single_space = re.sub(r'_+', ' ', underscores)\n trimmed = single_space.strip()\n first = trimmed[0:1]\n rest = trimmed[1:]\n return first.upper() + rest",
"def clean_username(self):\n username = self.cleaned_data.get('username')\n\n # Might be best to only strip out our XMPP domain, but this works too\n return username.split('@')[0]",
"def sanitize_filename(filename):\n filename = filename.replace(\"..\", \".\")\n for character in filename:\n if character not in (\"ABCDEFGHIJKLMNOPQRSTUVWXYZ\" +\n \"abcdefghijklmnopqrstuvwxyz\" + \n \"0123456789\" + \n \"._-\"):\n filename = filename.replace(character, \"\")\n return filename",
"def strip_nonalpha(word: str)->str:\n return re.sub('[^a-zA-Z]+', '', word)",
"def clean(s):\n return s.replace(' ', '_').replace('\\\\', '_').replace('/', '_')",
"def _strip_emoji_name(name):\n if name.startswith(':'):\n starts_at = 1\n else:\n starts_at = None\n \n if name.endswith(':'):\n ends_at = -1\n else:\n ends_at = None\n \n if (starts_at is not None) or (ends_at is not None):\n name = name[starts_at : ends_at]\n \n return name",
"def validate_username(username):\n for c in username:\n if c.isalnum() == False and c != '_':\n return False\n \n return bool(username and re.match('^\\w{2,30}$', username))",
"def clean_song_name(name):\r\n\tname = name.split(' ')\r\n\tcorrect_name = ''\r\n\tfor word in name:\r\n\t\tif word == '':\r\n\t\t\tcontinue\r\n\t\telif word[0] == '#':\r\n\t\t\tword = word[1:]\r\n\t\t\tcorrect_name += word\r\n\t\telif word[0] != '(':\r\n\t\t\tcorrect_name += word + ' '\r\n\t\telse:\r\n\t\t\tbreak\r\n\treturn correct_name[:-1]",
"def userName() -> str:\n return re.sub(\"^[a-zA-Z]-\", \"\", getpass.getuser())",
"def cleanForIRI(string):\n \n iri = \"\"\n \n for c in string:\n if c.isalnum() or c in [\"-\", \".\", \"_\", \"~\"]:\n iri+=c\n return iri",
"def remove_reserved_chars(word):\n return \"\".join(i for i in word if i not in r'\\/:*?\"<>|')",
"def clean_str(string):\n string = re.sub(r\"\\s\", \"_\", string.strip())\n return re.sub(r\"[^\\w]\", \"\", string)",
"def sanitize_arangodb_key(string):\n regex = r\"[^0-9A-Za-z_\\-:.+]\" # Valid characters\n return re.sub(regex, \"\", string)",
"def filter_string_alnum(string):\r\n return ''.join(char for char in string if char.isalnum())",
"def strip_non_alnum(string):\n return _re_non_alphanum.sub(u\" \", string)",
"def nonkwchar():\n return regex(\"[^a-zA-Z0-9_]\")",
"def sanitize_domain(domain):\n whitelist_pattern = re.compile(r\"[^\\.\\-_a-zA-Z0-9]\")\n return whitelist_pattern.sub(\"\", domain)",
"def author_clean(author):\n replace = [\".\", \";\", \" \", \",\", \"_\", \"-\"]\n author_split = author.strip().split(\",\")\n clean_author = \"\"\n if len(author_split) >= 2:\n last_name = author_split[0]\n first_name = author_split[1]\n for rep in replace:\n first_name = first_name.replace(rep, \"\")\n clean_author = last_name + \" \" + first_name\n else:\n for rep in replace:\n clean_author = author.replace(rep, \"\")\n\n return clean_author"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Checks if nickname already exists in DB. If so appends number to nickname and checks again until nickname does not exists in DB. Returns this nickname.
|
def make_unique_nickname(nickname):
if User.query.filter_by(nickname=nickname).first() is None:
return nickname
version = 2
while True:
new_nickname = nickname = str(version)
if User.query.filter_by(nickname=new_nickname).first() is None:
break
version += 1
return new_nickname
|
[
"def find_by_id(cls, name_id: int):\n nickname = None\n if name_id:\n nickname = cls.query.get(name_id)\n return nickname",
"def get_nickname():\n\n return User.query.get(nickname)",
"def _check_existing_nickname(nickname):\n return g.con.get_user(nickname) is not None",
"def clean_nickname(self):\n nickname = self.cleaned_data[\"nickname\"]\n if get_user_model().objects.filter(username=nickname).count():\n raise ValidationError(\"This login already exists.\")\n return nickname",
"def nickname_exists(user_nickname):\n with sqlite3.connect(DATABASE) as conn:\n cursor = conn.execute(\"SELECT \"\n \"user_nickname \"\n \"FROM users \"\n \"WHERE user_nickname = ?;\", (user_nickname,))\n row = cursor.fetchone()\n user_nickname = row\n if row == None:\n return False\n else:\n return True",
"def set_nickname(self, nickname):\n\n # this is just all IRC spec basics\n if len(nickname) > 9 or nickname[0] == \"-\" or nickname[0] == \"#\":\n print(\"Client tried to connect with invalid username\")\n code = \"432\"\n msg = f\":{nickname}\"\n self.send_code(code, nickname, msg)\n return False\n\n try:\n if int(nickname[0]):\n print(\"Client tried to connect with invalid username\")\n code = \"432\"\n msg = f\":{nickname}\"\n self.send_code(code, nickname, msg)\n return False\n except ValueError:\n pass\n\n for client in self.server_mem.clients:\n if self.server_mem.clients[client] == nickname:\n print(\"Client tried to connect with taken username\")\n code = \"433\"\n msg = f\":{nickname}\"\n self.send_code(code, nickname, msg)\n return False\n\n self.nickname = nickname\n self.nick_set = True\n\n msg = f\"NICK {nickname}\"\n self.send_message_from_server(msg)\n self.server_mem.clients[self.socket] = self.nickname\n return True",
"def register(self, nickname, passwordHash):\n # Checks in the DB that the nickname was not already used. If ok, create\n # the player in the DB.\n if self.playersColl.find_one({'nickname': nickname}) == None:\n # creates the players in the DB\n playerID = self.playersColl.insert_one({'nickname': nickname, \n 'passwordHash': passwordHash, \n 'totalScore': 0, 'gameID': None}).inserted_id\n result = {'status': \"ok\", 'nickname': nickname, 'playerID': playerID }\n else:\n result = {'status': \"ko\", 'reason': \"invalid nickname\"}\n return result",
"def checkNewNicks(self):\n\tquery = \"select address, data from posts where post_id > \" + str(self.savedAllPostId) + \" and data like 'nick:%'\"\n\trows = putQuery(self, query)\n\tif rows is False:\n\t\treturn False\n\tconn = sqlite3.connect('coinflow.db')\n\tc = conn.cursor()\n\tfor row in rows['rows']:\n\t\tc.execute('select id from nicks where address = ?;', (row[0],))\n\t\tid = c.fetchone()\n\t\tnick = row[1].split(':',1)\n\t\tif id is None:\n\t\t\tc.execute('insert into nicks (nick, address) values (?,?);', (nick[1], row[0]))\n\t\telse:\n\t\t\tc.execute('update nicks set nick = ? where address = ?;', (nick[1], row[0]))\n\t\t#also check follows for potential updates\n\t\tc.execute('select nick from follows where address = ?;', (row[0],))\n\t\tcheckNick = c.fetchone()\n\t\tif checkNick is not None:\n\t\t\tif nick[1] != checkNick[0]:\n\t\t\t\tc.execute('update follows set nick=? where address=?;', (nick[1], row[0]))\n\tconn.commit()\n\tconn.close()\n\treturn",
"def on_nicknameinuse(self, c, e):\n print(\"Nick in use, appending _\")\n c.nick(c.get_nickname() + \"_\")",
"def test_add_user_existing_nickname(self):\n print('(' + self.test_add_user_existing_nickname.__name__ + ')', self.test_add_user_existing_nickname.__doc__)\n request_data = ADD_USER_VALID_DATA.copy()\n request_data['nickname'] = 'Mystery'\n resp = self.client.post(resources.api.url_for(resources.Users),\n headers={CONTENT_TYPE: resources.JSON},\n data=json.dumps(request_data))\n self._assertErrorMessage(resp, 409, 'Nickname already exists')",
"def new_nick(self):\n old = self.nick\n self.nick = '%s_%s' % (self.base_nick, random.randint(1, 1000))\n self.logger.warn('Nick %s already taken, trying %s' % (old, self.nick))\n self.register_nick()\n self.handle_nick_change(old, self.nick)",
"def isNicknameAvailable(self, nickname):\n # test the validity of the nickname\n \n # test if the nickname already is in the database\n pp = self.playersColl.find_one({'nickname': nickname})\n if pp == None:\n result = {'status': \"ok\", 'nickname': nickname}\n else:\n result = {'status': \"ko\", 'reason': \"nickname already used\"}\n return result",
"def name_bot(irc):\n nick = sys.platform[:3] + '-' + str(int(time.time())) # platform + timestamp\n real_name = nick[3:]\n\n irc.send(('NICK ' + nick + '\\r\\n').encode('utf-8'))\n irc.send(('USER ' + nick + ' ' + nick +\n ' ' + nick + ' :' + real_name + '\\r\\n').encode('utf-8'))\n\n while True:\n receive = irc.recv(4096).decode('utf-8')\n\n if 'Nickname is already in use' in receive: # try another nickname\n nick = sys.platform[:3] + '-' + str(int(time.time()))\n irc.send(('NICK ' + nick + '\\r\\n').encode('utf-8'))\n\n elif nick in receive or 'motd' in receive.lower():\n # successfully connected\n return nick",
"def getNick(self, address):\n\tconn = sqlite3.connect('coinflow.db')\n\tc = conn.cursor()\n\tc.execute('select nick from nicks where address = ?;', (address,))\n\tnick = c.fetchone()\n\tconn.close()\n\tif nick is None:\n\t\treturn address\n\telse:\n\t\treturn nick[0]",
"async def get_account_id(self, nickname: str) -> int:\n try:\n nick = None\n server = None\n nick, server = nickname.split('@')\n debug(nick + ' @ '+ server)\n server = server.lower()\n if nick == None or server == None:\n raise ValueError('Invalid nickname given: ' + nickname)\n url = self.get_url_account_id(nick, server)\n\n json_data = await self.get_url_JSON(url, self.chk_JSON_status)\n for res in json_data['data']:\n if res['nickname'].lower() == nick.lower(): \n return res['account_id']\n error('No WG account_id found: ' + nickname)\n \n except Exception as err:\n error(exception=err)\n return None",
"def on_nicknameinuse(self, c, e):\n # Probably unnecessary, since sending a server password will\n # log us in regardless whether we have our main nick or not.\n c.nick(c.get_nickname() + \"_\")\n time.sleep(2) # latency problem?\n c.privmsg(\"NickServ\",\"GHOST %s %s\" % (self.nickname, self.password))\n c.nick(self.nickname)\n time.sleep(2) # latency problem?\n c.privmsg(\"NickServ\",\"IDENTIFY %s\" % self.password)",
"def get_nickname(self):\n return self.nickname",
"def CreateNickname(self, user_name, nickname):\n\n uri = self._nicknameURL()\n nickname_entry = gdata.apps.data.NicknameEntry()\n nickname_entry.login = gdata.apps.data.Login(user_name=user_name)\n nickname_entry.nickname = gdata.apps.data.Nickname(name=nickname)\n return self.Post(nickname_entry, uri)",
"def test_modify_user_existing_nickname(self):\n print('(' + self.test_modify_user_existing_nickname.__name__ + ')',\n self.test_modify_user_existing_nickname.__doc__)\n request_data = MODIFY_USER_VALID_DATA.copy()\n request_data['nickname'] = 'AxelW'\n nickname = 'Mystery'\n resp = self.client.put(resources.api.url_for(resources.User, nickname=nickname),\n headers={CONTENT_TYPE: resources.JSON},\n data=json.dumps(request_data))\n self._assertErrorMessage(resp, 409, 'Existing nickname')"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Returns the area of the ring Return the area of the outer ring with radius outer. The radius of the hole is inner.
|
def area_of_ring(outer, inner):
return area_of_disk(outer) - area_of_disk(inner)
|
[
"def calculate_area(self):\n return Circle.PI * self.radius**2",
"def area_of_a_circle(radius):\n return np.pi * radius ** 2",
"def circle_area(radius):\n return numpy.pi*radius**2",
"def area_of_circle(radius: float) -> float:\n return pi * pow(radius, 2)",
"def circumference_area(radius):\n return (round(math.pi * radius**2, 3))",
"def circle_area(r):\r\n area = 3.14159 * r**2\r\n return area",
"def surface_area(self):\n\t\treturn 4 * PI * power(self.r, 2)",
"def area( self ):\n\n return self.__sideAB * self.__sideDA * math.sin(math.radians(self.__angleA))",
"def soma_surface_area(morph):\n return 4.0 * math.pi * morph.soma.radius ** 2",
"def signed_area(ring):\n xs, ys = ring.T\n signed_area = (xs * (np.roll(ys, -1) - np.roll(ys, +1))).sum() / 2\n return signed_area",
"def get_area(box):\n x_max, x_min, y_max, y_min = box\n return (x_max - x_min) * (y_max - y_min)",
"def _get_area(self) -> \"double\" :\n return _core.SurfaceEvaluator__get_area(self)",
"def circlesector_area(angle, radius):\n return 2*numpy.pi*radius*sectorangle/360",
"def get_area(lon, lat, radius, np):\n xyz = lon_lat_to_xyz(lon, lat, np)\n lower_left = xyz[(slice(None, -1), slice(None, -1), slice(None, None))]\n lower_right = xyz[(slice(1, None), slice(None, -1), slice(None, None))]\n upper_left = xyz[(slice(None, -1), slice(1, None), slice(None, None))]\n upper_right = xyz[(slice(1, None), slice(1, None), slice(None, None))]\n return get_rectangle_area(\n lower_left, upper_left, upper_right, lower_right, radius, np\n )",
"def get_side_area(self):\n\t\treturn PI * self.get_forming * (self.r_1 + self.r_2)",
"def AreaOnSurface(self):\n return (self.Q*self.SpreadFactor*numpy.pi*(self.particleDiameter/2.)**2)/self.particleMass",
"def outer_area(box):\r\n return (box.position_x, box.position_y,\r\n box.margin_width(), box.margin_height())",
"def regular_hexagon_area(side):\n return (3 * math.sqrt(3) * side ** 2) / 2",
"def sphere_area(r):\n return 4*pi*r**2",
"def surface_area(self):\n l, h, w = self.size\n return 2 * (w * l + h * l + h * w)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Returns the lateral surface area of a right circular cone with height h and radius r
|
def area_of_cone(h, r):
return math.pi * r * math.sqrt(r ** 2 + h ** 2)
|
[
"def right_circular_cone(r,h):\n s = sqrt((r**2) + (h**2))\n return s",
"def cone_area(d, h):\n r = d / 2\n surface_area = np.pi * r * (r + (h ** 2 + r ** 2) ** (1 / 2)) # - np.pi * r**2\n return surface_area",
"def sphere_cap_area(h, R):\n return 2*np.pi*R*(R-h)",
"def circle_area(r):\r\n area = 3.14159 * r**2\r\n return area",
"def circle_cap_arclen(h, R):\n return 2*R*np.arccos(h / R)",
"def surface_area(self):\n\t\treturn 4 * PI * power(self.r, 2)",
"def sphere_area(r):\n return 4*pi*r**2",
"def circle_area(radius):\n return numpy.pi*radius**2",
"def cylinder(r,h):\n A = 2 * pi * r * (r+h)\n return A",
"def get_surface_from_h_coefs(h, radius):\r\n new_pol = 1 + h.deriv(m=1) ** 2\r\n rr, dh_dr_num = new_pol.linspace(n=1000, domain=np.array([0.0, radius]))\r\n \r\n to_int = rr * dh_dr_num ** 0.5\r\n \r\n return 2 * np.pi * integrate.trapz(to_int, rr)",
"def circle_corner_arclen(h1, h2, R):\n return R*(np.arccos(h2 / R) - np.arcsin(h1 / R))",
"def sphere_edge_area(x, y, R):\n p = np.sqrt(R**2 - x**2 - y**2)\n A = (R - x - y)*np.pi - 2*R*np.arctan(x*y/(p*R)) + \\\n 2*x*np.arctan(y/p) + 2*y*np.arctan(x/p)\n return A*R",
"def area_of_a_circle(radius):\n return np.pi * radius ** 2",
"def area_cyl_shell(r1, r2):\n area1 = area_circle(r1)\n area2 = area_circle(r2)\n area = np.abs(area1 - area2)\n return area",
"def area_sphere(r):\n check_positive(r)\n area = 4 * np.pi * r**2\n return area",
"def calculate_area(self):\n return Circle.PI * self.radius**2",
"def circumference_area(radius):\n return (round(math.pi * radius**2, 3))",
"def get_compartment_surface_area(self, compartment: Sequence[Dict]) -> float:\n\n length = self.get_compartment_length(compartment)\n radius_diff = compartment[1][\"radius\"] - compartment[0][\"radius\"]\n radius_sum = compartment[1][\"radius\"] + compartment[0][\"radius\"]\n\n slant_height = math.sqrt((radius_diff) ** 2 + length ** 2)\n return math.pi * radius_sum * slant_height",
"def get_ah_area(self):\n\t\treturn la.norm(cross(self.a, self.h))"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Return the volume of the smaller sphere within the bigger sphere
|
def hollow_sphere(bigger, smaller):
return volume_of_sphere(bigger) - volume_of_sphere(smaller)
|
[
"def sphere_volume(radius: Number) -> Number:\n return (4.0/3.0) * pi * radius * radius * radius",
"def sphere_volume(r):\n return (3.0/4.0)*pi*r**3",
"def multiple_spheres_volume(radius: float, num_spheres: int) -> float:\n\n #Your code here",
"def volume_spherical_shell(r1, r2):\n vol1 = volume_sphere(r1)\n vol2 = volume_sphere(r2)\n volume = np.abs(vol1 - vol2)\n return volume",
"def test1_find_sphere_subvolume(self):\n\n\n radius = 0.5\n center = 0.5 * np.ones(3)\n c = Sphere(center, radius)\n\n x_ax = np.linspace(0, 1, 10)\n y_ax = np.linspace(0, 1, 10)\n z_ax = np.linspace(0, 1, 10)\n\n x_ax_subvol, y_ax_subvol, z_ax_subvol = \\\n c.find_subvolume(x_ax, y_ax, z_ax)\n\n self.assertTrue(np.allclose(x_ax, x_ax_subvol))\n self.assertTrue(np.allclose(y_ax, y_ax_subvol))\n self.assertTrue(np.allclose(z_ax, z_ax_subvol))",
"def get_volume(self):\n\t\treturn abs(inner(cross(self.a, self.b), self.h))/2",
"def test3_find_sphere_subvolume(self):\n\n\n radius = 0.4\n center = 0.5 * np.ones(3)\n c = Sphere(center, radius)\n\n x_ax = np.linspace(0, 1, 10)\n y_ax = np.linspace(0, 1, 10)\n z_ax = np.linspace(0, 1, 10)\n\n x_ax_subvol, y_ax_subvol, z_ax_subvol = \\\n c.find_subvolume(x_ax, y_ax, z_ax)\n\n\n self.assertTrue(np.allclose(x_ax[1:-1], x_ax_subvol))\n self.assertTrue(np.allclose(y_ax[1:-1], y_ax_subvol))\n self.assertTrue(np.allclose(z_ax[1:-1], z_ax_subvol))",
"def sphere(n):\n X, Y, Z = _np.mgrid[-1:1:n*1j, -1:1:n*1j, -1:1:n*1j]\n R2 = X**2+Y**2+Z**2\n vol = 1/_np.sqrt(R2)\n vol[vol < 1] = 0\n vol = _ndarray_to_aims_volume(vol)\n\n return vol",
"def volume(self):\n return 4 / 3 * math.pi * (self.radius ** 3)",
"def sphere_radius(self) -> float:\n return self.GetSphereRadius()",
"def test2_generate_volume(self):\n\n radius = 0.5\n center = 2 * np.ones(3)\n\n\n x_ax = np.linspace(0, 1, 3)\n y_ax = np.linspace(0, 1, 3)\n z_ax = np.linspace(0, 1, 3)\n\n c = Sphere(center, radius)\n subvol = c.generate_volume(x_ax, y_ax, z_ax)\n\n self.assertTrue(np.allclose(np.zeros((3,3,3)), subvol))",
"def get_volume(self):\n\t\treturn abs(inner(cross(self.a, self.b), self.c))",
"def volume(self):\n if self._volume is None:\n i = self._vertices[2, :] - self._vertices[1, :]\n j = self._vertices[3, :] - self._vertices[1, :]\n k = self._vertices[5, :] - self._vertices[1, :]\n sys = np.array([i, j, k])\n self._volume = abs(np.linalg.det(sys))\n return self._volume",
"def sphere_area(r):\n return 4*pi*r**2",
"def phase_space_volume(self) -> float:",
"def ST_DistanceSphere(left, right):\n return arctern.ST_DistanceSphere(left, right)",
"def volume(self):\n\t\treturn (4/3) * PI * power(self.r, 3)",
"def calculate_volume(self):\r\n \r\n # Calculate the volume\r\n self.volume = math.pi * self.radius**2 * self.height",
"def cylinder_volume(radius, height):\n return pi * radius ** 2 * height"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Testing the get_channel method with specific ID and expected data
|
def test_get_channel(self):
channel = api.get_channel(self.channel["id"])
self.assertEqual(channel.id, self.channel["id"])
self.assertEqual(channel.name, self.channel["name"])
|
[
"def test_should_get_a_channel_by_id(self):\n\n response = self.client.get(\n '/api/v3/channel/1/',\n content_type='application/json',\n HTTP_AUTHORIZATION=self.auth)\n\n self.assertEqual(200, response.status_code)",
"def testRetrieveChannel(self):\n self.assert_(self.epg.channels())",
"def test_should_not_get_a_channel_by_id(self):\n\n response = self.client.get(\n '/api/v3/channel/0/',\n content_type='application/json',\n HTTP_AUTHORIZATION=self.auth)\n\n self.assertEqual(500, response.status_code)",
"def test_channel_created(self):\n self.assertTrue(Channel.objects.get(name=self.channel))",
"def testRetrieveChannelIds(self):\n self.assert_(self.epg.channelIds())",
"def test_getChannelMessages(channel_id: str = CHANNEL_ID) -> json:\r\n # Action\r\n # status, result = u.getChannelMessages(\"B4EF14CFE2782C1E94E82631F9B782E2\")\r\n status, result = u.getChannelMessages(channel_id)\r\n\r\n # Assertion\r\n AssertNotEmptyOrError(status, result)",
"def test_should_not_get_a_channel_by_name(self):\n response = self.client.get(\n '/api/v3/channel/fakechannel/',\n content_type='application/json',\n HTTP_AUTHORIZATION=self.auth)\n\n self.assertEqual(500, response.status_code)",
"def get_channel_info_by_id(self, channel_id, default_param='snippet,contentDetails,statistics'):\n url = f'{self.api_url}/channels?part={default_param}&id={channel_id}&key={self.api_key}'\n response = requests.get(url)\n return {'status_code': response.status_code, 'content': response.json()}",
"def test_should_update_a_channel(self):\n\n response = self.client.put(\n '/api/v3/channel/1/',\n content_type='application/json',\n HTTP_AUTHORIZATION=self.auth)\n\n self.assertEqual(200, response.status_code)",
"def test_channel_create(self):\n channels = Channel.objects.filter(pk=self.channel.id)\n self.assertTrue(channels.exists())\n self.assertEqual(channels.count(), 1)\n self.assertEqual(channels[0].name, self.channel.name)",
"def test_individual_channel_convenience():\n data = om.read(path=persist, channel='testing')\n assert_false(data == {})\n\n # Non-existing channel returns dictionary\n assert_is_instance(om.read(persist, 'NON_EXISTANT'), dict)",
"def get_channel_by_id_name(self,ID=None,name=None):\n\t\tyield\n\t\tif not ID : ID = None\n\t\tif not name: name = None\n\t\tif (ID == None) and (name == None):raise ValueError(\"ID and name can't both be None or empty\")\n\n\t\tif not (ID is None):\n\t\t\ttry:\n\t\t\t\tby_id = self.channels_by_id[ID]\n\t\t\texcept:\n\t\t\t\traise ValueError(\"Invalid ID: {ID}; does not correspond to any channel.\".format(ID=ID))\n\t\tif not (name is None):\n\t\t\ttry:\n\t\t\t\tby_name = self.channels_by_name[name]\n\t\t\texcept:\n\t\t\t\traise ValueError(\"Invalid name: {name}; does not correspond to any channel.\".format(name=name))\n\n\t\tif ID == None: # If user only specifies name,\n\t\t\tchannel = by_name # get channel by the name.\n\t\telif name == None: # If user only specifies ID,\n\t\t\tchannel = by_id # get channel by the ID.\n\t\telse: # If user specifies both, make sure they both validly point to the same channel.\n\t\t\tif by_id.ID != by_name.ID : raise ValueError(\"Name and ID point to different channels. If both specified they must point to the same channel.\")\n\t\t\tif by_id.name != by_name.name : raise ValueError(\"Name and ID point to different channels. If both specified they must point to the same channel.\")\n\t\t\tchannel = by_id # now that we know they point to the same channel, just set it to by_id\n\n\t\treturnValue(channel)",
"def test__VoiceChannelEffect__channel__0():\n channel_id = 202304040044\n \n voice_channel_effect = VoiceChannelEffect(channel_id = channel_id)\n \n output = voice_channel_effect.channel\n vampytest.assert_instance(output, Channel)\n vampytest.assert_eq(output.id, channel_id)\n vampytest.assert_is(output, voice_channel_effect.channel)",
"def test_store_channel_info(mocked_responses, dummy_scenario_runner, api_task_by_name):\n\n mocked_responses.add(\n \"GET\",\n f\"http://0/api/v1/channels/0x1{1:039d}/0x2{1:039d}\",\n json={\"something\": 1},\n status=200,\n )\n task_instance = api_task_by_name(\"store_channel_info\", {\"from\": 0, \"to\": 1, \"key\": \"test\"})\n\n task_instance()\n\n assert dummy_scenario_runner.task_storage[STORAGE_KEY_CHANNEL_INFO][\"test\"] == {\"something\": 1}",
"def get_channel(self,c,ID,name=\"\"):\n\t\tchannel = yield self.get_channel_by_id_name(ID,name)\n\t\tif not channel.has_get:\n\t\t\traise ValueError(\"Tried to get_channel on a channel that does not support get commands\")\n\n\t\tif len(channel.get_inputs) == 0: # If there are no inputs required, then \n\t\t\ttry: # we call the setting with context only (no inputs)\n\t\t\t\tret = yield self.client[channel.get_setting[0]][channel.get_setting[2]](context=channel.context)\n\t\t\texcept:\n\t\t\t\tyield self.client[channel.get_setting[0]].select_device(channel.get_setting[1],context=channel.context)\n\t\t\t\tret = yield self.client[channel.get_setting[0]][channel.get_setting[2]](context=channel.context)\n\n\t\telif len(channel.get_inputs) == 1: # If there's exactly one input required then\n\t\t\ttry: # we call the setting with (input, context)\n\t\t\t\tret = yield self.client[channel.get_setting[0]][channel.get_setting[2]](channel.get_inputs[0],context=channel.context)\n\t\t\texcept:\n\t\t\t\tyield self.client[channel.get_setting[0]].select_device(channel.get_setting[1],context=channel.context)\n\t\t\t\tret = yield self.client[channel.get_setting[0]][channel.get_setting[2]](channel.get_inputs[0],context=channel.context)\n\n\t\telse: # multiple inputs required, then they can be given as a list\n\t\t\ttry: # so we call the setting with ([inputs...], context)\n\t\t\t\tret = yield self.client[channel.get_setting[0]][channel.get_setting[2]](channel.get_inputs,context=channel.context)\n\t\t\texcept:\n\t\t\t\tret = yield self.client[channel.get_setting[0]][channel.get_setting[2]](channel.get_inputs,context=channel.context)\n\t\t\t\tyield self.client[channel.get_setting[0]].select_device(channel.get_setting[1],context=channel.context)\n\n\t\tret = ret._value if type(ret) is units.Value else ret\n\t\tself.signal__channel_get([channel.ID,channel.name,ret])\n\t\treturnValue(ret)",
"def _create_test_content_channel(self):\n url = reverse('list_details')\n self._random_uuid = uuid.uuid4()\n channel_data = {\n \"channel_id\": self._random_uuid,\n \"name\": \"Chennel name slash title (EN)\",\n \"description\": \"A test channel\",\n \"version\": 3,\n \"source_domain\": \"learningequality.org\",\n \"source_id\": \"The test channel v0.1\",\n \"user_registered_by\": \"content@learningequality.org\",\n \"user_token\": \"a92a8ff947c8423ed0cd11c6ce33ad6b95b65633\",\n \"content_server\": \"https://develop.contentworkshop.learningequality.org\"\n }\n response = self.client.post(url, channel_data, format='json')\n self.assertEqual(response.status_code, status.HTTP_201_CREATED, \"Can't register content channel\")",
"def test_delete_communication_channel_id(self):\r\n user_id = None # Change me!!\r\n id = None # Change me!!\r\n\r\n r = self.client.delete_communication_channel_id(id, user_id)",
"def id2channel(self, channel_id):\n channel = None\n nameloc = channel_id.split('@') + ['']\n name = nameloc[0]\n loc = nameloc[1]\n# try:\n# name, loc = channel_id.split('@')\n# except:\n# name = channel_id\n# loc = None\n\n if name:\n for d in self.devices.values():\n for c in d.channels:\n if c.name == name:\n channel = c\n if not channel:\n for d in self.devices.values():\n for c in d.channels:\n if c.loc == loc:\n channel = c\n\n if channel is None:\n message = 'could not find channel based on ID {}.'.format(channel_id)\n raise Exception(message)\n return channel",
"def test_notification_channel(self, account_id: str, channel_id: str, **kwargs) -> 'DetailedResponse':\n\n if account_id is None:\n raise ValueError('account_id must be provided')\n if channel_id is None:\n raise ValueError('channel_id must be provided')\n\n headers = {}\n if 'headers' in kwargs:\n headers.update(kwargs.get('headers'))\n sdk_headers = get_sdk_headers(service_name=self.DEFAULT_SERVICE_NAME, service_version='V1', operation_id='test_notification_channel')\n headers.update(sdk_headers)\n\n url = '/v1/{0}/notifications/channels/{1}/test'.format(*self._encode_path_vars(account_id, channel_id))\n request = self.prepare_request(method='GET',\n url=url,\n headers=headers)\n\n response = self.send(request)\n return response"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Testing the create_dm method with specific recipient ID and expected mock data
|
def test_create_dm(self):
dms = api.create_dm(406882130577063956)
self.assertEqual(int(dms.recipients[0].id), 406882130577063956)
|
[
"def test_dm_recipient(self):\n msg = {\n \"id_str\": \"1\",\n 'text': 'This is a dm.',\n \"sender_id\": 1,\n \"sender_id_str\": \"1\",\n \"sender_screen_name\": \"fakeuser\",\n \"sender\": {},\n \"recipient_id\": 2,\n \"recipient_id_str\": \"2\",\n \"recipient_screen_name\": \"fakeuser2\",\n \"recipient\": {\n \"id\": 2,\n \"id_str\": \"2\",\n \"screen_name\": \"fakeuser2\",\n },\n }\n self.assertEqual(msg['recipient'], self.messagetools.dm_recipient(msg))",
"def test_ensure_dm(self):\n msg = {\n \"id\": 1,\n \"id_str\": \"1\",\n 'text': 'This is a dm.',\n \"sender_id\": 1,\n \"sender_id_str\": \"1\",\n \"sender_screen_name\": \"fakeuser\",\n \"sender\": {},\n \"recipient_id\": 2,\n \"recipient_id_str\": \"2\",\n \"recipient_screen_name\": \"fakeuser2\",\n \"recipient\": {},\n }\n self.assertEqual(msg, self.messagetools.ensure_dm(msg))",
"def test_dm_id(self):\n msg = {\n \"id_str\": \"1\",\n 'text': 'This is a dm.',\n \"sender_id\": 1,\n \"sender_id_str\": \"1\",\n \"sender_screen_name\": \"fakeuser\",\n \"sender\": {},\n \"recipient_id\": 2,\n \"recipient_id_str\": \"2\",\n \"recipient_screen_name\": \"fakeuser2\",\n \"recipient\": {},\n }\n self.assertEqual('1', self.messagetools.dm_id(msg))",
"def test_dm_sender(self):\n msg = {\n \"id_str\": \"1\",\n 'text': 'This is a dm mentioning @fakeuser2.',\n \"sender_id\": 1,\n \"sender_id_str\": \"1\",\n \"sender_screen_name\": \"fakeuser\",\n \"sender\": {\n \"id\": 1,\n \"id_str\": \"1\",\n \"screen_name\": \"fakeuser\",\n },\n \"recipient_id\": 2,\n \"recipient_id_str\": \"2\",\n \"recipient_screen_name\": \"fakeuser2\",\n \"recipient\": {},\n }\n self.assertEqual(msg['sender'], self.messagetools.dm_sender(msg))",
"def test_is_dm(self):\n self.assertEqual(True, self.messagetools.is_dm({\n \"id\": 1,\n \"id_str\": \"1\",\n 'text': 'This is a dm.',\n \"sender_id\": 1,\n \"sender_id_str\": \"1\",\n \"sender_screen_name\": \"fakeuser\",\n \"sender\": {},\n \"recipient_id\": 2,\n \"recipient_id_str\": \"2\",\n \"recipient_screen_name\": \"fakeuser2\",\n \"recipient\": {},\n }))",
"def test_self_mailer_create(self):\n self.mock_api.self_mailer_create = MagicMock(return_value={\n \"id\": \"sfm_fakeId\"\n })\n created_self_mailer = self.mock_api.self_mailer_create(self.sfm_editable)\n self.assertIsNotNone(created_self_mailer)\n self.assertEqual(created_self_mailer[\"id\"], \"sfm_fakeId\")",
"def test_dm_text(self):\n msg = {\n \"id_str\": \"1\",\n 'text': 'This is a dm.',\n \"sender_id\": 1,\n \"sender_id_str\": \"1\",\n \"sender_screen_name\": \"fakeuser\",\n \"sender\": {},\n \"recipient_id\": 2,\n \"recipient_id_str\": \"2\",\n \"recipient_screen_name\": \"fakeuser2\",\n \"recipient\": {},\n }\n self.assertEqual('This is a dm.', self.messagetools.dm_text(msg))",
"def test_dm_recipient_nondm(self):\n msg = {'friends': []}\n self.assertRaises(ValueError, self.messagetools.dm_recipient, msg)",
"def test_create_recipient_minimal(self):\n test_recipient = Recipient(\n first_name = \"Test\",\n last_name = \"Recipient\",\n lab = Laboratory.objects.get(pk=1))\n test_recipient.save()\n self.assertEquals(test_recipient.__unicode__(), \"Test Recipient (Fixture Laboratory)\")",
"def test_send_dm(self):\n self.mock_sc.chat_postMessage = mock.MagicMock(return_value=OK_RESP)\n\n self.bot.send_dm(\"Hahahaha\", \"UD8UCTN05\")\n self.mock_sc.chat_postMessage.assert_called_with(\n text=\"Hahahaha\",\n channel=\"UD8UCTN05\",\n as_user=True\n )",
"def test_self_mailer_create_with_idempotency_key(self):\n self.mock_api.self_mailer_create = MagicMock(return_value={\n \"id\": \"sfm_fakeId\"\n })\n created_self_mailer = self.mock_api.self_mailer_create(self.sfm_editable, idempotency_key=\"fake idempotency\")\n self.assertIsNotNone(created_self_mailer)\n self.assertEqual(created_self_mailer[\"id\"], \"sfm_fakeId\")",
"def test_create_recipient_all_fields(self):\n test_recipient = Recipient(\n first_name = \"Test\",\n last_name = \"Recipient\",\n initials = \"E.\",\n lab = Laboratory.objects.get(pk=1))\n test_recipient.save()\n self.assertEquals(test_recipient.__unicode__(), \"Test Recipient (Fixture Laboratory)\")",
"def create_campaign_member():",
"def test_self_mailer_create_with_custom_headers(self):\n self.mock_api.self_mailer_create = MagicMock(return_value={\n \"id\": \"sfm_fakeId\"\n })\n created_self_mailer = self.mock_api.self_mailer_create(self.sfm_editable, _content_type=\"application/json\")\n self.assertIsNotNone(created_self_mailer)\n self.assertEqual(created_self_mailer[\"id\"], \"sfm_fakeId\")",
"def test_dm_id_nondm(self):\n msg = {'friends': []}\n self.assertRaises(ValueError, self.messagetools.dm_id, msg)",
"def test_dm_user_mentions(self):\n user_mention = {\n 'id_str': '123',\n 'screen_name': 'fakeuser2',\n 'name': 'Fake User 2',\n }\n msg = {\n \"id_str\": \"1\",\n 'text': 'This is a dm mentioning @fakeuser2.',\n \"sender_id\": 1,\n \"sender_id_str\": \"1\",\n \"sender_screen_name\": \"fakeuser\",\n \"sender\": {},\n \"recipient_id\": 2,\n \"recipient_id_str\": \"2\",\n \"recipient_screen_name\": \"fakeuser2\",\n \"recipient\": {},\n 'entities': {'user_mentions': [user_mention]},\n }\n self.assertEqual(\n [user_mention], self.messagetools.dm_user_mentions(msg))",
"def test_auth_create_participant_contact(self):\n pass",
"def test_create_wrong_recipients(self):\n data = [{\n 'program': {\n 'status': 'Draft',\n 'kind': 'Directive',\n 'send_by_default': True,\n 'managers': ['user@example.com'],\n 'recipients': 'Admin,Primary Contacts,Secondary Contacts',\n 'title': 'Program_Test',\n 'review': {\n 'status': 'Unreviewed',\n },\n 'access_control_list': [],\n 'slug': 'program_test'\n }\n }]\n response = self.api.post(all_models.Program, data=data)\n self.assert400(response)\n self.assertIn(\n u\"Value should be either empty or comma separated list of\",\n response.json[0][1]\n )",
"async def send_dm(bot, userid, message):\n\tuser = bot.get_user(userid)\n\tchannel = await user.create_dm()\n\tawait channel.send(message)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Testing the modify_current_user method with specific ID and expected mock data
|
def test_modify_current_user(self):
modified_user = api.modify_current_user({"username": "Ahnaf"})
self.assertEqual(modified_user.id, self.me["id"])
self.assertEqual(modified_user.username, "Ahnaf")
|
[
"def test_update_yourself_non_manager(self):\n user = User.objects.create_user(\n username=\"non-admin zeiyeGhaoXoh4awe3xai\",\n password=\"non-admin chah1hoshohN5Oh7zouj\",\n )\n client = APIClient()\n client.login(\n username=\"non-admin zeiyeGhaoXoh4awe3xai\",\n password=\"non-admin chah1hoshohN5Oh7zouj\",\n )\n\n response = client.put(\n reverse(\"user-detail\", args=[user.pk]),\n {\n \"username\": \"New username IeWeipee5mahpi4quupo\",\n \"last_name\": \"New name fae1Bu1Eyeis9eRox4xu\",\n \"about_me\": \"New profile text Faemahphi3Hilokangei\",\n },\n )\n\n self.assertEqual(response.status_code, 200)\n user = User.objects.get(pk=user.pk)\n self.assertEqual(user.username, \"New username IeWeipee5mahpi4quupo\")\n self.assertEqual(user.about_me, \"New profile text Faemahphi3Hilokangei\")\n # The user is not allowed to change some other fields (like last_name).\n self.assertNotEqual(user.last_name, \"New name fae1Bu1Eyeis9eRox4xu\")",
"def test_simple_update_via_patch(self):\n admin_client = APIClient()\n admin_client.login(username=\"admin\", password=\"admin\")\n # This is the builtin user 'Administrator' with username 'admin'. The pk is valid.\n user_pk = User.objects.get(username=\"admin\").pk\n\n response = admin_client.patch(\n reverse(\"user-detail\", args=[user_pk]),\n {\"last_name\": \"New name tu3ooh5Iez5Aec2laefo\"},\n )\n\n self.assertEqual(response.status_code, status.HTTP_200_OK)\n user = User.objects.get(pk=user_pk)\n self.assertEqual(user.last_name, \"New name tu3ooh5Iez5Aec2laefo\")\n self.assertEqual(user.username, \"admin\")",
"def test_edit_user(self):\n data = {\"first_name\": \"test1\", \"last_name\": \"user1\",\n \"email\": \"test1@test1.com\", \"type\": \"admin\"}\n response = self.c.post(\n '/core/users/1/edit/',\n data, content='application/json',\n **{\"HTTP_AUTHORIZATION\": \"Token testuser1\"})\n userobj = User.objects.get(id=1)\n self.assertEqual(response.status_code, 200)\n self.assertEqual(userobj.first_name, \"test1\")\n self.assertEqual(userobj.last_name, \"user1\")\n self.assertEqual(userobj.email, \"test1@test1.com\")\n self.assertEqual(userobj.userprofile.is_admin, True)",
"def test_update_user_by_random_logged_in_user(self):\n user = factories.UserFactory()\n\n self.assert_user_cant_update_user(user)",
"def test_update_user_fake_jwt(self, test_client, headers_fake):\n user = UserModel.query.filter_by(username=\"test\").first()\n response = test_client.patch(\"/api/user/\"+str(user.uuid), headers=headers_fake, json=dict(\n email=\"test@test.com\"\n ))\n res = json.loads(response.data)\n user = UserModel.query.filter_by(username=\"test\").first()\n\n assert response.status_code == 403\n assert res['status'] == False\n assert user.email == \"test@test.bzh\"",
"def test_015_edit_user_info( self ):\n self.logout()\n self.login( 'test11@bx.psu.edu' )\n user = sa_session.query( galaxy.model.User ) \\\n .filter( and_( galaxy.model.User.table.c.email=='test11@bx.psu.edu' ) ).first()\n self.edit_login_info( new_email='test11_new@bx.psu.edu', new_username='test11_new' )\n self.change_password('testuser', 'new_testuser')\n self.edit_user_info( ['Research', 'PSU'] )",
"def test_update(self):\n self.instance.update(permissions=\"admin\")\n\n self.session.patch.assert_called_once_with(\n url_for_inviter(), data='{\"permissions\": \"admin\"}'\n )",
"def mock_get_current_user():\n return {\n \"id\": \"123456-abcdef\",\n \"name\": \"Test User\",\n }",
"def test_task_update_user_profile(self, mock):\n task_update_user_profile('Dave')\n\n mock.assert_called_once_with('Dave')",
"def test_update_external_user(self):\n pass",
"def test_update_run_as_user(self):\n pass",
"def test_edit_user(self):\n\n with app.test_client() as client:\n\n edited_info = {\n \"first-name\": \"Tweety\", \n \"last-name\": \"Bird Jr\", \n \"image-url\": \"https://upload.wikimedia.org/wikipedia/en/thumb/0/02/Tweety.svg/320px-Tweety.svg.png\"}\n resp = client.post(f\"/users/{self.user_id}/edit\", data=edited_info, follow_redirects=True)\n\n html = resp.get_data(as_text=True)\n self.assertEqual(resp.status_code, 200)\n self.assertIn(\"<li>Tweety Bird Jr</li>\", html)",
"def test_user_edit(self):\n\n with app.test_client() as client:\n d = {\"first_name\": \"Jonathan\",\n \"last_name\": \"Pagac\",\n \"image_url\": \"\"}\n resp = client.post(f\"/users/{self.user_id}/edit\",\n data=d,\n follow_redirects=True)\n html = resp.get_data(as_text=True)\n\n self.assertEqual(resp.status_code, 200)\n self.assertIn(\"Jonathan\", html)\n self.assertIn(\"Pagac\", html)\n self.assertIn('id=\"user-info\"', html)",
"def test_update_user_level_access(self):\n pass",
"def test_user_cant_edit_other_users(self):\n other_user = mommy.make_recipe('backend.core.user', username='leonardo2')\n other_user.first_name = 'Trying to change other user data'\n data = model_to_dict(other_user)\n resp = self.client.put(reverse('user-update', kwargs={'pk': other_user.pk}), data,\n HTTP_AUTHORIZATION=self.jwt_authorization)\n self.assertEqual(403, resp.status_code)",
"def test_otoroshi_controllers_adminapi_users_controller_update_admin(self):\n pass",
"def test_modify(self):\n a = baker.make(\"User\")\n a.profile.aac = False\n a.profile.save()\n dept = baker.make(\"Department\")\n r = self.client.get(reverse('makeReports:aac-modify-account',kwargs={'pk':a.pk}))\n self.assertEquals(r.status_code,200)\n fD = {\n 'aac':'on',\n 'department':dept.pk,\n 'first_name':'Tina',\n 'last_name':'Fey',\n 'email':'tfey@g.com'\n }\n r = self.client.post(reverse('makeReports:aac-modify-account',kwargs={'pk':a.pk}),fD)\n a.refresh_from_db()\n self.assertEquals(a.profile.aac,True)\n self.assertEquals(a.profile.department,dept)\n self.assertEquals(a.first_name,'Tina')\n self.assertEquals(a.last_name,'Fey')\n self.assertEquals(a.email,'tfey@g.com')",
"def test_update_username(self):\r\n with app.test_request_context():\r\n with self.client.session_transaction() as sess:\r\n sess[self.CURR_USER_KEY] = self.u1.id\r\n sess[self.MEMBER_STATUS] = self.MEMBER_STATUS\r\n sess['csrf_token'] = self.Token\r\n g.user = sess[self.CURR_USER_KEY]\r\n g.member = sess[self.MEMBER_STATUS]\r\n json = {\r\n \"new_username\":\"broman\"\r\n }\r\n \r\n resp = self.client.patch(f\"/users/{self.id}/profile\",\r\n headers=self.headers,\r\n json=json)\r\n \r\n self.assertEqual(resp.status_code,200)\r\n self.assertEqual(resp.json[\"response\"][\"ok\"],\"OK\")",
"def test_edit(self):\n\n unit = CustomUnit.objects.first()\n\n # Try to edit without permission\n self.user.is_staff = False\n self.user.save()\n\n self.patch(\n reverse('api-custom-unit-detail', kwargs={'pk': unit.pk}),\n {\n 'name': 'new_unit_name',\n },\n expected_code=403\n )\n\n # Ok, what if we have permission?\n self.user.is_staff = True\n self.user.save()\n\n self.patch(\n reverse('api-custom-unit-detail', kwargs={'pk': unit.pk}),\n {\n 'name': 'new_unit_name',\n },\n # expected_code=200\n )\n\n unit.refresh_from_db()\n self.assertEqual(unit.name, 'new_unit_name')"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Testing the leave_guild method with specific ID and expected mock data.
|
def test_leave_guild(self):
left = api.leave_guild(self.leave_guild)
self.assertEqual(left, 204)
|
[
"def test_team_leave(self):\r\n self.test_team_join_approve()\r\n url = reverse('team_leave', args=[self.project.slug, self.language.code])\r\n DATA = {'team_leave' : 'Leave'}\r\n resp = self.client['registered'].post(url, DATA, follow=True)\r\n self.assertContains(resp, 'You left the', status_code=200)",
"def test_leave_group(self):\n resp = self.c.post('/groups/leave/', { 'groupid':self.group.pk })\n self.assertEqual(self.user.get_profile().group, None)",
"def IgmpMldLeave(self, *args, **kwargs):\n # type: (*Any, **Any) -> None\n payload = {\"Arg1\": self}\n for i in range(len(args)):\n payload[\"Arg%s\" % (i + 2)] = args[i]\n for item in kwargs.items():\n payload[item[0]] = item[1]\n return self._execute(\"igmpMldLeave\", payload=payload, response_object=None)",
"async def leave(self, ctx):\n # [p]leave\n\n message = ctx.message\n\n await self.bot.say(\"Are you sure you want me to leave this server? \"\n \"Type yes to confirm.\")\n response = await self.bot.wait_for_message(author=message.author, timeout=30)\n\n if response is not None:\n if response.content.lower().strip() == \"yes\":\n await self.bot.say(\"Alright. Bye :wave:\")\n log.debug('Leaving \"{}\"'.format(message.server.name))\n await self.bot.leave_server(message.server)\n else:\n await self.bot.say(\"Ok I'll stay here then.\")",
"def test_game_room_destroyed_last_player_leaves(self):\n GameRoom(name='test', password='test').save()\n Player(game_room_id=1, name='test').save()\n url = '/api/player/1/delete/'\n self.client.delete(url)\n self.assertEqual(len(Player.objects.all()), 0)\n self.assertEqual(len(GameRoom.objects.all()), 0)",
"async def leave(self, ctx):\n if not await self.check_pm(ctx.message):\n return\n if ctx.author not in self.players:\n await ctx.send(embed=self.make_embed(\"Avalon\", 0xff4055, \"Error\", \"You are not in a game..\"))\n return\n if self.game_status == 0:\n await ctx.send(embed=self.make_embed(\"Avalon\", 0xff4055, \"Error\", \"No game in progress.\"))\n return\n elif self.game_status == 2:\n await ctx.send(embed=self.make_embed(\"Avalon\", 0xff4055, \"Error\", \"You can not leave an in progress game.\"))\n return\n self.players.remove(ctx.author)\n await ctx.send(embed=self.make_embed(\"Avalon\", 0x77dd77, \"Avalon\", \"You have successfully left the game.\"))",
"async def on_guild_remove(self, guild):\n\n logger.info(\"Guild leave event for '%s' (%d)\", guild.name, guild.id)\n with self.sql.transaction():\n self.sql.guilds.deactivate_guild(guild)",
"async def _teamleave(self, ctx):\r\n if ctx.invoked_subcommand is None:\r\n await self.bot.send_cmd_help(ctx)\r\n return",
"def test__Guild__from_data__0():\n guild_id = 202306210065\n \n data = {\n 'id': str(guild_id),\n }\n \n guild = Guild.from_data(data)\n _assert_fields_set(guild)\n \n vampytest.assert_eq(guild.id, guild_id)",
"def test_leaveChannel(channel_id: str = \"C160AB99F292C98746C3EA6ABB6AC7CD\", passwd: str = \"utopia9\") -> bool:\r\n\r\n # Action\r\n status, result = u.leaveChannel(channel_id)\r\n u.joinChannel(channel_id, passwd)\r\n\r\n # Assert\r\n AssertResultIsTrue(status, result)",
"def test__Guild__from_data__3():\n guild_id = 202306210069\n \n data = {\n 'id': str(guild_id),\n }\n \n client = Client(\n token = 'token_20230621_0000',\n )\n \n try:\n guild = Guild.from_data(data, client)\n \n vampytest.assert_eq(guild.clients, [client])\n vampytest.assert_eq(client.guilds, {guild})\n \n # Cleanup\n finally:\n client._delete()\n client = None",
"def twitchleave(self, mask, target, args):\n if not (yield from self.__isNickservIdentified(mask.nick)):\n return\n self.createTwitchConIfNecessary()\n self.twitchthread.leave(args.get('<channel>'))",
"async def server(self, inter: disnake.GuildCommandInteraction, id : str = commands.Param()):\r\n try:\r\n gid = int(id)\r\n try:\r\n toleave = self.bot.get_guild(gid)\r\n await toleave.leave()\r\n except:\r\n pass\r\n if id not in self.bot.data.save['banned_guilds']:\r\n with self.bot.data.lock:\r\n self.bot.data.save['banned_guilds'].append(id)\r\n self.bot.data.pending = True\r\n await inter.response.send_message(embed=self.bot.util.embed(title=\"The command ran with success\", color=self.color), ephemeral=True)\r\n await self.guildList()\r\n except Exception as e:\r\n await self.bot.sendError('ban_server', e)\r\n await inter.response.send_message(embed=self.bot.util.embed(title=\"An unexpected error occured\", color=self.color), ephemeral=True)",
"def test_check_on_guild_returns_true_inside_of_guild(self):\n self.ctx.guild = \"lemon's lemonade stand\"\n self.assertTrue(self.cog.check_on_guild(self.ctx))",
"async def memberleave(self, ctx):\n status = await self.bot.pool.fetch(\"SELECT * FROM loggingsettings WHERE guildid = $1\", ctx.guild.id)\n\n if status[0][\"member_leave\"] == True:\n await self.bot.pool.execute(\"UPDATE loggingsettings SET member_leave = $1 WHERE guildid = $2\", False, ctx.guild.id)\n embed=discord.Embed(title=\"Done!\", color=discord.Color.blurple(), description=\"Logging has been turned off for members leaving.\")\n await ctx.send(embed=embed)\n return\n else:\n await self.bot.pool.execute(\"UPDATE loggingsettings SET member_leave = $1 WHERE guildid = $2\", True, ctx.guild.id)\n embed=discord.Embed(title=\"Done!\", color=discord.Color.blurple(), description=\"Logging has been turned on for members leaving.\")\n await ctx.send(embed=embed)",
"async def test_team_empty_mentions(bot):\n team_role_name = staff_role[0] # DCT-team\n\n dpytest.configure(bot, members=2)\n\n bot.log = CommandLog(\"test_log.json\")\n\n guild = bot.guilds[0] # Guild object\n team_role = await guild.create_role(name=team_role_name) # Role object\n bot.role_dcteam = team_role\n member1 = guild.members[0] # Member\n member2 = guild.members[1] # Member\n\n await bot.add_cog(Team(bot))\n\n # Before command\n assert team_role not in member2.roles # m2 doesn't have the role\n\n await member1.add_roles(team_role) # m1 has the role Team\n\n # test empty mentions -> nothing happens\n await dpytest.message('!team')\n assert dpytest.verify().message().nothing()",
"def test_handle_contract_send_channelunlock_already_unlocked():\n channel_identifier = 1\n token_network_identifier = make_address()\n token_address = make_address()\n participant = make_address()\n raiden = MockRaidenService()\n\n def detail_participants(participant1, participant2, channel_identifier):\n transferred_amount = 1\n locked_amount = 1\n locksroot = make_32bytes()\n balance_hash = hash_balance_data(transferred_amount, locked_amount, locksroot)\n our_details = ParticipantDetails(\n address=raiden.address,\n deposit=5,\n withdrawn=0,\n is_closer=False,\n balance_hash=balance_hash,\n nonce=1,\n locksroot=locksroot,\n locked_amount=locked_amount,\n )\n\n transferred_amount = 1\n locked_amount = 1\n # Let's mock here that partner locksroot is 0x0\n locksroot = EMPTY_HASH\n balance_hash = hash_balance_data(transferred_amount, locked_amount, locksroot)\n partner_details = ParticipantDetails(\n address=participant,\n deposit=5,\n withdrawn=0,\n is_closer=True,\n balance_hash=balance_hash,\n nonce=1,\n locksroot=locksroot,\n locked_amount=locked_amount,\n )\n return ParticipantsDetails(our_details, partner_details)\n\n # make sure detail_participants returns partner data with a locksroot of 0x0\n raiden.chain.token_network.detail_participants = detail_participants\n\n event = ContractSendChannelBatchUnlock(\n token_address=token_address,\n token_network_identifier=token_network_identifier,\n channel_identifier=channel_identifier,\n participant=participant,\n )\n # This should not throw an unrecoverable error\n RaidenEventHandler().on_raiden_event(raiden=raiden, event=event)",
"def test_post_leave_community(self, test_client):\n password = \"Mockpassword123!\"\n hashed_password = bcrypt.hash(password)\n app_user = AppUser(username=\"mockusername\", password=hashed_password)\n community = Community(\n name=\"mockcommunity\", description=\"mockdescription\", app_user=app_user\n )\n db.session.add(app_user)\n db.session.add(community)\n db.session.commit()\n helpers.login(test_client, app_user.username, password)\n\n response = test_client.post(\n f\"/community/{community.name}/leave\", follow_redirects=True\n )\n\n assert response is not None\n assert response.status_code == 200\n assert b\"Successfully left community\" in response.data",
"async def ask_leave(self, ctx):\r\n await ctx.send(\"If you would like to leave the game, type the command .leave\")"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
The module requires an email and password for EoBot to function, and will automatically lookup and store the user ID for use in future requests
|
def __init__(self, email, password):
self.url_base = "https://www.eobot.com/api.aspx?"
self.email = str(email)
self.password = str(password)
self.debug = 0
url = self.url_base + 'email=' + self.email + '&password=' + self.password
self.user_id = (requests.get(url, timeout=5)).text
self.timeout = 5
|
[
"def auth(client, email, password): # pragma: no cover\n user = User.authenticate(client, email, password)\n click.echo(user.meta.api_token)",
"def _fixture_user(self):\n user_model = get_user_model()\n user = user_model.objects.get(email='r2d2@naboo.gov') # r2's password = 'bleep'\n self.client.force_authenticate(user=user)\n return user",
"def set_credentials(self):\n addon = self.utils.get_addon()\n user = self.dialogs.show_email_dialog()\n password = self.dialogs.show_password_dialog()\n _mail = self.encode(user) if user != '' else user\n _password = self.encode(password) if password != '' else password\n addon.setSetting('email', _mail)\n addon.setSetting('password', _password)\n return (user, password)",
"def id():\n bot = get_bot_instance()\n\n logging.info('Getting bot ID...')\n\n bot_id = bot.get_id()\n\n if bot_id:\n logging.info('Bot ID is ' + bot_id)\n else:\n logging.error('Could not find bot user')",
"def user(ctx):\n pass",
"def auth_browserid_authenticate(email):\n return fetch_amo_user(email)",
"def user_id(self):\n return self.auth.get_user_by_session()[\"user_id\"]",
"def test_get_user_details(self):\n # register a user\n register_user(self, 'some', 'name', 'another@gmail.com', 'aaaAAA111')\n # log in registered user\n login_user(self, 'another@gmail.com', 'aaaAAA111')",
"def test_user_add_email(self):\n pass",
"def initialize_user():\n flask.g.user = readit.User(flask.session.get('session_key', None))\n flask.g.user.user_id = flask.session.get('user_id', None)",
"def test_ensure_user(self):\n user = {\n 'id_str': '12345',\n 'screen_name': 'luke'\n }\n self.assertEqual(user, self.messagetools.ensure_user(user))",
"def gae_cookie_authentication(_request):\n user = users.get_current_user()\n try:\n return model.Identity(model.IDENTITY_USER, user.email()) if user else None\n except ValueError:\n raise api.AuthenticationError('Unsupported user email: %s' % user.email())",
"def _prepare_user(self):\n user = self.client.factory.create('Client')\n user.username = self.username\n user.password = self.password\n return user",
"def get_single_user():",
"def find_user(self, username=None, email=None):\n raise NotImplementedError",
"def post_create_user(self, user_name, password, osutils):",
"def _get_user_id(self):\n return self._api_query_request('me')['id']",
"def setup_user_email_inbox(\n\temail_account, awaiting_password, email_id, enable_outgoing, used_oauth\n):\n\tfrom frappe.core.doctype.user.user import ask_pass_update\n\n\tdef add_user_email(user):\n\t\tuser = frappe.get_doc(\"User\", user)\n\t\trow = user.append(\"user_emails\", {})\n\n\t\trow.email_id = email_id\n\t\trow.email_account = email_account\n\t\trow.awaiting_password = awaiting_password or 0\n\t\trow.used_oauth = used_oauth or 0\n\t\trow.enable_outgoing = enable_outgoing or 0\n\n\t\tuser.save(ignore_permissions=True)\n\n\tupdate_user_email_settings = False\n\tif not all([email_account, email_id]):\n\t\treturn\n\n\tuser_names = frappe.db.get_values(\"User\", {\"email\": email_id}, as_dict=True)\n\tif not user_names:\n\t\treturn\n\n\tfor user in user_names:\n\t\tuser_name = user.get(\"name\")\n\n\t\t# check if inbox is alreay configured\n\t\tuser_inbox = (\n\t\t\tfrappe.db.get_value(\n\t\t\t\t\"User Email\", {\"email_account\": email_account, \"parent\": user_name}, [\"name\"]\n\t\t\t)\n\t\t\tor None\n\t\t)\n\n\t\tif not user_inbox:\n\t\t\tadd_user_email(user_name)\n\t\telse:\n\t\t\t# update awaiting password for email account\n\t\t\tupdate_user_email_settings = True\n\n\tif update_user_email_settings:\n\t\tUserEmail = frappe.qb.DocType(\"User Email\")\n\t\tfrappe.qb.update(UserEmail).set(UserEmail.awaiting_password, (awaiting_password or 0)).set(\n\t\t\tUserEmail.enable_outgoing, (enable_outgoing or 0)\n\t\t).set(UserEmail.used_oauth, (used_oauth or 0)).where(\n\t\t\tUserEmail.email_account == email_account\n\t\t).run()\n\n\telse:\n\t\tusers = \" and \".join([frappe.bold(user.get(\"name\")) for user in user_names])\n\t\tfrappe.msgprint(_(\"Enabled email inbox for user {0}\").format(users))\n\task_pass_update()",
"def post(self):\n test_user = api.payload\n if 'username' in test_user:\n username = test_user['username']\n if 'password' in test_user:\n password = test_user['password']\n res = User.login(username=username, password=password, registered_users=registered_users)\n return res"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Return the current value for a Coin, expects the EoBot coin ID string
|
def get_coin_value(self, coin):
url = self.url_base + 'coin=' + str(coin)
if self.debug == 1:
print url
try:
result = requests.get(url, timeout=self.timeout)
except requests.exceptions.RequestException as exception:
print exception
return "ERROR"
return float(result.text)
|
[
"def coins(player):\n return player['coins']",
"def get_coin_balance(self, coin):\r\n totals = self.get_all_balances()\r\n if coin in totals.keys():\r\n if self.debug == 1:\r\n print coin\r\n\r\n return float(totals[coin])\r\n else:\r\n return 'Bad Coin'",
"def get_mining_coin(self):\r\n url = self.url_base + \"idmining=\" + self.user_id\r\n\r\n if self.debug == 1:\r\n print url\r\n\r\n try:\r\n coin = (requests.get(url, timeout=self.timeout)).text\r\n except requests.exceptions.RequestException as exception:\r\n print exception\r\n return \"ERROR\"\r\n\r\n return coin",
"def pick_coin(self):\n coin = round(random.uniform(0,1))\n if coin == 0:\n picked_coin = \"normal\"\n else: \n picked_coin = \"biased\"\n return picked_coin",
"def _get_val(self):\n return self.stock_owned.dot(self.stock_price) + self.cash_in_hand",
"def get_account_information(self, coin):\n\n accounts = self.auth_client.get_accounts()\n for account in accounts:\n if coin in account['currency']:\n return float(account['available'])\n\n return None",
"def get_price(coin, base_currency):\n\n try:\n url = \"https://api.cryptonator.com/api/ticker/{}-{}\".format(\n coin, base_currency)\n request = requests.get(url)\n if request.status_code == 200:\n data = request.json()\n except requests.exceptions.RequestException:\n return \"Coin not found\"\n\n if not data['success']:\n raise Exception(\"Coin not found\")\n else:\n return data['ticker']['price']",
"def get_coin_info():\n query = iroha.query('GetAssetInfo', asset_id='coin#domain')\n IrohaCrypto.sign_query(query, admin_private_key)\n\n response = net.send_query(query)\n data = response.asset_response.asset\n print('Asset id = {}, precision = {}'.format(data.asset_id, data.precision))",
"def get_deposit_address(self, coin):\r\n url = self.url_base + \"id=\" + self.user_id + '&deposit=' + str(coin)\r\n\r\n if self.debug == 1:\r\n print url\r\n\r\n try:\r\n result = requests.get(url, timeout=self.timeout)\r\n except requests.exceptions.RequestException as exception:\r\n print exception\r\n return \"ERROR\"\r\n\r\n return result.text",
"def get_money(self, *args):\n for coin in args:\n self.value_entered += coin.value",
"def getbalance(url):\n return Channel.get(url).our.nValue",
"def get_value_coins(area):\n if area > 3550 and area < 3750:\n print(area)\n return '2E', 2\n if area > 2950 and area < 3150:\n return '1E', 1\n if area > 2350 and area < 2550:\n return '5cnt', 0.05\n if area > 3200 and area < 3400:\n return '50cnt', 0.5\n if area > 2600 and area < 2800:\n return '20cnt', 0.2\n if area > 1400 and area < 1600:\n return '1cnt', 0.01\n if area > 2050 and area < 2250:\n return '10cnt', 0.1\n if area > 1800 and area < 2000:\n return '2cnt', 0.02\n return '0',0",
"def add_get(self, coin):\n if coin.symbol is None or len(coin.symbol) == 0:\n raise Exception(\"coin could not be added because it symbol was missing\")\n if coin.hash_value is None or len(coin.hash_value) == 0:\n coin.hash_value = self.hash(coin.symbol)\n if not self.coin_exist(coin):\n self.active_session.add(coin)\n self.active_session.commit()\n return coin",
"async def getBalance(self, guildID: str, userID) -> int:\n c = await self.getBankCursor()\n\n cursor = await c.execute('SELECT mcoins FROM bank WHERE guildID = ? and userID = ?', (guildID, str(userID)))\n result = await cursor.fetchone()\n\n coins = -1\n\n if result is None:\n cursor = await c.execute('INSERT INTO bank VALUES (?, ?, ?, NULL)', (guildID, str(userID), DEFAULT_AMOUNT))\n await self.commitBank()\n coins = DEFAULT_AMOUNT\n else:\n coins = result[0]\n\n return coins",
"def value_current(self):\n # get current value from Stockexchange\n #TODO: Transform to € if $\n value = self.history.iloc[-1]\n if self.info['currency'] != self.currency:\n currency = Converter(\n self.info['currency'], self.currency\n )\n value = currency.convert(value)\n\n return value",
"def get_value(self):\n if self.card:\n return self.card.get_value()\n return 0",
"def getCash(self):\n return self.cash",
"def get_btcprice():\n bitcoin_api_url = \"https://api.alternative.me/v2/ticker/bitcoin/?convert=CAD\"\n response = requests.get(bitcoin_api_url)\n response_json = response.json()\n price_cad = parse_float(response_json[\"data\"][\"1\"][\"quotes\"][\"CAD\"][\"price\"])\n return price_cad",
"def income(player: Player) -> None:\n player.coin += 1"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Return set email, shouldn't need this, maybe for debugging
|
def get_email(self):
return self.email
|
[
"def email(self, value):\n match = email_pattern(value)\n if match:\n self._email = value\n return\n assert 0, 'Invalid email'",
"def set_Email(self, value):\n super(UpdateTicketInputSet, self)._set_input('Email', value)",
"def email(self):\n return '{}.{}@email.com'.format(self.first, self.last)",
"def get_email():\n from six.moves.configparser import NoOptionError\n\n email = ''\n\n gitConfig = get_gitConfig()\n if gitConfig:\n try:\n email = gitConfig.get('user', 'email')\n except (KeyError, NoOptionError):\n pass\n\n # if not successful, we improvise\n if not email:\n import socket\n user = get_userName()\n host = socket.gethostname()\n email = \"{user}@{host}\".format(user=user, host=host)\n\n return email",
"def email_address(self) -> pulumi.Output[str]:\n return pulumi.get(self, \"email_address\")",
"def get_default_email_address(self):\n return self.teams[\"Default\"].email",
"def get_email(self, email):\n return self.db.one(\"\"\"\n SELECT *\n FROM emails\n WHERE participant_id=%s\n AND address=%s\n \"\"\", (self.id, email))",
"def thread_email(self):\n return self._thread_email",
"def test_account_set_email(self):\r\n \r\n # Create dummy account\r\n account = Account.objects.create(name='Foo Bar inc.')\r\n account.primary_email = 'first@account.com'\r\n \r\n # assert email is not saved yet\r\n email = None\r\n try:\r\n email = account.email_addresses.get(is_primary=True)\r\n email = email.email_address \r\n except EmailAddress.DoesNotExist:\r\n pass \r\n self.assertEqual(None, email)\r\n \r\n # Save email\r\n account.save()\r\n \r\n # assert email equals first@account.com\r\n email = None\r\n try:\r\n email = account.email_addresses.get(is_primary=True)\r\n email = email.email_address \r\n except EmailAddress.DoesNotExist:\r\n pass \r\n self.assertEqual('first@account.com', email)\r\n \r\n # change and save email\r\n account.primary_email = 'second@account.com'\r\n account.save()\r\n \r\n # assert email equals second@account.com\r\n email = None\r\n try:\r\n email = account.email_addresses.get(is_primary=True)\r\n email = email.email_address \r\n except EmailAddress.DoesNotExist:\r\n pass \r\n self.assertEqual('second@account.com', email)\r\n \r\n # change email (don't save)\r\n account.primary_email = 'third@account.com'\r\n \r\n # assert email still equals second@user.com \r\n email = None\r\n try:\r\n email = account.email_addresses.get(is_primary=True)\r\n email = email.email_address \r\n except EmailAddress.DoesNotExist:\r\n pass \r\n self.assertEqual('second@account.com', email)",
"def getMail(self):\n return self._mail",
"def test_getExternalEmail(self):\n email = self.reset.getExternalEmail(self.loginAccount)\n self.assertEquals(email, 'joe@external.com')",
"def default_email_address():\n import socket\n import getpass\n hostname = socket.gethostname()\n username = getpass.getuser()\n return '%s@%s'%(username, hostname)",
"def master_account_email(self) -> str:\n return pulumi.get(self, \"master_account_email\")",
"def edit_email(self, email, new_email):\n runner = self.get_runner(email)\n runner.set_email(new_email)",
"def get_email(self, author):\n if not self.context['request'].user.is_superuser:\n return None\n\n return author.user.email",
"def save(self, *args, **kwargs):\n u = self.instance\n u.email = self.cleaned_data['email']\n u.save()\n profile = super(HackDoUserEmailChangeForm, self).save(*args, **kwargs)\n return profile",
"def environ_email():\n username = os.environ.get(\"SUDO_USER\")\n if not username:\n username = getpass.getuser()\n\n return f\"{username}@scilifelab.se\"",
"def get_email_htmlinfo(self, request):\n\n if ((self.email == None) or (self.email == '')):\n # there is no email address on file at all\n rethtml = \"No email address provided (\" + \"provide one now\" +\").\"\n else:\n rethtml = self.email\n # we have one, now is it verified?\n if (self.isverified_email):\n rethtml += \" (verified)\"\n else:\n rethtml += \" (not yet verified)\"\n # now let's check for pending change to their email\n verification = request.sitecomp_verificationmanager().find_valid_by_type_and_userid(mconst.DEF_VFTYPE_userfield_verification, self.id, 'email')\n if (verification != None):\n if (verification.verification_varval != self.email):\n rethtml += \" [pending change to {0}]\".format(verification.verification_varval)\n else:\n # it's initial email verification, so nothing extra to display\n pass\n\n # return it\n return rethtml",
"def smtpAddress(self):\r\n return self._ensureSet('_smtpAddress', '__substg1.0_39FE')"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Returns the currently mining coin for the user account
|
def get_mining_coin(self):
url = self.url_base + "idmining=" + self.user_id
if self.debug == 1:
print url
try:
coin = (requests.get(url, timeout=self.timeout)).text
except requests.exceptions.RequestException as exception:
print exception
return "ERROR"
return coin
|
[
"def get_account_information(self, coin):\n\n accounts = self.auth_client.get_accounts()\n for account in accounts:\n if coin in account['currency']:\n return float(account['available'])\n\n return None",
"def coins(player):\n return player['coins']",
"async def getBalance(self, guildID: str, userID) -> int:\n c = await self.getBankCursor()\n\n cursor = await c.execute('SELECT mcoins FROM bank WHERE guildID = ? and userID = ?', (guildID, str(userID)))\n result = await cursor.fetchone()\n\n coins = -1\n\n if result is None:\n cursor = await c.execute('INSERT INTO bank VALUES (?, ?, ?, NULL)', (guildID, str(userID), DEFAULT_AMOUNT))\n await self.commitBank()\n coins = DEFAULT_AMOUNT\n else:\n coins = result[0]\n\n return coins",
"def pick_coin(self):\n coin = round(random.uniform(0,1))\n if coin == 0:\n picked_coin = \"normal\"\n else: \n picked_coin = \"biased\"\n return picked_coin",
"def get_coin_balance(self, coin):\r\n totals = self.get_all_balances()\r\n if coin in totals.keys():\r\n if self.debug == 1:\r\n print coin\r\n\r\n return float(totals[coin])\r\n else:\r\n return 'Bad Coin'",
"def set_mining_coin(self, coin):\r\n url = self.url_base + \"id=\" + self.user_id + \"&email=\" + self.email + \"&password=\" + self.password + \\\r\n \"&mining=\" + coin\r\n\r\n if self.debug == 1:\r\n print url\r\n\r\n try:\r\n requests.post(url, timeout=self.timeout)\r\n except requests.exceptions.RequestException as exception:\r\n print exception\r\n return \"ERROR\"\r\n\r\n if self.get_mining_coin() == coin:\r\n return \"Success\"\r\n else:\r\n return \"Error\"",
"def get_net(self) -> float:\n return self.coin * self.currentPrice - self.coinOwed * self.currentPrice + self.balance",
"def get_user_bid(self):\n if self.good.deal == AUCTION:\n bid = AuctionBids.objects.filter(good=self.good, user=self.user).latest('updated')\n return bid.user_price",
"def get_coin_value(self, coin):\r\n url = self.url_base + 'coin=' + str(coin)\r\n \r\n if self.debug == 1:\r\n print url\r\n\r\n try:\r\n result = requests.get(url, timeout=self.timeout)\r\n except requests.exceptions.RequestException as exception:\r\n print exception\r\n return \"ERROR\"\r\n\r\n return float(result.text)",
"def getClientBalance(self, client, bot_config):\n currency = str(bot_config['currency'])\n pair = currency[len(currency)-4:len(currency)]\n if(pair == 'USDT'):\n balance = client.get_asset_balance(asset='USDT')\n else:\n balance = client.get_asset_balance(asset='BTC')\n return balance['free']",
"def get_coin_info():\n query = iroha.query('GetAssetInfo', asset_id='coin#domain')\n IrohaCrypto.sign_query(query, admin_private_key)\n\n response = net.send_query(query)\n data = response.asset_response.asset\n print('Asset id = {}, precision = {}'.format(data.asset_id, data.precision))",
"def get_balance(self):\n query = 'select sum(amount) from pizza_transactions where user_id=%s'\n self.cursor.execute(query, (self.user,))\n result = self.cursor.fetchall()\n balance = result[0][0]\n if balance is None:\n balance = 0.0\n return balance",
"def get_buy_amount(self):\r\n return self.balance / 3",
"def wallet(self):\n\t\tdat = self.conn.call('GET', '/api/wallet/').json()\n\t\tbalance = float(dat['data']['total']['balance'])\n\t\tsendable = float(dat['data']['total']['sendable'])\n\t\treturn (balance, sendable)",
"def get_checkin(self):\n\t\treturn self.checkin",
"def get_account_buying_power(self) -> float:\n return self.trader.account['buying_power']",
"def testnet():\n return wallet['obj'].testnet",
"def acceptable_coins():\n return (Coin(0.01 * 10 ** multiplier * coinsDeg) for multiplier in range(4) for coinsDeg in [1, 2, 5])",
"def pickup_coin(self, x, y):\n \n # ADD CODE HERE\n if self.coins[y][x] > 0:\n coins = self.coins[y][x]\n self.coins[y][x] = 0\n return coins\n else:\n return 0"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Returns a specific coin balance for your account, requires a EoBot Coin String
|
def get_coin_balance(self, coin):
totals = self.get_all_balances()
if coin in totals.keys():
if self.debug == 1:
print coin
return float(totals[coin])
else:
return 'Bad Coin'
|
[
"def balance(ctx, address):\n if address == '':\n address = config.PUBLIC_KEY.to_bytes().hex()\n id__address, address = normalize_address(address, asHex=True)\n if VERBOSE:\n app_log.info(f\"Get balance for address {address}\")\n assert(len(address) == 64) # TODO: better user warning\n\n url = \"{}/balance?walletId={}&action=run\".format(ctx.obj['client'], address)\n if VERBOSE:\n app_log.info(f\"Calling {url}\")\n res = get(url)\n if VERBOSE:\n app_log.info(res)\n if path.isdir(\"tmp\"):\n # Store for debug purposes\n with open(\"tmp/answer.txt\", \"w\") as fp:\n fp.write(res.text)\n # print(json.dumps(fake_table_to_list(res.text)))\n try:\n data = list(fake_table_to_list(res.text))[0]\n balance = data[\"balance\"].replace(\"\\u2229\", \"\")\n if ctx.obj['json']:\n print(json.dumps({\"block\": data[\"block height\"], \"balance\": balance,\n \"address\": address,\n \"id__\": id__address}))\n else:\n print(f\"At block: {data['block height']}\")\n print(f\"Your Balance is: {balance}\")\n return float(balance)\n except:\n data = {}\n if ctx.obj['json']:\n print(json.dumps({\"block\": \"N/A\", \"balance\": 0,\n \"address\": address, \"id__\": id__address}))\n else:\n print(f\"At block: N/A\")\n print(f\"Your Balance is: N/A\")\n return 0",
"def getClientBalance(self, client, bot_config):\n currency = str(bot_config['currency'])\n pair = currency[len(currency)-4:len(currency)]\n if(pair == 'USDT'):\n balance = client.get_asset_balance(asset='USDT')\n else:\n balance = client.get_asset_balance(asset='BTC')\n return balance['free']",
"def get_deposit_address(self, coin):\r\n url = self.url_base + \"id=\" + self.user_id + '&deposit=' + str(coin)\r\n\r\n if self.debug == 1:\r\n print url\r\n\r\n try:\r\n result = requests.get(url, timeout=self.timeout)\r\n except requests.exceptions.RequestException as exception:\r\n print exception\r\n return \"ERROR\"\r\n\r\n return result.text",
"def get_account_information(self, coin):\n\n accounts = self.auth_client.get_accounts()\n for account in accounts:\n if coin in account['currency']:\n return float(account['available'])\n\n return None",
"def getAccountBalance(self, currency={}):\n data = self.getInfo()\n\n if currency.__contains__(\"BTC\"):\n return Decimal(data['return']['funds']['btc'])\n elif currency.__contains__(\"USD\"):\n return Decimal(data['return']['funds']['usd'])\n else:\n return {'BTC': Decimal(data['return']['funds']['btc']), 'USD': Decimal(data['return']['funds']['usd'])}",
"def get_balance(self, address, chain_id=None, token_id=None, issuer_id=None):\n params = FATd.check_id_params(chain_id, token_id, issuer_id)\n params[\"address\"] = address\n return self._request(\"get-balance\", params)",
"def getbalance(url):\n return Channel.get(url).our.nValue",
"def get_account_balance(self):\n return self.execute_private_api(\"/api/accounts/balance\", \"GET\")",
"def get_balance(address: 'Address'):\n return IcxEngine.get_balance(None, address)",
"def withdraw_currency(self, coin, amount, wallet):\r\n\r\n url = self.url_base + 'id=' + self.user_id + '&email=' + self.email + '&password=' + self.password + \\\r\n '&manualwithdraw=' + coin + '&amount=' + str(amount) + '&wallet=' + wallet\r\n\r\n if self.debug == 1:\r\n print url\r\n\r\n try:\r\n result = requests.get(url, timeout=self.timeout)\r\n except requests.exceptions.RequestException as exception:\r\n print exception\r\n return \"ERROR\"\r\n\r\n return result.text",
"def get_coin_value(self, coin):\r\n url = self.url_base + 'coin=' + str(coin)\r\n \r\n if self.debug == 1:\r\n print url\r\n\r\n try:\r\n result = requests.get(url, timeout=self.timeout)\r\n except requests.exceptions.RequestException as exception:\r\n print exception\r\n return \"ERROR\"\r\n\r\n return float(result.text)",
"def get_balance(self, address=''):\n params = {'address': address}\n r = self._make_request('getBalance', **params)\n return r",
"def get_price(coin, base_currency):\n\n try:\n url = \"https://api.cryptonator.com/api/ticker/{}-{}\".format(\n coin, base_currency)\n request = requests.get(url)\n if request.status_code == 200:\n data = request.json()\n except requests.exceptions.RequestException:\n return \"Coin not found\"\n\n if not data['success']:\n raise Exception(\"Coin not found\")\n else:\n return data['ticker']['price']",
"async def getBalance(self, guildID: str, userID) -> int:\n c = await self.getBankCursor()\n\n cursor = await c.execute('SELECT mcoins FROM bank WHERE guildID = ? and userID = ?', (guildID, str(userID)))\n result = await cursor.fetchone()\n\n coins = -1\n\n if result is None:\n cursor = await c.execute('INSERT INTO bank VALUES (?, ?, ?, NULL)', (guildID, str(userID), DEFAULT_AMOUNT))\n await self.commitBank()\n coins = DEFAULT_AMOUNT\n else:\n coins = result[0]\n\n return coins",
"async def balance(self, currency: str) -> int:\n\n return (await self.balances()).get(currency, 0)",
"def balanceOf(acct, tokenId):\n return Get(GetContext(), _concatkey(_concatkey(BALANCE_PREFIX, tokenId), acct))",
"def get_current_account_balance(account_id, access_token):\n response = requests.get(\n f\"https://api.monzo.com/balance?account_id={account_id}\",\n headers={\"Authorization\": f\"Bearer {access_token}\"},\n )\n return response.json()[\"balance\"]",
"def confirmed_balance(account=None):\n return wallet['obj'].confirmed_balance(account)",
"def get_btcprice():\n bitcoin_api_url = \"https://api.alternative.me/v2/ticker/bitcoin/?convert=CAD\"\n response = requests.get(bitcoin_api_url)\n response_json = response.json()\n price_cad = parse_float(response_json[\"data\"][\"1\"][\"quotes\"][\"CAD\"][\"price\"])\n return price_cad"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Returns a dict with all mining speeds
|
def get_all_speeds(self):
url = self.url_base + "idspeed=" + self.user_id
if self.debug == 1:
print url
try:
speed_raw = (requests.get(url, timeout=self.timeout)).text
except requests.exceptions.RequestException as exception:
print exception
return "ERROR"
speed = {}
for line in speed_raw.split(';'):
if self.debug == 1:
print line
if ':' in line:
line_array = line.split(':')
speed[line_array[0]] = line_array[1]
return speed
|
[
"def get_speed(self):\n std_out, _, _ = self.run_command(\"speedtest-cli --simple\", default_asserts=True)\n print(std_out)\n\n current_ping = float(std_out[0].replace('Ping: ', '').replace(' ms', ''))\n current_download = float(std_out[1].replace('Download: ', '').replace(' Mbit/s', ''))\n current_upload = float(std_out[2].replace('Upload: ', '').replace(' Mbit/s', ''))\n\n return {'date': datetime.datetime.now(),\n 'ping': current_ping,\n 'download': current_download,\n 'upload': current_upload}",
"def best_performance(self):\n return list()",
"def time(self):\n\n return {p: sim.time for p, sim in self.simulators.items()}",
"def torrent_stats( self, torrents ):\n \n return dict( ( key, {\n \"uploadRatio\" : val[ \"uploadRatio\" ],\n \"percentDone\" : (\n # Convert NaN to `None`\n val[ \"percentDone\" ]\n if val[ \"percentDone\" ] == val[ \"percentDone\" ]\n else None\n ),\n \"trackerStats\" : val[ \"trackerStats\" ],\n } ) for key, val in self.mapped_rpc(\n torrents,\n (\n \"uploadRatio\",\n \"percentDone\",\n \"trackerStats\",\n )\n ).items() )",
"def getBenchmarkDictionary(self):\n\n return self.benchmarks",
"def stream_utility_prices(self) -> dict[str, float]:\n return bst.stream_utility_prices",
"def __call__(self):\n # For each frequency, we apply the function x -> tanh(x / 10).\n stats = {}\n for network in self.networks.keys():\n stats[network] = {\"rate\" : math.tanh(self.networks[network][\"rate\"] / 10.), \"level\" : self.networks[network][\"level\"]}\n return stats",
"def get_timings(prog_name) :\n\n [prob_sizes, timings] = db.get_timings(prog_name)\n \n return [prob_sizes, timings]",
"def speed_list(self) -> list:\n if NEW_FAN:\n return None\n else:\n return list(self._ctrl_params['speed'].keys())",
"def get_workers_reported_hashrate() -> dict:\n response = requests.get(f'{BASE_ETH_URL}reportedhashrates/{ETH_MINER_ADDRESS}')\n response: dict = response.json()\n\n return response['data']",
"def get_pool_hashrate():\n dt = datetime.datetime.utcnow()\n twelve_ago = dt - datetime.timedelta(minutes=12)\n two_ago = dt - datetime.timedelta(minutes=2)\n ten_min = (OneMinuteShare.query.filter_by(user='pool')\n .filter(OneMinuteShare.time >= twelve_ago, OneMinuteShare.time <= two_ago))\n ten_min = sum([min.value for min in ten_min])\n # shares times hashes per n1 share divided by 600 seconds and 1000 to get\n # khash per second\n return (float(ten_min) * (2 ** 16)) / 600000",
"def smt_params(self):\n cpucount = 0\n SMTLIST = []\n SMT = {}\n if self.GENERAL_SNAP:\n self.GENERAL_SNAP.seek(0)\n while True:\n CUR_SMT = {}\n line = self.GENERAL_SNAP.readline()\n if not line:\n break\n if 'smt_enabled' in line:\n CUR_SMT.update({'smt_enabled' : line.split()[1]})\n line = self.GENERAL_SNAP.readline()\n CUR_SMT.update({'smt_threads' : line.split()[1]})\n if len(SMTLIST) > 0:\n for item in SMTLIST:\n if not(item == CUR_SMT):\n SMTLIST.append(CUR_SMT)\n else:\n SMTLIST.append(CUR_SMT)\n cpucount += 1\n# (cpucount == len(self.__snap_proc_list())) and\n\n if (len(SMTLIST) == 1):\n if SMTLIST[0]['smt_enabled'] == 'true':\n SMT.update({'smt_threads_count' : SMTLIST[0]['smt_threads']})\n else:\n SMT.update({'smt_threads_count' : '0'})\n else:\n return None\n return SMT",
"def look_up_speed_by_runner(self, runner):\n\t\treturn self.runner_speed_cate[runner]",
"def getInfoOnWorker(self):\n self.memory = PerfUtils.readMeminfo()\n cpus = PerfUtils.readCPUInfo()\n [ self.addCPU(x['Core'], x['MHz'], x['Model']) for x in cpus ]\n return",
"def list_minions(request):\n keys = request.subreq('salt_key', cmd='list_keys')\n minions = {}\n for name in keys['minions']:\n minions[name] = {\n 'name': name,\n 'enabled': not bool(request.db.query(MinionDisabled)\n .filter_by(name=name).first()),\n }\n return minions",
"def min_speed(self):\n result = List(7)\n node = self._graphs_data_list.head().third_way[0].head().next\n while node is not None:\n result.add(node.item)\n node = node.next\n return result",
"async def block_to_mine_info(self):\n if self.block_factory is None:\n # await self.refresh()\n return {}\n res = {\n \"target\": hex(int(self.block_factory.target))[2:].rjust(\n 64, \"0\"\n ), # target is now in hex format\n \"special_target\": hex(int(self.block_factory.special_target))[2:].rjust(\n 64, \"0\"\n ), # target is now in hex format\n # TODO this is the network target, maybe also send some pool target?\n \"special_min\": self.block_factory.special_min,\n \"header\": self.block_factory.header,\n \"version\": self.block_factory.version,\n \"height\": self.block_factory.index, # This is the height of the one we are mining\n \"previous_time\": self.config.LatestBlock.block.time, # needed for miner to recompute the real diff\n }\n return res",
"def stats(self):\n return dict(watch=self.watch_data.as_dict, exec=self.exec_data.as_dict)",
"def format_getstat1(self):\n\n raw_response = self.getstat1()\n response = {\n \"miner\": dict(),\n \"eth_pool\": dict(),\n \"dcr_pool\": dict(),\n \"GPUs\": dict(),\n }\n\n response[\"miner\"][\"version\"] = raw_response[0]\n hours = int(raw_response[1]) // 60\n minutes = int(raw_response[1]) % 60\n response[\"miner\"][\"runtime\"] = \"{:02d}:{:02d}\".format(hours, minutes)\n\n [\n response[\"eth_pool\"][\"total_hashrate\"],\n response[\"eth_pool\"][\"accepted\"],\n response[\"eth_pool\"][\"rejected\"],\n ] = [int(val) for val in raw_response[2].split(\";\")]\n if response[\"eth_pool\"][\"total_hashrate\"] > 0:\n response[\"eth_pool\"][\"total_hashrate\"] *= 1000\n\n [\n response[\"dcr_pool\"][\"total_hashrate\"],\n response[\"dcr_pool\"][\"accepted\"],\n response[\"dcr_pool\"][\"rejected\"],\n ] = [int(val) for val in raw_response[4].split(\";\")]\n if response[\"dcr_pool\"][\"total_hashrate\"] > 0:\n response[\"dcr_pool\"][\"total_hashrate\"] *= 1000\n\n response[\"eth_pool\"][\"pool\"] = raw_response[7]\n\n [\n response[\"eth_pool\"][\"invalid\"],\n response[\"eth_pool\"][\"pool_switches\"],\n response[\"dcr_pool\"][\"invalid\"],\n response[\"dcr_pool\"][\"pool_switches\"],\n ] = [int(val) for val in raw_response[8].split(\";\")]\n\n percard_eth_hashrate = [\n (int(val) * 1000) if val != \"off\" else 0\n for val in raw_response[3].split(\";\")\n ]\n\n percard_dcr_hashrate = [\n (float(val) * 1000) if val != \"off\" else 0\n for val in raw_response[5].split(\";\")\n ]\n\n tempsfans = raw_response[6].split(\";\")\n tempsfans = [\n [int(value), int(tempsfans[index + 1])]\n for index, value in enumerate(tempsfans)\n if not index % 2\n ]\n\n for gpu in range(len(percard_eth_hashrate)):\n response[\"GPUs\"][\"GPU {}\".format(gpu)] = {\n \"eth_hashrate\": percard_eth_hashrate[gpu],\n \"dcr_hashrate\": percard_dcr_hashrate[gpu],\n \"temp\": tempsfans[gpu][0],\n \"fan\": tempsfans[gpu][1],\n }\n response[\"miner\"][\"ip\"] = self.ip\n response[\"miner\"][\"port\"] = self.port\n\n return response"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Returns a specific mining speed, requires a EoBot mining type string
|
def get_one_speed(self, m_type):
speeds = self.get_all_speeds()
if m_type in speeds.keys():
if self.debug == 1:
print m_type
return speeds[m_type]
else:
return 'Bad Mining Type'
|
[
"def _get_speed(self):\n reply = self.query(command = b'/1?37\\r', port = self.port)\n number = reply['value']\n debug('get_speed(): reply = {}, and number = {}'.format(reply,number))\n return reply",
"def way_speed(way):\n return way['tags'].get('maxspeed_mph',DEFAULT_SPEED_LIMIT_MPH[way['tags']['highway']])",
"def get_speed(lines, word):\n\n line = next(line for line in lines if line.startswith(word))\n return float(line.split()[1])",
"def get_speed(self):\n return float(self.send('speed?'))",
"def get_speed(self):\n reply = self._speed\n return reply",
"def speed_unit(self) -> str:\n system_unit = self.core_config[\"system_unit\"]\n if system_unit == METRIC:\n speed_unit = METERS_PER_SECOND\n else:\n speed_unit = MILES_PER_HOUR\n\n return speed_unit",
"def min_speed(self):\n out = self.__fcobj._execute_transceiver_cmd()\n if self.__swobj.is_connection_type_ssh():\n shintd = ShowInterfaceTransceiverDetail(out)\n return int(shintd.min_speed)\n supported_speed = get_key(interfacekeys.SUPP_SPEED, self._SW_VER)\n supp_speed = out.get(supported_speed, None)\n if supp_speed is not None:\n pat = \"Min speed: (\\d+) Mb/s, Max speed: (\\d+) Mb/s\"\n match = re.match(pat, supp_speed)\n if match:\n return int(match.group(1))\n return None",
"def speedMultiplier(self) -> float:\n return self._getMultiplier('speed')",
"def getDifficulty(self):\n stepsList = self.getSteps()\n difficultyNumber = self.scorer.scoreHit(stepsList,2, .01, self)\n difficulty = \"\"\n if difficultyNumber<= self.difficultyBenchmarks[\"easy\"]:\n difficulty = \"easy\"\n elif difficultyNumber <= self.difficultyBenchmarks[\"medium\"]:\n difficulty = \"medium\"\n elif difficultyNumber <= self.difficultyBenchmarks[\"hard\"]:\n difficulty = \"hard\"\n \n return difficulty",
"def look_up_speed_by_runner(self, runner):\n\t\treturn self.runner_speed_cate[runner]",
"async def get_laser_scan_speed(self):\n\n return unpack('I', await self._execute_command('#GetLaserScanSpeed').content)[0]",
"def get_fan_speed(gpu_number):\n command = 'ethos-smi -g {0} | grep \"* Fan Speed\" | cut -f 5 -d \" \"'.format(gpu_number)\n fan_speed = subprocess.check_output(command, shell=True).decode('utf-8')\n return int(fan_speed[:-2])",
"def Pick(self, string):\n if WEIGHTREGEX.search(string) is not None:\n return self.PickWeighted(string)\n\n if \"~\" in string:\n return random.choice(string.split('~'))\n return random.choice(string.split(','))",
"def max_speed(self):\n out = self.__fcobj._execute_transceiver_cmd()\n if self.__swobj.is_connection_type_ssh():\n shintd = ShowInterfaceTransceiverDetail(out)\n return int(shintd.max_speed)\n supported_speed = get_key(interfacekeys.SUPP_SPEED, self._SW_VER)\n supp_speed = out.get(supported_speed, None)\n if supp_speed is not None:\n pat = \"Min speed: (\\d+) Mb/s, Max speed: (\\d+) Mb/s\"\n match = re.match(pat, supp_speed)\n if match:\n return int(match.group(2))\n return None",
"def getSpeedOnStep(self, timeStep):\n if self.hasSpeedOnStep(timeStep):\n return self._speed[timeStep]\n else: # default case zero value\n return 0",
"def get_speed(self):\n std_out, _, _ = self.run_command(\"speedtest-cli --simple\", default_asserts=True)\n print(std_out)\n\n current_ping = float(std_out[0].replace('Ping: ', '').replace(' ms', ''))\n current_download = float(std_out[1].replace('Download: ', '').replace(' Mbit/s', ''))\n current_upload = float(std_out[2].replace('Upload: ', '').replace(' Mbit/s', ''))\n\n return {'date': datetime.datetime.now(),\n 'ping': current_ping,\n 'download': current_download,\n 'upload': current_upload}",
"def readactspindlespeed(self):\n\t\tst=self._req_rdsingle(1,1,0x25)\n\t\treturn self._decode8(st['data']) if st['len']==8 else None",
"def _avg_taxi_speed(time: float):\n # TODO Check int\n steps_per_minute = 60 / UPDATE_MOBILITY_INTERVAL\n minute = (time / steps_per_minute) % len(TAXI_SPEED_DISTRIBUTION)\n return TAXI_SPEED_DISTRIBUTION[int(minute)]",
"def get_power_unit(type_, log=False):\n if type_ not in UNITS:\n raise Exception('Unknown data type')\n if log:\n return 'dB/Hz'\n else:\n return UNITS[type_]['power_unit']"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Sets the mining coin on your account, requires a EoBot Coin String Will return string Success on success and ERROR if not.
|
def set_mining_coin(self, coin):
url = self.url_base + "id=" + self.user_id + "&email=" + self.email + "&password=" + self.password + \
"&mining=" + coin
if self.debug == 1:
print url
try:
requests.post(url, timeout=self.timeout)
except requests.exceptions.RequestException as exception:
print exception
return "ERROR"
if self.get_mining_coin() == coin:
return "Success"
else:
return "Error"
|
[
"def get_mining_coin(self):\r\n url = self.url_base + \"idmining=\" + self.user_id\r\n\r\n if self.debug == 1:\r\n print url\r\n\r\n try:\r\n coin = (requests.get(url, timeout=self.timeout)).text\r\n except requests.exceptions.RequestException as exception:\r\n print exception\r\n return \"ERROR\"\r\n\r\n return coin",
"def pick_coin(self):\n coin = round(random.uniform(0,1))\n if coin == 0:\n picked_coin = \"normal\"\n else: \n picked_coin = \"biased\"\n return picked_coin",
"async def addcoin(self, ctx, amount: int, member: discord.Member):\n data = await BonfideCoin(self.bot).get(ctx.guild.id, member.id)\n if data is None:\n await self.add_to_db(ctx.guild.id, member.id)\n\n if amount > 10000 or amount < 0:\n return await ctx.send(\"You can not add more than 10000 or less than 0.\")\n query = \"\"\" UPDATE bonafidecoin SET wallet = wallet + $3 WHERE guild_id = $1 AND user_id = $2\"\"\"\n await self.bot.db.execute(query, member.guild.id, member.id, amount)\n await ctx.send(\n f\"Successfully added <:coin:853891390537465858> {amount} to <@{member.id}>\"\n )",
"def get_coin_value(self, coin):\r\n url = self.url_base + 'coin=' + str(coin)\r\n \r\n if self.debug == 1:\r\n print url\r\n\r\n try:\r\n result = requests.get(url, timeout=self.timeout)\r\n except requests.exceptions.RequestException as exception:\r\n print exception\r\n return \"ERROR\"\r\n\r\n return float(result.text)",
"def income(player: Player) -> None:\n player.coin += 1",
"def validate_coin(self, value):\n if value != 1:\n raise serializers.ValidationError('This field must be 1.')\n return value",
"async def ask_bet(self, ctx):\r\n await ctx.send(\"What is the big blind (minimum bet) amount?\")",
"async def set_chance(msg):\n if len(msg.content.split()) < 2:\n return await embeds.desc_only(msg.channel, 'You need to specify an Amount to which the Chance should be set!')\n try:\n amount = int(msg.content.split()[1])\n except ValueError:\n return await embeds.desc_only(msg.channel, 'That is not a valid amount.')\n\n if not 0 <= amount <= 20:\n return await embeds.desc_only(msg.channel, 'Chance must be within 0 and 20%.')\n data.set_currency_chance(msg.guild.id, amount)\n return await embeds.desc_only(msg.channel, f'Set **Chime Spawn Chance** to **{amount} %**!')",
"def take_coins(choice):\r\n coin_amounts = []\r\n coin_values = {\"quarters\": 0.25, \"dimes\": 0.10, \"nickels\": 0.05, \"pennies\": 0.01}\r\n price = MENU[choice][\"cost\"]\r\n\r\n print(\"Please insert coins.\")\r\n for coin in coin_values:\r\n valid_response = False\r\n while not valid_response:\r\n num_of_coins = input(f\"How many {coin}?: \")\r\n if not check_for_off_command(num_of_coins):\r\n return False\r\n else:\r\n try:\r\n coin_amount = int(num_of_coins) * coin_values[coin]\r\n coin_amounts.append(coin_amount)\r\n valid_response = True\r\n except ValueError:\r\n print(\"Invalid response\")\r\n\r\n total_amount = sum(coin_amounts)\r\n\r\n if total_amount >= price:\r\n print(f\"Your total is ${'{:.2f}'.format(round(price, 2))}.\")\r\n change = total_amount - price\r\n print(f\"Here is ${'{:.2f}'.format(round(change, 2))} of change.\")\r\n resources[\"money\"] += float('{:.2f}'.format(round(price, 2)))\r\n return True\r\n else:\r\n print(\"Sorry, that's not enough money. Money refunded.\")\r\n return False",
"def handle_coin(command: Command):\n if command.has_arg() and command.arg.isnumeric():\n flips = min(max(int(command.arg), 1), 500)\n else:\n flips = 1\n\n response = []\n emoji = (':heads:', ':tails:')\n for i in range(flips):\n response.append(choice(emoji))\n\n bot.post_message(command.channel_id, \"\".join(response))",
"def insert_coin(self, value):\n self.amount += value",
"def withdraw_currency(self, coin, amount, wallet):\r\n\r\n url = self.url_base + 'id=' + self.user_id + '&email=' + self.email + '&password=' + self.password + \\\r\n '&manualwithdraw=' + coin + '&amount=' + str(amount) + '&wallet=' + wallet\r\n\r\n if self.debug == 1:\r\n print url\r\n\r\n try:\r\n result = requests.get(url, timeout=self.timeout)\r\n except requests.exceptions.RequestException as exception:\r\n print exception\r\n return \"ERROR\"\r\n\r\n return result.text",
"def process_coins():\n quarters = float(input(\"How many quarters? \"))\n dimes = float(input(\"How many dimes? \"))\n nickles = float(input(\"How many nickles? \"))\n pennies = float(input(\"How many pennies? \"))\n\n globals()[\"inserted_money\"] = round((quarters * 0.25) + (dimes * 0.10) + (nickles * 0.05) + (pennies * 0.01), 2)",
"def freeze_utxo(self, coin: str):\n assertOutpoint(coin)\n self.wallet.set_frozen_coin_state([coin], True)\n return True",
"def testnet():\n return wallet['obj'].testnet",
"def change_currency(self):\n if self.user_can_update_information():\n selected_currency = get_currency(acronym=get_currency_from_input())\n self.user.currency_id = selected_currency.get_id()\n print_message(f\"The currency has been set to the {selected_currency.name} ({selected_currency.acronym}).\")\n else:\n print_error(\"Password is incorrect. Cannot update currency.\")",
"def confirm_bitcoin_tx_online(self, hash, sender_gid, network):\n\n if network == 't' :\n url = \"https://api.samourai.io/test/v2/tx/\" + hash ## default testnet txtenna-server\n else :\n url = \"https://api.samourai.io/v2/tx/\" + hash ## default txtenna-server\n \n try:\n r = requests.get(url)\n ## print(r.text)\n\n while r.status_code != 200:\n sleep(60) # sleep for a minute\n r = requests.get(url)\n\n ## send zero-conf message back to tx sender\n rObj = TxTennaSegment('', '', tx_hash=hash, block=0)\n arg = str(sender_gid) + ' ' + rObj.serialize_to_json()\n self.do_send_private(arg) \n\n print(\"\\nSent to GID: \" + str(sender_gid) + \": Transaction \" + hash + \" added to the mempool.\") \n\n r_text = \"\".join(r.text.split()) # remove whitespace\n obj = json.loads(r_text)\n while not 'block' in obj.keys():\n sleep(60) # sleep for a minute\n r = requests.get(url)\n r_text = \"\".join(r.text.split())\n obj = json.loads(r_text)\n\n ## send block height message back to tx sender\n blockheight = obj['block']['height']\n rObj = TxTennaSegment('', '', tx_hash=hash, block=blockheight)\n arg = str(sender_gid) + ' ' + rObj.serialize_to_json()\n self.do_send_private(arg)\n\n print(\"\\nSent to GID: \" + str(sender_gid) + \": Transaction \" + hash + \" confirmed in block \" + str(blockheight) + \".\")\n\n except:\n traceback.print_exc()",
"def test_coin_info(self):",
"def send_money(self):\n pass"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Returns a desposit wallet address for the EoBot Coin String
|
def get_deposit_address(self, coin):
url = self.url_base + "id=" + self.user_id + '&deposit=' + str(coin)
if self.debug == 1:
print url
try:
result = requests.get(url, timeout=self.timeout)
except requests.exceptions.RequestException as exception:
print exception
return "ERROR"
return result.text
|
[
"async def get_deposit_address(self, **params):\r\n return await self.client_helper(\"get_deposit_address\", **params)",
"def current_address():\n return wallet['obj'].current_address",
"def get_address_for_account(email):\n query = (email, )\n conn = sqlite3.connect(WALLET_KEYS)\n c = conn.cursor()\n c.execute('SELECT wallet_key from wallet_keys WHERE email=?', query)\n wallet_key = c.fetchone()[0]\n wallet = Wallet.Wallet.from_wallet_key(wallet_key)\n return wallet.address()",
"def get_payout_address(account=None):\n return wallet['obj'].get_payout_address(account)",
"async def btc_address(self, *_):\n if self.bitcoin_address:\n return self.bitcoin_address\n return await self.exec(GetBTCAddress())",
"def get_address(self):\n return self.account.address",
"def backAddress(wallet):\n wallet.backAddress()",
"def get_address(self, address: str) -> Address:",
"def get_change_address(account=None):\n return wallet['obj'].get_change_address(account)",
"def createnewaddress(self):\n return self.wallet.create_new_address(False).to_ui_string()",
"def test_get_deposit_address(self):\n pass",
"def get_address(self, offset):\n donglePath = self._parse_bip32_path(offset)\n\n apdu = bytes.fromhex('e0020000') \n apdu += bytes([len(donglePath) + 1])\n apdu += bytes([len(donglePath) // 4])\n apdu += donglePath\n\n result = self.dongle.exchange(apdu, timeout=60)\n\n\n # Parse result\n offset = 1 + result[0]\n\n address = result[offset + 1 : offset + 1 + result[offset]]\n\n return f't0{address.decode()}'",
"async def fetch_deposit_address(self, code: str, params={}):\n await self.load_markets()\n currency = self.currency(code)\n request = {\n 'symbol': currency['id'],\n }\n response = await self.privateGetDeposit(self.extend(request, params))\n #\n # {\n # \"address\": \"0x449889e3234514c45d57f7c5a571feba0c7ad567\",\n # \"paymentId\": \"10002653\"\n # }\n #\n address = self.safe_string(response, 'address')\n tag = self.safe_string(response, 'paymentId')\n self.check_address(address)\n return {\n 'currency': code,\n 'address': address,\n 'tag': tag,\n 'network': None,\n 'info': response,\n }",
"def seed_to_address(seed: str) -> str:\n return Keypair.from_seed(seed).address().decode()",
"def get_genesis_contract_address_string(self):\n chain_status = self.get_chain_status()\n return chain_status['GenesisContractAddress']",
"def germanaddress(adict):\n return (get_entry(\"street\", adict) + \" \"\n + get_entry(\"houseNumber\", adict)\n + r\"\\\\\" + \"%\\n \"\n + get_entry(\"postalCode\", adict)\n + \" \"\n + get_entry(\"city\", adict)\n + get_country(adict)\n )",
"async def create_deposit_address(self, code: str, params={}):\n await self.load_markets()\n currency = self.currency(code)\n accounts = self.safe_value(self.options, 'coinbaseAccounts')\n if accounts is None:\n accounts = await self.privateGetCoinbaseAccounts()\n self.options['coinbaseAccounts'] = accounts # cache it\n self.options['coinbaseAccountsByCurrencyId'] = self.index_by(accounts, 'currency')\n currencyId = currency['id']\n account = self.safe_value(self.options['coinbaseAccountsByCurrencyId'], currencyId)\n if account is None:\n # eslint-disable-next-line quotes\n raise InvalidAddress(self.id + \" createDepositAddress() could not find currency code \" + code + \" with id = \" + currencyId + \" in self.options['coinbaseAccountsByCurrencyId']\")\n request = {\n 'id': account['id'],\n }\n response = await self.privatePostCoinbaseAccountsIdAddresses(self.extend(request, params))\n address = self.safe_string(response, 'address')\n tag = self.safe_string(response, 'destination_tag')\n return {\n 'currency': code,\n 'address': self.check_address(address),\n 'tag': tag,\n 'info': response,\n }",
"def get_contract_address(self) -> Address:\n return self.contract.address",
"async def address(self, ctx):\n await ctx.send('{} Send Coins to: `{}`'.format(ctx.author.mention, self.grlc.get_user_address(ctx.author.id)))"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Withdraw currency from the specified coin string, in the specified amount, to the specified wallet
|
def withdraw_currency(self, coin, amount, wallet):
url = self.url_base + 'id=' + self.user_id + '&email=' + self.email + '&password=' + self.password + \
'&manualwithdraw=' + coin + '&amount=' + str(amount) + '&wallet=' + wallet
if self.debug == 1:
print url
try:
result = requests.get(url, timeout=self.timeout)
except requests.exceptions.RequestException as exception:
print exception
return "ERROR"
return result.text
|
[
"async def deposit(self, ctx, amount):\n data = await BonfideCoin(self.bot).get(ctx.guild.id, ctx.author.id)\n if data is None:\n await self.add_to_db(ctx.guild.id, ctx.author.id)\n\n data = await BonfideCoin(self.bot).get(ctx.guild.id, ctx.author.id)\n\n # return error if balance is 0\n if data.get(\"wallet\") == 0:\n return await ctx.send(\"You don't have sufficient balance to deposit.\")\n\n query = \"\"\"UPDATE bonafidecoin SET bank = $3 + bank, wallet = wallet - $3 WHERE guild_id = $1 AND user_id\n = $2\"\"\"\n if amount.lower() == \"all\":\n await self.bot.db.execute(\n query, ctx.guild.id, ctx.author.id, data.get(\"wallet\")\n )\n return await ctx.send(\n f\"Successfully deposited <:coin:853891390537465858> **{data.get('wallet')}**.\"\n )\n\n else:\n try:\n # check if money being deposited is equal to or less than wallet\n if 0 < data.get(\"wallet\") >= int(amount):\n await self.bot.db.execute(\n query, ctx.guild.id, ctx.author.id, int(amount)\n )\n return await ctx.send(\n f\"Successfully deposited <:coin:853891390537465858> **{amount}**.\"\n )\n return await ctx.send(\"You don't have sufficient balance to deposit.\")\n except ValueError:\n return await ctx.send(\"Enter a valid amount.\")",
"async def withdraw(self, ctx, amount: int):\n data = await BonfideCoin(self.bot).get(ctx.guild.id, ctx.author.id)\n if data is None:\n await self.add_to_db(ctx.guild.id, ctx.author.id)\n\n data = await BonfideCoin(self.bot).get(ctx.guild.id, ctx.author.id)\n if amount <= data.get(\"bank\"):\n query = \"\"\"UPDATE bonafidecoin SET bank = bank - $3, wallet = wallet + $3 WHERE guild_id = $1 AND user_id\n = $2 \"\"\"\n await self.bot.db.execute(query, ctx.guild.id, ctx.author.id, amount)\n return await ctx.send(\n f\"Successfully withdrawn <:coin:853891390537465858> **{amount}**.\"\n )\n\n return await ctx.send(\"You don't have sufficient balance to withdraw.\")",
"def deposit(self, amount):\n self.wallet += amount",
"def transfer_wallet(self, currency, amount, wallet_from, wallet_to):\n body = {\n 'currency': currency,\n 'amount': str(amount),\n 'walletfrom': wallet_from,\n 'walletto': wallet_to,\n }\n return self.auth_req('v1/transfer', body)",
"def withdrawToAddress(self, address, amount):\n data = self.api_call(\"WithdrawCoin\", {'coinName': \"BTC\", 'address': address, 'amount': amount})\n\n if \"error\" in data:\n return {'success': 0, 'error': data['error']}\n else:\n return {'success': 1, 'id': data['tID']}",
"def withdraw_money(self, amount):\n self.balance -= amount",
"async def addcoin(self, ctx, amount: int, member: discord.Member):\n data = await BonfideCoin(self.bot).get(ctx.guild.id, member.id)\n if data is None:\n await self.add_to_db(ctx.guild.id, member.id)\n\n if amount > 10000 or amount < 0:\n return await ctx.send(\"You can not add more than 10000 or less than 0.\")\n query = \"\"\" UPDATE bonafidecoin SET wallet = wallet + $3 WHERE guild_id = $1 AND user_id = $2\"\"\"\n await self.bot.db.execute(query, member.guild.id, member.id, amount)\n await ctx.send(\n f\"Successfully added <:coin:853891390537465858> {amount} to <@{member.id}>\"\n )",
"def withdraw(self, account, amount):\n # Take the amount of money our of the account\n self.accounts[account].balance -= amount\n # Return the amount of money we withdrew\n return amount",
"async def removecoin(self, ctx, amount: int, member: discord.Member):\n data = await BonfideCoin(self.bot).get(ctx.guild.id, member.id)\n if data is None:\n await self.add_to_db(ctx.guild.id, member.id)\n\n if amount > 10000 or amount < 0:\n return await ctx.send(\"You can not remove more than 10000 or less than 0.\")\n query = \"\"\" UPDATE bonafidecoin SET wallet = wallet - $3 WHERE guild_id = $1 AND user_id = $2\"\"\"\n await self.bot.db.execute(query, member.guild.id, member.id, amount)\n await ctx.send(\n f\"Successfully removed <:coin:853891390537465858> {amount} from <@{member.id}>\"\n )",
"def deposit(self, account, amount):\n self.accounts[account].balance += amount",
"def deposit(self, amount):\n bal = self.get_balance()\n bal += amount\n return bal",
"def withdrawCash(self, amount): # withdrawCash function\n amount_f = float(amount)\t\t\t\t\t\t\n if amount_f > self.cash:\t\t\t\t\t\t # if there is not enough cash to withdraw\n \t self.tr += \"Failed to withdraw cash\"\t\t\t # record of failed transaction\n \t return \"Not enough cash in portfolio\" \n self.cash -= amount_f\t\t\t\t\t\t\t # subtract the amount when enough\n self.tr += \"Withdrew ${0} of cash\\n\".format(amount) # record of transaction",
"def withdraw(self, amount: int): # METHOD\n if self.check_withdraw(amount): # Inputs the output from check-withdrawal(amount)\n self._balance -= amount # Balance is decremented after each withdrawal\n return self._balance # New balance is shown\n else:\n message = f'Insufficient funds.'\n raise ValueError(message)",
"def deposit(self, amount):\n if amount < 0:\n raise ValueError('Negative deposit')\n else:\n self.bal += amount",
"def transfer(self, amount, account):\n \n if ((self.getBalance()) >= amount):\n self.withdraw(amount, \"Transfer to \" + account.name)\n account.deposit(amount, \"Transfer from \" + self.name)\n\n print(\"Transferred $\" + \"{:.2f}\".format(amount) + \" from \" + self.name + \" to \" + account.name)\n\n else:\n print(\"Insufficient Balance\")",
"def convert_then_withdraw(self, amount, currency, description):\n if isinstance(amount, (int, float)) == False:\n raise TypeError(\"The inserted amount is not numeric\")\n \n exchange = currency + '_USD'\n api = 'https://free.currencyconverterapi.com/api/v5/convert'\n query = '?q=' + exchange + '&compact=ultra'\n\n response = requests.get(api + query)\n \n while not response:\n time.sleep(0.1)\n \n rate = response.json()[exchange]\n amount_after_conversion = round(amount * rate, 2)\n \n if amount_after_conversion > self._balance:\n raise ValueError(\"Insufficient funds\")\n \n self._balance -= amount_after_conversion\n self.history.append('Withdraw after conversion of an amount of {} '.format(amount) \n + currency \n + ' to {} $ at date {} : {}'.format(amount_after_conversion, datetime.datetime.now().date(), description))\n self.save()",
"def debit(self, amount):\n if self._is_asset_or_expenses:\n self.balance += amount\n else:\n self.balance -= amount",
"def send_btc(amount, address):\n # Don't debug with httpbin while the headers are enabled in\n # execute_coinbase_http.\n #url = \"http://httpbin.org/post\"\n\n url = \"https://coinbase.com/api/v1/transactions/send_money\"\n\n body = json.dumps({\n \"transaction\": {\n \"to\": address,\n \"amount\": amount,\n },\n })\n\n response = execute_coinbase_http(url, body=body)\n content = json.loads(response.read())\n return content",
"def withdraw(self, amount):\n self._balance -= amount\n\n if self._balance < 10:\n self._balance -= 5\n self._fees += 5"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Generates and prints n words, starting with the word w, and following the distribution of the language model.
|
def generate(self, w, n):
# YOUR CODE HERE
w = w.lower()
res = w + " "
ix = self.index[w]
for _ in range(n-1):
choices = []
weights = []
if ix in self.bigram_prob:
for k, v in self.bigram_prob[ix].items():
choices.append(k)
weights.append(math.exp(v))
ix = random.choices(population=choices, weights=weights)[0]
w = self.word[ix]
res = res + w + " "
else:
ix = random.randint(0, self.unique_words)
print(res)
|
[
"def easy_words():\n length = random.randint(4,6)\n constraints = init_constraint(length)\n return ''.join(constraints)",
"def wordGenerator(maxLength=12):\n s=''\n wordLength=random.randint(4,maxLength)\n for i in range(wordLength):\n # return random integer\n s += chr(random.randint(ord('a'), ord('j')))\n s += \"\\n\"\n return s",
"def sentence_gen(corpora, n, priority, length=15):\n \n counted_ngrams = {}\n sorted_ngrams = {}\n \n counted_ngrams = corpora.ngrams(n)\n sorted_ngrams = sorted(counted_ngrams.iteritems(), key=operator.itemgetter(1))[::-1]\n \n words = [None]\n while len(filter(lambda w: w is not None, words)) < length:\n index = random.randint(priority, priority+2)\n \n filtered_ngrams = filter(lambda k: k[0][0] == words[-1], sorted_ngrams[n])\n if len(words) + n >= length:\n filtered_ngrams = filter(lambda item: item[0][-1] is None, filtered_ngrams)\n \n if filtered_ngrams:\n ngram = filtered_ngrams[min(index, len(filtered_ngrams)-1)]\n ngram_words = ngram[0][1:]\n \n words += ngram_words\n else:\n ngram = sorted_ngrams[n][index]\n words += [\".\"] + list(ngram[0])\n \n words = filter(lambda w: w is not None, words)\n \n return \" \".join(words)",
"def generate_sentence(model, n):\n text = [None] * (n-1)\n sentence_finished = False\n\n # generate random sentences\n while not sentence_finished:\n r = random.random()\n accumulator = .0\n\n for word in model[tuple(text[1-n:])].keys():\n accumulator += model[tuple(text[1-n:])][word]\n if accumulator >= r:\n text.append(word)\n break\n\n if text[1-n:] == [None] * (n-1):\n sentence_finished = True\n\n return ' '.join([t for t in text if t])",
"def generate_word(self) -> str:\n\n from random import choice, randint\n\n ret = choice(self.inits)\n count = randint(self.min, self.max)\n\n while len(ret) < count:\n try:\n arr = self.pairs[ret[-2:]]\n ret += choice(arr)[1:]\n except KeyError:\n ret = ret[:-2]\n\n if len(ret) < 2:\n ret = choice(self.inits)\n\n return ret.title()",
"def blooms_words(level):\n create_words = ['design', 'assemble', 'construct', 'conjecture', 'develop',\n 'formulate', 'author', 'investigate', 'create', 'adapt', 'plan',\n 'produce', 'build', 'solve', 'compose', 'think', 'theorize', 'modify',\n 'improve']\n evaluate_words = ['appraise', 'argue', 'defend', 'judge', 'select', 'support',\n 'value', 'critique', 'weigh', 'evaluate', 'assess', 'compare', 'conclude',\n 'debate', 'decide', 'measure', 'opinion', 'prove', 'support', 'test', \n 'validate', 'interpret']\n analyze_words = ['differentiate', 'organize', 'relate', 'compare', 'contrast',\n 'distinguish', 'examine', 'experiment', 'question', 'test',\n 'analyze', 'arrange', 'breakdown', 'categorize', 'differences',\n 'dissect', 'inspect', 'research', 'highlight', 'find', 'question']\n apply_words = ['execute', 'implement', 'solve', 'use', \n 'interpret', 'operate', 'schedule', 'sketch', 'apply',\n 'act', 'administer', 'build', 'choose', 'connect', 'construct', 'develop',\n 'teach', 'plan', 'employ', 'demonstrate', 'show']\n understand_words = ['describe', 'explain', 'identify', 'locate', 'recognize', 'report', \n 'select', 'translate', 'understand', 'ask', 'cite', 'classify', \n 'compare', 'contrast', 'discuss', 'rephrase', 'infer', 'summarize', \n 'purpose', 'show', 'demonstrate', 'express', 'examples']\n remember_words = ['define', 'duplicate', 'list', 'memorize', 'repeat', 'state',\n 'remember', 'copy', 'recognize', 'tell', 'reproduce', 'retell',\n 'recite', 'read', 'knowledge']\n if(level==\"KN\"):\n return remember_words\n elif(level==\"CO\"):\n return understand_words\n elif(level==\"AP\"):\n return apply_words\n elif(level==\"AN\"):\n return analyze_words\n elif(level==\"SN\"):\n return create_words\n elif(level==\"EV\"):\n return evaluate_words",
"def make_word(phonology, num_syllables, distro='zipf')->str:\n\n # Construct the word\n word = ''\n for i in range(num_syllables):\n word += make_syllable(phonology)\n return word",
"def generate_text(word_count=5, lang=\"eng\"):\n text = TEXTS[lang].replace(\"\\n\", \"\").split(\" \")\n generated_text_lst = []\n for _ in range(word_count):\n generated_text_lst.append(random.choice(text))\n generated_text = ' '.join(generated_text_lst)\n return generated_text",
"def topic_words(model, feature_names, n_top_words):\n for num_topic, topic in enumerate(model.components_):\n words = np.argsort(topic)[::-1][:n_top_words]\n print('Topic ' + str(num_topic) + ':')\n print(' '.join([feature_names[i] for i in words]))",
"def print_words(L):\n # Checks to see if the given input can be cast as an integer.\n try:\n N = int(input(\"N: \"))\n except ValueError:\n print (\"ERROR: Could not read N\")\n exit(1)\n # Ends the program if the given number is negative.\n assert N >= 0\n N_word_count = L[N].count()\n # Prints every word that has a count greater than or equal to the count of\n # the object at position N.\n for item in L:\n if item.count() >= N_word_count:\n print (\"{} : {:d}\".format(item.word(), item.count()))\n else:\n break",
"def _number_to_words(n: int) -> str:\n assert 0 <= n < 100\n try:\n return _num2words[n]\n except KeyError:\n try:\n return _num2words[n - n % 10] + _num2words[n % 10]\n except KeyError:\n raise Exception('Number out of range')",
"def generate( table ) :\n\n\t\t# set our \"start\" condition\n\tw1 = w2 = NONWORD;\n\n\tline = \"\"\t# to accumulate words, print a line at a time\n\n\tfor i in range( MAXGEN ) :\n\t\t\t# get our hands on the list\n\t\tkey = (w1,w2)\n\t\tsufList = table[key]\n\t\t\t# choose a suffix from the list\n\t\tsuf = random.choice( sufList )\n\n\t\tif suf == NONWORD :\t# caught our \"end story\" marker. Get out\n\t\t\tif len( line ) > 0 :\n\t\t\t\tprint line\n\t\t\tbreak\n\t\tif len( line ) + len( suf ) > MAX_LINE_LEN :\n\t\t\tprint line\n\t\t\tline = \"\"\n\t\tline = line + \" \" + suf\n\n\t\tw1, w2 = w2, suf",
"def important_words(model, n):\n theta = np.array(model.theta.toArray())\n dictionary = np.array(CountVectorizerModel.load('./cv_model').vocabulary)\n ind = np.argpartition(theta, -n)[-n:]\n return dictionary[ind]",
"def print_model(self):\n for tokens, gram in self.grams.iteritems():\n print('{}'.format(tokens))\n for successor, count in gram.successors.iteritems():\n probability = count / gram.count\n print('\\t{} {:.3f}'.format(successor, probability))",
"def gen_mnemonic(num_words:int)->str:\n if num_words < 12 or num_words > 24 or num_words%3 != 0:\n raise RuntimeError(\"Invalid word count\")\n return bip39.mnemonic_from_bytes(rng.get_random_bytes(num_words*4//3))",
"def gen_words(self, doc):\r\n doc = re.sub(\"[\\s+\\.\\!\\/_,$%^*(+\\\"\\']+|[+——！，。？、~@#”“￥：%……&*（）]+\".decode(\"utf8\"),\r\n \"\".decode(\"utf8\"), doc.decode('utf8'))\r\n suffix_indexes = extract_cand_words(doc, self.max_word_len)\r\n word_cands = {}\r\n # compute frequency and neighbors\r\n for suf in suffix_indexes:\r\n word = doc[suf[0]:suf[1]]\r\n if word not in word_cands:\r\n word_cands[word] = GetWordInfo(word)\r\n word_cands[word].update_att(doc[suf[0]-1:suf[0]], doc[suf[1]:suf[1]+1])\r\n\r\n # compute the tf and info_entropy\r\n doc_lens = len(doc)\r\n for word in word_cands:\r\n word_cands[word].compute_indexes(doc_lens)\r\n\r\n # compute PMI for every word, if len(word)>1\r\n values = sorted(word_cands.values(), key=lambda x: len(x.text))\r\n\r\n for v in values:\r\n if len(v.text) == 1:\r\n continue\r\n v.compute_info_entropy(word_cands)\r\n return sorted(values, key=lambda v: v.freq, reverse=True)",
"def get_random_words(n: int, word_site: str = \"https://www.mit.edu/~ecprice/wordlist.10000\") -> List[str]:\n response = requests.get(word_site)\n result = [x.decode(\"utf-8\") for x in random.sample(list(response.content.splitlines()), n)]\n return get_random_words(n) if not result else result",
"def generate(weight_path, output_path, num_sentences=20):\n # generate textgenrnn results to file\n textgen = textgenrnn(weight_path)\n textgen.generate_to_file(output_path, n=num_sentences)",
"def genPhrase(self):\n words = [\"\"] * randint(*self.CODE_LENGTH)\n p = 1\n with file(self.DICT_PATH, \"r\") as f:\n for line in f.readlines():\n #for each word, replace it with the pth dictionary word with P() = 1/p\n for i in xrange(len(words)):\n if randint(1, p) == 1:\n words[i] = line.rstrip(\"\\n\")\n p += 1\n return \" \".join(words)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Is this a simulation.
|
def is_simulator(self) -> bool:
...
|
[
"def has_been_simulated(self):\n return self.simulated",
"def is_simulate(submodule):\r\n try: # Attempt to retrieve the key from the config file\r\n is_sim = config[submodule]['simulate']\r\n if not type(is_sim) is bool: # The key is not a boolean\r\n return False\r\n else:\r\n return is_sim\r\n except KeyError: # The key does not exist, assume not in simulation mode\r\n return False",
"def getSimulation(self):\r\n raise NotImplementedError()",
"def is_species(self) -> bool:\n return True",
"def is_stationary(self):\n ...",
"def _simulation_should_continue(self):\n if len(self.newly_infected) == 0:\n return False\n else:\n return True",
"def _is_smv_run_config(self):\n pass",
"def is_spawned(self):\n return self.spawned",
"def can_generate_on_machine(self):\n\n # Check that all the structs can actually be generated\n for struct in self.__neuron_impl.structs:\n if not struct.is_generatable:\n # If this is false, we can't generate anything on machine\n return False\n\n if (not _all_gen(self.__parameters) or\n not _all_gen(self.__state_variables)):\n return False\n\n _check_random_dists(self.__parameters)\n _check_random_dists(self.__state_variables)\n return True",
"def is_start(self) -> bool:\n return self.num_river == 1 and self.num_coast == 0",
"def get_simulator(self):\n return self.simulator",
"def get_simulation_state(self):\n return self._state",
"def is_periodic(self):\n return self.thurston_type() == 'periodic'",
"def _is_shared_agent_instance(self):\n return isinstance(self._actor, SimpleActor) and id(self._actor.agents) == id(self._agent_manager)",
"def test_multiple_simulationobject():\n sim = Sim()\n sys = MassSpringDamper()\n sys.store(\"x1\")\n sys.inputs.b = 50\n sys.inputs.f = 0\n sim.add_system(sys)\n sim.simulate(5, 0.1)\n xref = sys.res.x1\n for dummy in range(60):\n #Create Simulaton\n sim = Sim()\n sys = MassSpringDamper()\n sys.store(\"x1\")\n sys.inputs.b = 50\n sys.inputs.f = 0\n sim.add_system(sys)\n sim.simulate(5, 0.1)\n x = sys.res.x1\n assert np.all(xref == x)",
"def is_pssm(self) -> bool:\n return False",
"def is_specific(self):\n return True",
"def test_niculescu2003_sim(self):\r\n sim = Simulation(self.net)\r\n sim.run()\r\n for node in self.net.nodes():\r\n self.assertTrue(len(node.memory.get('pos', [None, None])) == 2\\\r\n or 'tp' in node.memory)",
"def ismultims(self):\n return _ms.ms_ismultims(self)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Create a Mark10 driver.
|
def create(cls, port: str, baudrate: int = 115200, timeout: float = 1) -> "Mark10":
conn = Serial()
conn.port = port
conn.baudrate = baudrate
conn.timeout = timeout
return Mark10(connection=conn)
|
[
"def create_generator(instr_info):\n from visa_generator import VisaGenerator\n from anritsu_generator import AnritsuGenerator\n \n # check if instrument is proper or simulated\n if instr_info['type'] == 'sim':\n rm = visa.ResourceManager('@sim')\n else:\n rm = visa.ResourceManager('@py')\n \n # try to connect to instrument\n try:\n instr = rm.open_resource(instr_info['connection'])\n except socket.error:\n print(\"Unable to connect to instrument \" + instr_info['connection'])\n exit()\n\n # create the proper generator object with the correct inctruction keywords\n if instr_info['type'] == 'visa':\n return VisaGenerator(instr, instr_info)\n elif instr_info['type'] == 'anritsu':\n return AnritsuGenerator(instr, instr_info)\n else: # default to visa\n return VisaGenerator(instr, instr_info)",
"def new_driver(name):\n return drivers.new_driver_object(name)",
"def __init__(self,kim_code,*args,**kwargs):\n super(ModelDriver,self).__init__(kim_code,*args,**kwargs)",
"def createDriver(self, newDbConnection):\n driver = TerminalDriver(newDbConnection, self)\n driver.start()\n\n return driver",
"def __init__(self, name, basedir=None):\n # Guess the dtype based on the class name\n dtype = guess_type(self)\n self.m80 = FreezableAPI(dtype, name, basedir)",
"def New(*args, **kargs):\n obj = itkPointSetPD22S.__New_orig__()\n import itkTemplate\n itkTemplate.New(obj, *args, **kargs)\n return obj",
"def New(*args, **kargs):\n obj = itkPointSetPD33S.__New_orig__()\n import itkTemplate\n itkTemplate.New(obj, *args, **kargs)\n return obj",
"def create_testbed_device_instance(self, dev_name_info, hint):\n testbed_dev = None\n if hint == \"AP\":\n testbed_dev = TestBedAP(self.prog_name)\n testbed_dev.dev_name = dev_name_info\n testbed_dev.dev_type = \"AP\"\n if hint == \"STA\":\n testbed_dev = TestBedSTA(self.prog_name)\n testbed_dev.dev_name = dev_name_info\n testbed_dev.dev_type = \"STA\"\n if hint == \"DUT\":\n testbed_dev = DUT(self.prog_name)\n testbed_dev.dev_name = dev_name_info\n testbed_dev.dev_type = \"DUT\"\n if hint == \"SNIFFER\":\n testbed_dev = Sniffer(self.prog_name)\n testbed_dev.dev_name = dev_name_info\n testbed_dev.dev_type = \"SNIFFER\"\n if hint == \"PCENDPOINT\":\n testbed_dev = PCEndpoint(self.prog_name)\n testbed_dev.dev_name = dev_name_info\n testbed_dev.dev_type = \"PCENDPOINT\"\n if hint == \"APCONFIG\":\n testbed_dev = APConfig(self.prog_name)\n testbed_dev.dev_name = dev_name_info\n testbed_dev.dev_type = \"APCONFIG\"\n if hint == \"RADIUSSERVER\":\n testbed_dev = RadiusServer(self.prog_name)\n testbed_dev.dev_name = dev_name_info\n testbed_dev.dev_type = \"RADIUSSERVER\"\n if hint == \"OSUSERVER\":\n testbed_dev = OSUServer(self.prog_name)\n testbed_dev.dev_name = dev_name_info\n testbed_dev.dev_type = \"OSUSERVER\"\n if hint == \"ATTENUATOR\":\n testbed_dev = Attenuator(self.prog_name)\n testbed_dev.dev_name = dev_name_info\n testbed_dev.dev_type = \"ATTENUATOR\"\n if hint == \"POWERSWITCH\":\n testbed_dev = PowerSwitch(self.prog_name)\n testbed_dev.dev_name = dev_name_info\n testbed_dev.dev_type = \"POWERSWITCH\"\n if hint == \"WFAEMT\":\n testbed_dev = WFAEMT(self.prog_name)\n testbed_dev.dev_name = dev_name_info\n testbed_dev.dev_type = \"WFAEMT\"\n return testbed_dev",
"def launch_new_instance():\n binifier = Binifier()\n binifier.main()",
"def create_driver(ob, path, index, target, target_path):\n driver = ob.driver_add(path, index)\n setup_driver(driver, target, target_path)\n return driver",
"def __init__(self, address=None):\n # open resource manager\n self.rm = visa.ResourceManager()\n\n if address:\n addresses = [address]\n else:\n addresses = self.rm.list_resources()\n\n print(\"Looking for Tektronix AWG7122B\")\n self.inst = None\n for inst_str in addresses:\n print(\"Checking resource at {}\".format(inst_str))\n try:\n inst = self.rm.open_resource(inst_str)\n query = inst.query(\"*IDN?\")\n if \"TEKTRONIX,AWG7122B\" in query:\n print(\"Found {}\".format(query))\n self.inst = inst\n # set parameters necessary for binary data sending\n self.inst.read_termination = None\n self.inst.write_termination = \"\\r\\n\"\n self.inst.encoding = \"utf-8\"\n self.inst.timeout = 10000\n break\n except Exception:\n pass\n if self.inst is None:\n print(\"Couldn't find Tektronix AWG7122B\")\n self.inst = None",
"def test_station_creation():\n \n SO = ISO(\"System Operator\")\n RZ = ReserveZone(\"RZ\", SO)\n ND = Node(\"ND\", SO, RZ)\n CO = Company(\"CO\")\n \n ST = Station(\"ST\", ND, SO, CO, spinning=True, capacity=400)\n \n assert ST.name == \"ST\"\n assert ST,capacity == 400\n assert ST.spinning == True\n assert ST.band_names == []\n assert ST.band_offers == {}\n assert ST.band_prices == {}\n \n assert ST.node == ND\n \n assert ST.rband_names == []\n assert ST.rband_offers == {}\n assert ST.rband_prices == {}\n assert ST.rband_proportions == {}",
"def create_driver(context):\n global _driver\n driver_name = context.config.userdata.get('browser', 'phantomjs')\n cls = DRIVER_MAP[driver_name]\n _driver = cls()\n return _driver",
"def _create_driver(self):\n driver_module = self._driver_config['dvr_mod']\n driver_class = self._driver_config['dvr_cls']\n\n assert self._platform_id is not None, \"must know platform_id to create driver\"\n\n if log.isEnabledFor(logging.DEBUG):\n log.debug('%r: creating driver: driver_module=%s driver_class=%s' % (\n self._platform_id, driver_module, driver_class))\n\n try:\n module = __import__(driver_module, fromlist=[driver_class])\n classobj = getattr(module, driver_class)\n driver = classobj(self._pnode, self.evt_recv)\n\n except Exception as e:\n msg = '%r: could not import/construct driver: module=%r, class=%r' % (\n self._platform_id, driver_module, driver_class)\n log.exception(\"%s\", msg) #, exc_Info=True)\n raise CannotInstantiateDriverException(msg=msg, reason=e)\n\n self._plat_driver = driver\n\n if log.isEnabledFor(logging.DEBUG):\n log.debug(\"%r: driver created: %s\" % (self._platform_id, str(driver)))",
"def help_create(self):\n\n self.__print(\n 'Usage: create CLASS',\n 'Creates a new instance of the given data model class.',\n sep='\\n'\n )",
"def init_driver(cls):\n pass",
"def create(\n markersX, markersY, markerLength, markerSeparation, dictionary, firstMarker=...\n ) -> retval:\n ...",
"def training_x10(self):\n result = run_swift_benchmark(name=self.benchmark_name, variety='training', backend='x10')\n self.report_benchmark(**result)",
"def make_drivers(self):\n\n bpy.ops.object.mode_set(mode ='OBJECT')\n pose_bones = self.obj.pose.bones\n\n # Add mouth_lock property on jaw_master #\n jaw_master = pose_bones[self.bones['jaw_ctrl']['jaw']]\n prop_name = 'mouth_lock'\n jaw_master[prop_name] = 0.0\n prop = rna_idprop_ui_prop_get(jaw_master, prop_name)\n prop[\"min\"] = 0.0\n prop[\"max\"] = 1.0\n prop[\"soft_min\"] = 0.0\n prop[\"soft_max\"] = 1.0\n prop[\"description\"] = prop_name\n\n for bone in self.bones['jaw_mch']['jaw_masters'][:-1]:\n drv = pose_bones[bone].constraints[1].driver_add(\"influence\").driver\n drv.type = 'SUM'\n\n var = drv.variables.new()\n var.name = prop_name\n var.type = \"SINGLE_PROP\"\n var.targets[0].id = self.obj\n var.targets[0].data_path = jaw_master.path_from_id() + '[' + '\"' + prop_name + '\"' + ']'"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Sends an email via IFTTT webhook integration.
|
def send_email(msg: str) -> int:
url = f'https://maker.ifttt.com/trigger/qseek_post/with/key/{os.environ.get("IFTTT_KEY")}'
data = {"value1": msg}
logger.info(f'Sending email with body "{msg}"')
resp = requests.post(url, data=data)
if not resp.ok:
logger.error(f'Sending email failed with status code {resp.status_code}')
return resp.status_code
|
[
"def email_callback(self, ch, method, properties, body):\n send_email_message = SendEmailMessage.try_create_from_body(body, self.config)\n if send_email_message:\n email_send_id = send_email_message.send_email_id\n try:\n print(\"Sending email {} to bespin-api.\".format(email_send_id))\n self.bespin_api.email_message_send(email_send_id)\n print(\"Success sending email {} to bespin-api.\".format(email_send_id))\n except requests.HTTPError as err:\n print(\"Bespin API sending email {} failed with {}\".format(email_send_id, err))\n self.send_email_retry(send_email_message)\n else:\n print(\" [x] Received invalid SendEmail request {}\".format(pickle.loads(body)))",
"def send_feedback_email_task():\n print(\"Sent feedback email\")\n return",
"def send_email(user):\n data = get_weather_json(user)\n\n # Exctract necessary variables from JSON\n location = data['current_observation']['display_location']['full']\n weather_now = data['current_observation']['weather']\n temp_now = float(data['current_observation']['temp_f'])\n avg_high = float(data['almanac']['temp_high']['normal']['F'])\n icon_url = data['current_observation']['icon_url']\n readable_weather = '{} degrees, {}.'.format(temp_now, weather_now.lower())\n\n email = user.email\n # Set email's subject based on current conditions\n # NOTE: We are using the average high temperature in our comparison...\n # -- This could be done a variety of ways including using the median of the\n # -- average high and low temperature, or using the average low in the\n # -- morning/night and the average high during the day.\n subject = REGULAR_SUBJECT\n if (temp_now >= avg_high+5) or ('clear' in weather_now.lower()):\n subject = NICE_OUT_SUBJECT\n if (temp_now <= avg_high-5) or ('rain' in weather_now.lower()):\n subject = POOR_OUT_SUBJECT\n\n text = get_template('email/newsletter.txt')\n html = get_template('email/newsletter.html')\n context = Context(\n {\n 'location': location,\n 'icon_url': icon_url,\n 'weather': readable_weather\n }\n )\n html_content = html.render(context)\n text_content = text.render(context)\n\n message = EmailMultiAlternatives(\n subject,\n text_content,\n settings.EMAIL_HOST_USER,\n [email]\n )\n message.attach_alternative(html_content, 'text/html')\n message.send()",
"def handle_test_email(self, msg):\n logger.debug(\"sending test email\")\n txt = \"%s test email\" % msg.fabric\n msg.wf.send_notification(\"any_email\", txt, txt)",
"def send_email(cls, recipient, mail_subject, mail_body):\n pass",
"def send_email():\n name = request.form[\"name_input\"]\n email = request.form[\"email_input\"]\n message = request.form[\"message_input\"]\n body = message + f\" email: {email}, name: {name}\"\n sender = app.config[\"ADMINS\"]\n recipients = [app.config[\"RECIPIENT\"]]\n email_out(\"Question\", sender, recipients, body)\n return _(\"Email sent!\")",
"def _execute_send(self, email):\n pass",
"def trigger_notification(self, url, message):\n # Trigger the webhook\n response = requests.post(\n url,\n data=json.dumps(message),\n headers={'Content-Type': 'application/json'}\n )",
"def test_emailservice_send():\n emailservice = EmailService()\n status, message = emailservice.send_email(\"marco.zingales@gmail.com\", [\"marco.zingales@gmail.com\"],\n [\"marco.zingales@gmail.com\"],\n \"marzi@dtu.dk\", \"test subject 101\", \"test content 102\")\n _test('send email', status == 0)",
"def send_test_email(self, config, as_json=True, timestamp_format=APITimestampFormat.NANOSECOND):\n return self._xjtrans(\"/settings/notification/send_test_mail\", \"POST\", config, as_json, timestamp_format)",
"def send_email(self, to, subject, body):\n message = {\n 'command': 'send-email',\n 'to': to,\n 'subject': subject,\n 'body': body,\n }\n\n send_message_to_server(message=message)",
"def send_email_request(self, request,):\n\n assert self.context == 'request'\n\n # Generate text\n from django.template import Context, Template\n from django.template.loader import get_template\n ctx = Context({\n 'prefix': settings.EMAIL_SUBJECT_PREFIX,\n 'request': request,\n 'sender': settings.USER_EMAIL_SIGNATURE,\n })\n tmpl = get_template(self.template)\n body = tmpl.render(ctx)\n subject_tmpl = Template(self.subject_template)\n subject = subject_tmpl.render(ctx)\n\n # Generate recipients\n recipients = []\n for rt in self.recipients:\n if rt == 'recipient':\n recipients.append(request.check_to_email)\n elif rt == 'area':\n recipients.append(request.budget_area.owner_address())\n elif rt == 'admins':\n pass # you don't *actually* have a choice...\n for name, addr in settings.ADMINS:\n recipients.append(addr)\n\n # Send mail!\n from django.core.mail import send_mail\n send_mail(\n subject,\n body,\n settings.SERVER_EMAIL,\n recipients,\n )",
"def send_mail_task(mail):\n mail._send()",
"def mail_ticket(ticket_id, fake=False): \n try:\n ticket = lookup_ticket_by_id(ticket_id)\n event = get_event_of_ticket(ticket)\n order = ticket.ticket_order.order\n \n env = Environment(loader=PackageLoader('tickee', 'templates'),\n extensions=['jinja2.ext.with_'])\n body = env.get_template('mail_ticket.html')\\\n .render(ticket=ticket, \n account=order.account,\n event=event, \n order=order, \n as_guest=False)\n \n body_plain = env.get_template('mail_ticket.txt')\\\n .render(ticket=ticket, \n account=order.account,\n event=event, \n order=order, \n as_guest=False)\n \n # send generated mail\n blogger.info('sending mail for ticket %s to user %s (%s)' % (ticket.id, \n ticket.user.id, \n ticket.user.email))\n \n validate_email(ticket.user.email)\n \n if not ticket.user.email:\n raise ex.OrderError(\"user has no email.\")\n \n if not fake:\n send_email(\"Tickee Ticketing <tickets@tick.ee>\", \n ticket.user.email, \n \"Your ticket for '%s' is here!\" % event.name, \n body,\n body_plain)\n \n log_crm(\"ticket\", ticket.id, dict(action=\"mailed\",\n addressee=ticket.user.email))\n transaction.commit()\n return True\n \n \n except Exception as e:\n try:\n email = ticket.user.email\n except:\n email = \"no mail found.\"\n log_crm(\"ticket\", ticket_id, dict(action=\"mail failed\",\n addressee=email))\n transaction.commit()\n tlogger.exception(\"failed sending mail for ticket %s: %s\" % (ticket_id, e))\n return False",
"async def send_alert_email(event_id: str):\n sended = await MailController.send_alert(event_id)\n\n if sended == 404:\n exceptions.not_fount_404(\"Event not found\")\n\n return {\"detail\": \"Email sended\", \"target\": f\"Event: {event_id}\"}",
"def send_post(event, context):\n jobId = event['CodePipeline.job']['id']\n\n #Get userparameters string and decode as json\n user_parameters = event['CodePipeline.job']['data']['actionConfiguration']['configuration']['UserParameters']\n\n # decoded_parameters = json.loads(user_parameters, object_hook=ascii_encode_dict)\n decoded_parameters = json.loads(user_parameters)\n print(decoded_parameters)\n\n webhook = decoded_parameters['webhooks']\n message = decoded_parameters['message']\n\n #Slack webhook post\n try:\n response = requests.post(webhook, headers={\"Content-Type\": \"application/json\"}, data=json.dumps({\"text\": message}))\n print response.text\n response.raise_for_status()\n code_pipeline.put_job_success_result(jobId=jobId)\n except requests.ConnectionError:\n \tcode_pipeline.put_job_failure_result(jobId=jobId)",
"def email(given_email):\n print('email action')\n\n text = \"Your email is \" + str(given_email)\n return text",
"def test_users_send_emails(self):\n pass",
"async def send_special_email(\n event_id: str = Form(...),\n subject: str = Form(...),\n message: str = Form(...),\n file: Optional[UploadFile] = Form(None),\n user: dict = Depends(get_current_user),\n):\n if not file:\n file = None\n\n sended = await MailController.send_special(event_id, subject, message, file, user)\n\n if sended == 403:\n exceptions.forbidden_403(\"Operation forbidden\")\n if sended == 404:\n exceptions.not_fount_404(\"Event not found\")\n\n return {\"detail\": \"Email sended\", \"target\": f\"Event: {event_id}\"}"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Perform batch lookup on matrix M using indices idx.
|
def batch_lookup(M, idx, vector_output=True):
batch_size, w = M.size()
batch_size2, sample_size = idx.size()
assert(batch_size == batch_size2)
if sample_size == 1 and vector_output:
samples = torch.gather(M, 1, idx).view(-1)
else:
samples = torch.gather(M, 1, idx)
return samples
|
[
"def batch_lookup_3D(M, idx):\n batch_size, seq_len, dim = M.size()\n _, sample_size = idx.size()\n M = M.view(batch_size*seq_len, dim)\n offset = long_var_cuda(torch.arange(batch_size).unsqueeze(1))\n idx = idx + offset * seq_len\n idx = idx.view(-1)\n # [batch_size*sample_size, dim]\n features = torch.index_select(M, 0, idx)\n return features.view(batch_size, sample_size, dim)",
"def batch_binary_lookup(M, b_idx, pad_value):\n batch_size = M.size(0)\n seq_len = b_idx.sum(1, keepdim=True)\n max_seq_len = int(seq_len.max())\n output_masks = batch_arange_cuda(batch_size, max_seq_len) >= seq_len\n pad_len = max_seq_len - seq_len\n max_pad_len = int(pad_len.max())\n M = torch.cat([M, fill_var_cuda([batch_size, max_pad_len], pad_value, dtype=M.dtype)], dim=1)\n pad_b_idx = batch_arange_cuda(batch_size, max_pad_len) < pad_len\n b_idx = torch.cat([b_idx, pad_b_idx], dim=1)\n output = M[b_idx].view(batch_size, max_seq_len)\n return output, output_masks",
"def map_idx(tensor_unfl, idx_fl, gpu):\n #row_number of unflattened tensor is index of flattened tensor // amount of columns of unflattened tensor\n #col_number of unflattened tensor is index of flattened tensor % amount of columns of unflattened tensor\n n_cols = tensor_unfl.size()[-1]\n row_idx_unfl = idx_fl // n_cols\n col_idx_unfl = idx_fl % n_cols\n result = torch.tensor([row_idx_unfl, col_idx_unfl])\n if gpu:\n if torch.cuda.is_available():\n result = result.to('cuda')\n return result",
"def batch_binary_lookup_3D(M, b_idx, pad_value):\n # Pad binary indices\n batch_size = M.size(0)\n hidden_dim = M.size(2)\n seq_len = b_idx.sum(1, keepdim=True)\n max_seq_len = int(seq_len.max())\n output_masks = batch_arange_cuda(batch_size, max_seq_len) >= seq_len\n pad_len = max_seq_len - seq_len\n max_pad_len = int(pad_len.max())\n M = torch.cat([M, fill_var_cuda([batch_size, max_pad_len, hidden_dim], pad_value, dtype=M.dtype)], dim=1)\n pad_b_idx = batch_arange_cuda(batch_size, max_pad_len) < pad_len\n b_idx = torch.cat([b_idx, pad_b_idx], dim=1)\n output = M[b_idx].view(batch_size, max_seq_len, hidden_dim)\n return output, output_masks",
"def csr_gather_np(indptr, indices, dense, shape):\n import scipy.sparse\n sparse_data = scipy.sparse.csr_matrix((np.zeros(indices.shape), indices, indptr), shape[:2])\n coo = sparse_data.tocoo()\n coo_idx = np.stack((coo.row, coo.col))\n expect = dense[tuple(coo_idx.tolist())]\n return expect",
"def flat_indices(m: Mat2, indices: List[int]) -> Tuple[List[Tuple[int, int]], int]:\n if len(indices) == 0:\n return [], -1\n rows = {i: m.data[i] for i in indices}\n weights: Dict[int,int] = {i: sum(r) for i, r in rows.items()}\n result = []\n next_indices = []\n while len(indices) > 1:\n best = (-1, -1)\n reduction = -10000\n for i in indices:\n for j in indices:\n if j <= i: continue\n w = sum(xor_rows(rows[i], rows[j]))\n if weights[i] - w > reduction:\n best = (j, i) # \"Add row j to i\"\n reduction = weights[i] - w\n if weights[j] - w > reduction:\n best = (i, j)\n reduction = weights[j] - w\n result.append(best)\n control, target = best\n rows[target] = xor_rows(rows[control], rows[target])\n weights[target] = weights[target] - reduction\n indices.remove(control)\n indices.remove(target)\n next_indices.append(target)\n if len(indices) <= 1:\n if len(indices) == 1:\n next_indices.append(indices[0])\n indices = next_indices\n next_indices = []\n return result, indices[0]",
"def lookup(indexable, idx):\n return indexable[idx]",
"def __getitem__(self, idx):\n\n sample = self.numpy_dataset[idx]\n\n it = self.transformations\n for transformation_fn, transformation_fn_kwargs in it:\n transformation_fn_kwargs = transformation_fn_kwargs.copy()\n sample_keys = transformation_fn_kwargs.pop('sample_keys')\n\n sample = apply_transformation(\n transformation_fn, sample, sample_keys,\n transformation_fn_kwargs\n )\n\n inputs = [\n sample[input_key] for input_key in self.numpy_dataset.input_keys\n ]\n targets = [\n sample[target_key] for target_key in self.numpy_dataset.target_keys\n ]\n\n if len(inputs) == 1:\n inputs = inputs[0]\n if len(targets) == 1:\n targets = targets[0]\n\n return inputs, targets",
"def evaluate_dataloader_item(dataloader,model,indx):\n etl = enumerate(dataloader)\n with inference_context(model), torch.no_grad():\n found = False\n for idx, inputs in etl:\n if idx==indx:\n outputs = model(inputs)\n return outputs\n if found == False:\n return \"Index not found\"",
"def index_select_multidim_jit(input, indices):\n n = indices.size()[-1]\n input_size = input.size()\n\n if n == 1:\n return input[(\n indices[...,0].clamp(0, input_size[0]-1),\n ...)]\n elif n == 2:\n return input[(\n indices[...,0].clamp(0, input_size[0]-1),\n indices[...,1].clamp(0, input_size[1]-1),\n ...)]\n elif n == 3:\n return input[(\n indices[...,0].clamp(0, input_size[0]-1),\n indices[...,1].clamp(0, input_size[1]-1),\n indices[...,2].clamp(0, input_size[2]-1),\n ...)]\n else:\n raise NotImplemented",
"def idx_by_dim(x: Any, idx: int, dim: int):\n if is_torch_tensor(x) or is_numpy_array(x):\n if dim == 0:\n return x[idx]\n else:\n loc = tuple([_LOC[:]] * dim + [idx])\n return x[loc]\n else:\n raise ValueError",
"def __getitem__(self, idx):\n if isinstance(idx, int):\n batch = [self.dataset[idx]]\n else:\n batch = self.dataset[idx]\n\n images, targets = zip(*batch)\n\n if self.no_background:\n\n images = [process_img(i) for i in images]\n\n else:\n n_trials = len(images)\n n_back = len(self.backgrounds)\n back_inds = np.random.choice(n_back, n_trials)\n backgrounds = self.backgrounds[back_inds]\n\n images = [self.overlay(back, img)\n for back,img in zip(backgrounds, images)]\n\n if self.vae:\n targets = [resize(i, (64,64)) for i in images]\n\n pairs = list(zip(images, targets))\n if isinstance(idx, int):\n pairs = pairs[0]\n return pairs",
"def _perform_batch_lookup():\n state = _runstate.current()\n batch = state.batches.pop(_BATCH_LOOKUP, None)\n if batch is None:\n return\n\n rpc = _datastore_lookup(batch.keys())\n _eventloop.queue_rpc(rpc, BatchLookupCallback(batch))",
"def _find_node_by_index(nodes, idx):\n for node in nodes:\n if node.idx == idx:\n return node",
"def _index(t, index):\n if not isinstance(index, (tuple, list)):\n index = list(index)\n for i in index:\n t = tf.gather(t, i)\n return t",
"def _copy_labelindex_batch(src_triple, dest_triple, labels_batch):\n indexes_batch = fetch_labelindices(*src_triple, labels_batch)\n post_labelindices(*dest_triple, indexes_batch)",
"def _gather_for_multidim_indexing(args: GatherArgs):\n # Guess the axis.\n axis = args.dnums.collapsed_slice_dims[0]\n squeezed_indices = tf.squeeze(args.start_indices, -1)\n op_shape = jax2tf._eval_shape(args.op_shape)\n start_indices = _clip((op_shape[axis],), squeezed_indices, (1,))\n return tf.gather(args.operand, start_indices, axis=axis, batch_dims=0)",
"def _index(t, index):\n if not isinstance(index, (tuple, list)):\n index = list(index)\n for i in index:\n t = tf.gather(t, i)\n #t = tf.gather(t, index[0])\n return t",
"def idxs_map(idxs, cmd, *args, **kwargs):\r\n # XXX: consider insisting on sorted idxs\r\n # XXX: use np.searchsorted instead of dct\r\n\r\n if 0: # these should all be true, but evaluating them is slow\r\n for ii, (idxs_ii, vals_ii) in enumerate(args):\r\n for jj in idxs: assert jj in idxs_ii\r\n for kw, (idxs_kw, vals_kw) in kwargs.items():\r\n for jj in idxs: assert jj in idxs_kw\r\n\r\n args_imap = []\r\n for idxs_j, vals_j in args:\r\n if len(idxs_j):\r\n args_imap.append(dict(zip(idxs_j, vals_j)))\r\n else:\r\n args_imap.append({})\r\n\r\n kwargs_imap = {}\r\n for kw, (idxs_j, vals_j) in kwargs.items():\r\n if len(idxs_j):\r\n kwargs_imap[kw] = dict(zip(idxs_j, vals_j))\r\n else:\r\n kwargs_imap[kw] = {}\r\n\r\n f = scope._impls[cmd]\r\n rval = []\r\n for ii in idxs:\r\n try:\r\n args_nn = [arg_imap[ii] for arg_imap in args_imap]\r\n except:\r\n ERR('args_nn %s' % cmd)\r\n ERR('ii %s' % ii)\r\n ERR('arg_imap %s' % str(arg_imap))\r\n ERR('args_imap %s' % str(args_imap))\r\n raise\r\n try:\r\n kwargs_nn = dict([(kw, arg_imap[ii])\r\n for kw, arg_imap in kwargs_imap.items()])\r\n except:\r\n ERR('args_nn %s' % cmd)\r\n ERR('ii %s' % ii)\r\n ERR('kw %s' % kw)\r\n ERR('arg_imap %s' % str(arg_imap))\r\n raise\r\n try:\r\n rval_nn = f(*args_nn, **kwargs_nn)\r\n except:\r\n ERR('error calling impl of %s' % cmd)\r\n raise\r\n rval.append(rval_nn)\r\n return rval",
"def __getitem__(self, index):\n return self.__matrix[index]"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Perform batch look up on a 3D tensor M using indices idx.
|
def batch_lookup_3D(M, idx):
batch_size, seq_len, dim = M.size()
_, sample_size = idx.size()
M = M.view(batch_size*seq_len, dim)
offset = long_var_cuda(torch.arange(batch_size).unsqueeze(1))
idx = idx + offset * seq_len
idx = idx.view(-1)
# [batch_size*sample_size, dim]
features = torch.index_select(M, 0, idx)
return features.view(batch_size, sample_size, dim)
|
[
"def batch_binary_lookup_3D(M, b_idx, pad_value):\n # Pad binary indices\n batch_size = M.size(0)\n hidden_dim = M.size(2)\n seq_len = b_idx.sum(1, keepdim=True)\n max_seq_len = int(seq_len.max())\n output_masks = batch_arange_cuda(batch_size, max_seq_len) >= seq_len\n pad_len = max_seq_len - seq_len\n max_pad_len = int(pad_len.max())\n M = torch.cat([M, fill_var_cuda([batch_size, max_pad_len, hidden_dim], pad_value, dtype=M.dtype)], dim=1)\n pad_b_idx = batch_arange_cuda(batch_size, max_pad_len) < pad_len\n b_idx = torch.cat([b_idx, pad_b_idx], dim=1)\n output = M[b_idx].view(batch_size, max_seq_len, hidden_dim)\n return output, output_masks",
"def map_idx(tensor_unfl, idx_fl, gpu):\n #row_number of unflattened tensor is index of flattened tensor // amount of columns of unflattened tensor\n #col_number of unflattened tensor is index of flattened tensor % amount of columns of unflattened tensor\n n_cols = tensor_unfl.size()[-1]\n row_idx_unfl = idx_fl // n_cols\n col_idx_unfl = idx_fl % n_cols\n result = torch.tensor([row_idx_unfl, col_idx_unfl])\n if gpu:\n if torch.cuda.is_available():\n result = result.to('cuda')\n return result",
"def idx_by_dim(x: Any, idx: int, dim: int):\n if is_torch_tensor(x) or is_numpy_array(x):\n if dim == 0:\n return x[idx]\n else:\n loc = tuple([_LOC[:]] * dim + [idx])\n return x[loc]\n else:\n raise ValueError",
"def _index(t, index):\n if not isinstance(index, (tuple, list)):\n index = list(index)\n for i in index:\n t = tf.gather(t, i)\n #t = tf.gather(t, index[0])\n return t",
"def __getitem__(self, idx):\n if isinstance(idx, int):\n batch = [self.dataset[idx]]\n else:\n batch = self.dataset[idx]\n\n images, targets = zip(*batch)\n\n if self.no_background:\n\n images = [process_img(i) for i in images]\n\n else:\n n_trials = len(images)\n n_back = len(self.backgrounds)\n back_inds = np.random.choice(n_back, n_trials)\n backgrounds = self.backgrounds[back_inds]\n\n images = [self.overlay(back, img)\n for back,img in zip(backgrounds, images)]\n\n if self.vae:\n targets = [resize(i, (64,64)) for i in images]\n\n pairs = list(zip(images, targets))\n if isinstance(idx, int):\n pairs = pairs[0]\n return pairs",
"def batch_binary_lookup(M, b_idx, pad_value):\n batch_size = M.size(0)\n seq_len = b_idx.sum(1, keepdim=True)\n max_seq_len = int(seq_len.max())\n output_masks = batch_arange_cuda(batch_size, max_seq_len) >= seq_len\n pad_len = max_seq_len - seq_len\n max_pad_len = int(pad_len.max())\n M = torch.cat([M, fill_var_cuda([batch_size, max_pad_len], pad_value, dtype=M.dtype)], dim=1)\n pad_b_idx = batch_arange_cuda(batch_size, max_pad_len) < pad_len\n b_idx = torch.cat([b_idx, pad_b_idx], dim=1)\n output = M[b_idx].view(batch_size, max_seq_len)\n return output, output_masks",
"def _index(t, index):\n if not isinstance(index, (tuple, list)):\n index = list(index)\n for i in index:\n t = tf.gather(t, i)\n return t",
"def test_ravel_multi_index_3d(self):\n indices = [[0, 0, 0], [0, 1, 1], [2, 2, 3], [3, 1, 2]]\n expected = [0, 5, 43, 54]\n\n result = array_ops.ravel_multi_index(indices, [4, 4, 4])\n self.assertAllEqual(result, expected)",
"def _gather_for_multidim_indexing(args: GatherArgs):\n # Guess the axis.\n axis = args.dnums.collapsed_slice_dims[0]\n squeezed_indices = tf.squeeze(args.start_indices, -1)\n op_shape = jax2tf._eval_shape(args.op_shape)\n start_indices = _clip((op_shape[axis],), squeezed_indices, (1,))\n return tf.gather(args.operand, start_indices, axis=axis, batch_dims=0)",
"def gather_cols_3d(params, indices, pad_elem=0, name=None):\n with tf.name_scope(name, \"gather_cols_3d\", [params, indices, pad_elem]):\n params = tf.convert_to_tensor(params, name=\"params\")\n ind_2D = False\n if isinstance(indices[0], collections.Iterable):\n # Convert indices into a list of 1D np.arrays\n indices = [np.asarray(ind) for ind in indices]\n ind_2D = True\n else:\n indices = [np.asarray(indices)]\n # Check params\n param_shape = params.get_shape()\n param_dims = param_shape.ndims\n if param_dims == 1:\n param_size = param_shape[0].value\n elif param_dims == 2:\n param_size = param_shape[1].value\n else:\n raise ValueError(\"'params' must be 1D or 2D\")\n # We need the size defined for optimizations\n if param_size is None:\n raise RuntimeError(\"The indexed dimension of 'params' is not specified\")\n # Check indices\n if any(ind.ndim != 1 for ind in indices):\n raise ValueError(\"Each 'indices' must be 1D\")\n if any(ind.size < 1 for ind in indices):\n raise ValueError(\"None of the 'indices' can be empty\")\n if any(not np.issubdtype(ind.dtype, np.integer) for ind in indices):\n raise ValueError(\"'indices' can only be integer type\")\n if any(np.any((ind < 0) | (ind >= param_size)) for ind in indices):\n raise ValueError(\"All 'indices' must fit the the indexed dimension\")\n\n # Define op\n if len(indices) == 1:\n # Single indices (1D)\n if param_size == 1 and indices[0].size == 1:\n # Single column tensor, with a single column to be gathered,\n # indices should include it, so just forward tensor\n return_tensor = params\n elif indices[0].size == param_size and np.all(np.ediff1d(indices[0]) == 1):\n # Indices contains all the columns, and in the correct order. So\n # just forward tensor\n return_tensor = params\n else:\n # If not, then just pass it to gather_cols() function\n return_tensor = tf.gather(params, indices[0], axis=-1)\n\n if ind_2D:\n # Indices is 2D, so insert an extra dimension to the output\n return tf.expand_dims(return_tensor, axis=-2)\n else:\n return return_tensor\n else:\n # Multiple rows of indices\n indices_cols = max([ind.size for ind in indices])\n padding = False\n for i, ind in enumerate(indices):\n if ind.size < indices_cols:\n padding = True\n indices[i] = np.append(ind, np.ones(indices_cols-ind.size,\n dtype=ind.dtype)*-1)\n # Convert the list of indices arrays into an indices matrix\n indices = np.vstack(indices)\n if not padding and indices_cols == param_size and \\\n all(np.all(np.ediff1d(ind) == 1) for ind in indices):\n indices_rows = indices.shape[0]\n if param_dims == 1:\n return tf.reshape(tf.tile(params, [indices_rows]),\n (-1, indices_cols))\n else:\n return tf.reshape(tf.tile(params, [1, indices_rows]),\n (-1, indices_rows, indices_cols))\n else:\n if param_dims == 1:\n axis = 0\n if padding:\n augmented = tf.concat([[tf.constant(pad_elem, dtype=params.dtype)],\n params], axis=axis)\n gathered = tf.gather(augmented, indices=indices.ravel() + 1, axis=axis)\n else:\n gathered = tf.gather(params, indices=indices.ravel(), axis=axis)\n return tf.reshape(gathered, indices.shape)\n # else:\n axis = 1\n if padding:\n augmented = tf.concat([\n tf.fill((tf.shape(params)[0], 1), value=tf.constant(\n pad_elem, dtype=params.dtype)),\n params\n ], axis=axis)\n gathered = tf.gather(augmented, indices=indices.ravel() + 1, axis=axis)\n else:\n gathered = tf.gather(params, indices=indices.ravel(), axis=axis)\n return tf.reshape(gathered, (-1,) + indices.shape)",
"def shared_embedding_lookup(params, indices, name=None):\n if not isinstance(params, (list, tuple)):\n params = [params]\n with tf.name_scope(name, 'shared_embedding', list(params) + list(indices)):\n params = [tf.convert_to_tensor(p, name='params') for p in params]\n indices = [tf.convert_to_tensor(ids, name='ids') for ids in indices]\n all_ids = tf.concat([tf.reshape(ids, [-1]) for ids in indices], 0)\n all_results = layers.embedding_lookup_unique(params, all_ids)\n dim = params[0].get_shape()[1].value\n dim_shape = tf.constant([dim])\n results = []\n parts = tf.split(all_results, [tf.size(ids) for ids in indices])\n for ids, part in zip(indices, parts):\n result = tf.reshape(part, tf.concat([tf.shape(ids), dim_shape], 0))\n result.set_shape(ids.get_shape().concatenate([dim]))\n results.append(result)\n return results",
"def __getitem__(self, idx):\n\n sample = self.numpy_dataset[idx]\n\n it = self.transformations\n for transformation_fn, transformation_fn_kwargs in it:\n transformation_fn_kwargs = transformation_fn_kwargs.copy()\n sample_keys = transformation_fn_kwargs.pop('sample_keys')\n\n sample = apply_transformation(\n transformation_fn, sample, sample_keys,\n transformation_fn_kwargs\n )\n\n inputs = [\n sample[input_key] for input_key in self.numpy_dataset.input_keys\n ]\n targets = [\n sample[target_key] for target_key in self.numpy_dataset.target_keys\n ]\n\n if len(inputs) == 1:\n inputs = inputs[0]\n if len(targets) == 1:\n targets = targets[0]\n\n return inputs, targets",
"def index_select_multidim_jit(input, indices):\n n = indices.size()[-1]\n input_size = input.size()\n\n if n == 1:\n return input[(\n indices[...,0].clamp(0, input_size[0]-1),\n ...)]\n elif n == 2:\n return input[(\n indices[...,0].clamp(0, input_size[0]-1),\n indices[...,1].clamp(0, input_size[1]-1),\n ...)]\n elif n == 3:\n return input[(\n indices[...,0].clamp(0, input_size[0]-1),\n indices[...,1].clamp(0, input_size[1]-1),\n indices[...,2].clamp(0, input_size[2]-1),\n ...)]\n else:\n raise NotImplemented",
"def csr_gather_np(indptr, indices, dense, shape):\n import scipy.sparse\n sparse_data = scipy.sparse.csr_matrix((np.zeros(indices.shape), indices, indptr), shape[:2])\n coo = sparse_data.tocoo()\n coo_idx = np.stack((coo.row, coo.col))\n expect = dense[tuple(coo_idx.tolist())]\n return expect",
"def lookup(indexable, idx):\n return indexable[idx]",
"def get_element_from_batch(tt_batch, idx):\n tt_cores = []\n if not hasattr(tt_batch, 'batch_size'):\n print('input not a tt batch!')\n if tt_batch.is_tt_matrix:\n for core_idx in range(tt_batch.ndims):\n tt_cores.append(tt_batch.tt_cores[core_idx][idx, :, :, :, :])\n else:\n for core_idx in range(tt_batch.ndims):\n tt_cores.append(tt_batch.tt_cores[core_idx][idx, :, :, :])\n #print('get_element rank:', TensorTrain(tt_cores).ranks)\n # if TensorTrain(tt_cores).ranks[4] == 1:\n # print('idx unnormal:', idx)\n # else:\n # print('idx normal:', idx)\n return TensorTrain(tt_cores)",
"def test_ravel_multi_index_3d_scalar(self):\n indices = [2, 2, 1]\n expected = 41\n\n result = array_ops.ravel_multi_index(indices, [4, 4, 4])\n self.assertAllEqual(result, expected)",
"def batch_gather(tensor, indices):\n shape = list(tensor.shape)\n flat_first = tf.reshape(tensor, [shape[0] * shape[1]] + shape[2:])\n indices = tf.convert_to_tensor(indices)\n offset_shape = [shape[0]] + [1] * (indices.shape.ndims - 1)\n offset = tf.reshape(tf.range(shape[0]) * shape[1], offset_shape)\n output = tf.gather(flat_first, indices + offset)\n return output",
"def flat_indices(m: Mat2, indices: List[int]) -> Tuple[List[Tuple[int, int]], int]:\n if len(indices) == 0:\n return [], -1\n rows = {i: m.data[i] for i in indices}\n weights: Dict[int,int] = {i: sum(r) for i, r in rows.items()}\n result = []\n next_indices = []\n while len(indices) > 1:\n best = (-1, -1)\n reduction = -10000\n for i in indices:\n for j in indices:\n if j <= i: continue\n w = sum(xor_rows(rows[i], rows[j]))\n if weights[i] - w > reduction:\n best = (j, i) # \"Add row j to i\"\n reduction = weights[i] - w\n if weights[j] - w > reduction:\n best = (i, j)\n reduction = weights[j] - w\n result.append(best)\n control, target = best\n rows[target] = xor_rows(rows[control], rows[target])\n weights[target] = weights[target] - reduction\n indices.remove(control)\n indices.remove(target)\n next_indices.append(target)\n if len(indices) <= 1:\n if len(indices) == 1:\n next_indices.append(indices[0])\n indices = next_indices\n next_indices = []\n return result, indices[0]"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Perform batch look up on a 2D tensor M using a binary mask.
|
def batch_binary_lookup(M, b_idx, pad_value):
batch_size = M.size(0)
seq_len = b_idx.sum(1, keepdim=True)
max_seq_len = int(seq_len.max())
output_masks = batch_arange_cuda(batch_size, max_seq_len) >= seq_len
pad_len = max_seq_len - seq_len
max_pad_len = int(pad_len.max())
M = torch.cat([M, fill_var_cuda([batch_size, max_pad_len], pad_value, dtype=M.dtype)], dim=1)
pad_b_idx = batch_arange_cuda(batch_size, max_pad_len) < pad_len
b_idx = torch.cat([b_idx, pad_b_idx], dim=1)
output = M[b_idx].view(batch_size, max_seq_len)
return output, output_masks
|
[
"def batch_binary_lookup_3D(M, b_idx, pad_value):\n # Pad binary indices\n batch_size = M.size(0)\n hidden_dim = M.size(2)\n seq_len = b_idx.sum(1, keepdim=True)\n max_seq_len = int(seq_len.max())\n output_masks = batch_arange_cuda(batch_size, max_seq_len) >= seq_len\n pad_len = max_seq_len - seq_len\n max_pad_len = int(pad_len.max())\n M = torch.cat([M, fill_var_cuda([batch_size, max_pad_len, hidden_dim], pad_value, dtype=M.dtype)], dim=1)\n pad_b_idx = batch_arange_cuda(batch_size, max_pad_len) < pad_len\n b_idx = torch.cat([b_idx, pad_b_idx], dim=1)\n output = M[b_idx].view(batch_size, max_seq_len, hidden_dim)\n return output, output_masks",
"def mask_data(token_tensor, mask_inds):\n for i in range(token_tensor.input_ids.shape[0]):\n token_tensor.input_ids[i, mask_inds[i]] = 103",
"def batch_lookup_3D(M, idx):\n batch_size, seq_len, dim = M.size()\n _, sample_size = idx.size()\n M = M.view(batch_size*seq_len, dim)\n offset = long_var_cuda(torch.arange(batch_size).unsqueeze(1))\n idx = idx + offset * seq_len\n idx = idx.view(-1)\n # [batch_size*sample_size, dim]\n features = torch.index_select(M, 0, idx)\n return features.view(batch_size, sample_size, dim)",
"def apply_mapping(mask, mapping):\n K, F = mapping.shape\n assert K < 20, (K, mapping.shape)\n assert mask.shape[:2] == mapping.shape, (mask.shape, mapping.shape)\n return mask[mapping, range(F)]",
"def test_permutation_and_input_mask(self):\n seq_length = 4\n batch_size = 1\n memory_length = 0\n\n input_mask = np.array([[1, 1, 0, 0]])\n permutation_mask = np.array([[\n [0, 1, 1, 1],\n [1, 0, 1, 1],\n [1, 1, 0, 1],\n [1, 1, 1, 0],\n ]])\n\n expected_query_mask = np.array([[[\n [0, 1, 0, 0],\n [1, 0, 0, 0],\n [1, 1, 0, 0],\n [1, 1, 0, 0]]]])\n expected_content_mask = np.array([[[\n [1, 1, 0, 0],\n [1, 1, 0, 0],\n [1, 1, 1, 0],\n [1, 1, 0, 1]]]])\n query_mask, content_mask = xlnet_base._compute_attention_mask(\n input_mask=input_mask,\n permutation_mask=permutation_mask,\n attention_type=\"bi\",\n seq_length=seq_length,\n memory_length=memory_length,\n batch_size=batch_size,\n dtype=tf.float32)\n\n self.assertAllClose(query_mask, expected_query_mask)\n self.assertAllClose(content_mask, expected_content_mask)",
"def test_permutation_mask_no_input_mask(self):\n seq_length = 2\n batch_size = 1\n memory_length = 0\n\n input_mask = None\n permutation_mask = np.array([\n [[1, 0],\n [1, 0]],\n ])\n\n expected_query_mask = permutation_mask[:, None, :, :]\n expected_content_mask = np.array([[[\n [1, 0],\n [1, 1]]]])\n\n query_mask, content_mask = xlnet_base._compute_attention_mask(\n input_mask=input_mask,\n permutation_mask=permutation_mask,\n attention_type=\"bi\",\n seq_length=seq_length,\n memory_length=memory_length,\n batch_size=batch_size,\n dtype=tf.float32)\n\n self.assertAllClose(query_mask, expected_query_mask)\n self.assertAllClose(content_mask, expected_content_mask)",
"def test_input_mask_no_permutation(self):\n seq_length = 4\n batch_size = 1\n memory_length = 0\n\n input_mask = np.array([[1, 1, 0, 0]])\n permutation_mask = None\n\n expected_query_mask = input_mask[None, None, :, :]\n expected_content_mask = np.array([[[\n [1, 1, 0, 0],\n [1, 1, 0, 0],\n [1, 1, 1, 0],\n [1, 1, 0, 1]]]])\n\n query_mask, content_mask = xlnet_base._compute_attention_mask(\n input_mask=input_mask,\n permutation_mask=permutation_mask,\n attention_type=\"bi\",\n seq_length=seq_length,\n memory_length=memory_length,\n batch_size=batch_size,\n dtype=tf.float32)\n\n self.assertAllClose(query_mask, expected_query_mask)\n self.assertAllClose(content_mask, expected_content_mask)",
"def compute_mask_map_over_batch(pixels_with_depth):\n img_wh = 64\n num_vertices = pixels_with_depth.get_shape().as_list()[0] # num_vertices\n indices = tf.expand_dims(tf.range(num_vertices, dtype='float32'), axis=1) # num_vertices x 1\n pixels_with_depth_and_index = tf.concat([pixels_with_depth, indices], axis=1) # num_vertices x 4\n\n i = tf.range(0, img_wh)\n j = tf.range(0, img_wh)\n\n t1, t2 = tf.meshgrid(i, j)\n grid = tf.cast(tf.stack([t1, t2], axis=2), dtype='float32') # img_wh x img_wh x 2\n pixel_coords = tf.reshape(grid, [-1, 2]) # img_wh^2 x 2\n expanded_pixels_with_depth_and_index = tf.tile(tf.expand_dims(pixels_with_depth_and_index,\n axis=0, name='big_tile1'),\n [img_wh*img_wh, 1, 1]) # img_wh^2 x num_vertices x 4\n\n min_depth_verts = tf.map_fn(get_min_depth_vert_index_at_pixel,\n [pixel_coords, expanded_pixels_with_depth_and_index],\n back_prop=False,\n dtype='float32',\n parallel_iterations=128) # img_wh^2 x 1 x 1 x 4\n\n min_depth_verts = tf.squeeze(tf.cast(min_depth_verts, dtype='int32')) # img_wh^2 x 4\n min_indices, _ = tf.unique(min_depth_verts[:, 3]) # (?,), ? is number of visible vertices\n\n mask = K.variable(np.ones(num_vertices) * 500)\n ones = tf.ones_like(min_indices, dtype='float32')\n mask = tf.scatter_update(mask, min_indices, ones) # (num_vertices,)\n\n return mask",
"def sparse_mask(self, input, mask): # real signature unknown; restored from __doc__\n pass",
"def _extract_and_mask_tensor(self, multivec, start_pos, end_pos):\n device = multivec.device\n\n # First get the leftmost and rightmost indices, and extract the relevant columns from multivec\n left_lim = torch.min(start_pos)\n right_lim = torch.max(end_pos)\n extracted_segment = multivec[:, left_lim:right_lim]\n\n # modifiers_count represents the batch size, mask_length is the TOTAL amount of relevant columns, but\n # note it may be sparse (we'll make this vector more dense later on).\n # i.e: extracted_segment may contain:\n # [ [1, 2, 3, 0, 0, 0], [0, 0, 0, 3, 4, 5] ].\n # so mask_length is 6, but ultimately we'll want to return: [ [1, 2, 3], [3, 4, 5] ]\n modifiers_count = end_pos.shape[0]\n mask_length = right_lim - left_lim\n\n # Create a mask of: [start_pos, start_pos + 1, .., end_pos] for EACH row.\n tiled_indices = torch.arange(right_lim - left_lim, device=device).repeat(modifiers_count, 1) + left_lim\n\n # Create a mask of [start_pos[i], start_pos[i], .. start_pos[i], for each row. Same goes for end_pos.\n # The binary mask is obtained where the indices are between the start and end positions.\n left_mask_lim = start_pos.unsqueeze(1).repeat(1, mask_length)\n right_mask_lim = end_pos.unsqueeze(1).repeat(1, mask_length)\n mask = torch.mul(tiled_indices >= left_mask_lim, tiled_indices < right_mask_lim)\n\n # -- At this point extracted_segment may contain the result, and mask the actual mask --\n # However, extracted_segment may be sparse, so we wish to \"dilate\" it.\n # ---\n\n # First extract the real length of the dense vector. This is determined by the maximal range: end-start.\n # Then create a mask of dims_per_row: for each row we keep how many \"real\" columns should be extracted\n # Then we obtain a short binary mask, containing a 1 bit for each real value we should extract.\n # So for input: [ [1, 2, 3, 0, 0, 0], [0, 0, 0, 3, 4, 5] ]\n # We get: real_length = 3, and dims_per_row = [ [ 3, 3, 3], [ 3, 3, 3,]],\n # and the short_mask is [ [1, 1, 1], [1, 1, 1] ]\n real_length = torch.max(end_pos - start_pos).item()\n dims_per_row = (right_mask_lim - left_mask_lim)[:, :real_length]\n short_mask = torch.arange(real_length, device=device).repeat(modifiers_count, 1) < dims_per_row\n\n # We pad the original mask with an inverted mask, and the original extracted_segment with empty zero\n # values, to get \"empty dimensions\" we can pick from.\n # Later when we use mask_selection, we'll pick those empty values if this specific row has less columns than\n # other rows.\n # (in other words - for modifiers with less parameters, we append a \"dummy\" mask of ones to make sure all rows\n # contain an equal number of selected columns, but those are empty zero entries)\n inverted_mask = torch.ones_like(short_mask) - short_mask\n padded_mask = torch.cat((mask, inverted_mask), dim=1)\n empty_entries_padding = torch.zeros(modifiers_count, real_length, device=multivec.device)\n padded_segment = torch.cat((extracted_segment, empty_entries_padding), dim=1)\n\n # Finally use mask select to extract the real values and obtain a shorter extracted segment.\n # The real dimensions of this tensor are exactly like the padding we added in the previous stage\n # (think of an empty modifier: it would need the entire padding we've added).\n short_extracted_segment = torch.masked_select(padded_segment, padded_mask).reshape_as(empty_entries_padding)\n\n # This shouldn't be required, but to be on the safe side: zero out elements that fall out of the mask\n short_mask = short_mask.float()\n short_extracted_segment.mul_(short_mask)\n\n return short_extracted_segment, short_mask",
"def masked_scatter(self, mask, tensor): # real signature unknown; restored from __doc__\n pass",
"def _relabel_tile(\n inp_tile: numpy.ndarray,\n mapping: dict[int, int],\n) -> numpy.ndarray:\n out_tile = numpy.copy(inp_tile)\n for k, v in mapping.items():\n mask = inp_tile == k\n out_tile[mask] = v\n return out_tile",
"def one_cold_mask(idx, tensor):\n result = np.ones([tensor.get_shape()[-1].value], dtype='bool')\n result[idx] = False\n return tf.tile(tf.expand_dims(result, axis=0), [tf.shape(tensor)[0], 1])",
"def bilinear_attention(query_tensor, mem_tensor, mem_dim,\n valid_memory_length=None,\n max_mem_seq_len=None, mode=None,\n hard_attention=False, activation_fn=None,\n project_query=True, project_mem=True, scope=None):\n with tf.variable_scope(scope or 'bilinear_attention'):\n # Projects the query tensor if desired.\n if project_query:\n query_tensor = tf.contrib.layers.fully_connected(\n query_tensor, mem_dim, activation_fn=activation_fn,\n scope='query_projection'\n )\n\n if project_mem:\n mem_tensor = tf.contrib.layers.fully_connected(\n mem_tensor, mem_dim, activation_fn=activation_fn,\n scope='mem_projection'\n )\n # This mulitplication results in a [batch_size, query_seq_len,\n # mem_seq_len] sized tensor of unnormalized similarity.\n sim_logits = tf.matmul(query_tensor, mem_tensor, transpose_b=True)\n if valid_memory_length:\n # A [batch_size, mem_seq_length] sized boolean tensor.\n valid_mem_seq = tf.sequence_mask(valid_memory_length,\n maxlen=max_mem_seq_len)\n mem_seq_mask = tf.where(\n valid_mem_seq,\n tf.zeros_like(valid_mem_seq, dtype=tf.float32),\n VERY_NEG * tf.ones_like(valid_mem_seq, dtype=tf.float32))\n\n # Expands the query_seq_length dimension for broadcasting.\n mem_seq_mask = tf.expand_dims(mem_seq_mask, 1)\n sim_logits += mem_seq_mask\n\n sim_logits /= tf.sqrt(tf.to_float(mem_dim))\n sim_softmax = tf.nn.softmax(sim_logits)\n\n if hard_attention:\n batch_size = tf.shape(mem_tensor)[0]\n max_indices = tf.argmax(sim_softmax, axis=-1)\n offset = tf.expand_dims(tf.range(tf.to_int64(batch_size),\n dtype=tf.int64), -1)\n max_indices += offset\n max_indices = tf.stop_gradient(max_indices)\n\n flat_mem_tensor = tf.reshape(mem_tensor, [-1, mem_dim])\n mix_mem_tensor = tf.nn.embedding_lookup(flat_mem_tensor,\n max_indices)\n else:\n mix_mem_tensor = tf.matmul(sim_softmax, mem_tensor)\n\n return mix_mem_tensor, sim_logits, sim_softmax",
"def filtered_by_cell_mask(self, mask, both_cells_required = True):\n\n assert len(self.grid_list) == 1, 'attempt to filter multi-grid connection set by cell mask'\n grid = self.grid_list[0]\n flat_extent = grid.cell_count()\n flat_mask = mask.reshape((flat_extent,))\n where_0 = flat_mask[self.cell_index_pairs[:, 0]]\n where_1 = flat_mask[self.cell_index_pairs[:, 1]]\n if both_cells_required:\n where_both = np.logical_and(where_0, where_1)\n else:\n where_both = np.logical_or(where_0, where_1)\n indices = np.where(where_both)[0] # indices into primary axis of original arrays\n if len(indices) == 0:\n log.warning('no connections have passed filtering')\n return None\n masked_gcs = GridConnectionSet(self.model, grid = grid)\n masked_gcs.count = len(indices)\n masked_gcs.cell_index_pairs = self.cell_index_pairs[indices, :]\n masked_gcs.face_index_pairs = self.face_index_pairs[indices, :]\n masked_gcs.feature_indices = self.feature_indices[indices]\n masked_gcs.feature_list = self.feature_list.copy()\n masked_gcs.clean_feature_list()\n return masked_gcs",
"def multi_hot_encoding(self, mask: np.ndarray) -> np.ndarray:\n encoded_mask = np.zeros((len(self.class_indexes), *mask.shape))\n for i, label in enumerate(self.class_indexes):\n encoded_mask[i,:,:,:] = np.where(mask == label, 1, 0)\n return encoded_mask",
"def _insert_sparse_mask_ops(cls, main_program, params):\n block = main_program.global_block()\n asp_info = cls._get_program_asp_info(main_program)\n for param in params:\n if param.name in asp_info.mask_vars:\n block.append_op(\n type='elementwise_mul',\n inputs={\"X\": param, 'Y': asp_info.mask_vars[param.name]},\n outputs={'Out': param},\n attrs={\n 'axis': -1,\n 'use_mkldnn': False,\n OP_ROLE_KEY: int(OpRole.Optimize),\n },\n )",
"def bitmasks2tensor(self, bitmasks, target_sz):\n assert check_argument.is_type_list(bitmasks, BitmapMasks)\n assert isinstance(target_sz, tuple)\n\n batch_size = len(bitmasks)\n num_masks = len(bitmasks[0])\n\n results = []\n\n for level_inx in range(num_masks):\n kernel = []\n for batch_inx in range(batch_size):\n mask = torch.from_numpy(bitmasks[batch_inx].masks[level_inx])\n # hxw\n mask_sz = mask.shape\n # left, right, top, bottom\n pad = [\n 0, target_sz[1] - mask_sz[1], 0, target_sz[0] - mask_sz[0]\n ]\n mask = F.pad(mask, pad, mode='constant', value=0)\n kernel.append(mask)\n kernel = torch.stack(kernel)\n results.append(kernel)\n\n return results",
"def __apply_input_mask(self):\n with torch.no_grad():\n # apply the input mask\n for tid, in_tensor in enumerate(self.dummy_input):\n if isinstance(in_tensor, torch.Tensor) and self.in_masks[tid] is not None:\n # in_tensor.data = in_tensor.data * \\\n # self.in_masks[tid] + \\\n # (1-self.in_masks[tid]) * self.in_constants[tid]\n # issue-4540 when two tensors are multiplied, the constants part make\n # the propagation weaker, and lead to shape misaligment. Currently, we\n # donnot support the constant folding, so, we just remove the constant here\n in_tensor.data = in_tensor.data * \\\n self.in_masks[tid]"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Perform batch look up on a 3D tensor M using a binary mask.
|
def batch_binary_lookup_3D(M, b_idx, pad_value):
# Pad binary indices
batch_size = M.size(0)
hidden_dim = M.size(2)
seq_len = b_idx.sum(1, keepdim=True)
max_seq_len = int(seq_len.max())
output_masks = batch_arange_cuda(batch_size, max_seq_len) >= seq_len
pad_len = max_seq_len - seq_len
max_pad_len = int(pad_len.max())
M = torch.cat([M, fill_var_cuda([batch_size, max_pad_len, hidden_dim], pad_value, dtype=M.dtype)], dim=1)
pad_b_idx = batch_arange_cuda(batch_size, max_pad_len) < pad_len
b_idx = torch.cat([b_idx, pad_b_idx], dim=1)
output = M[b_idx].view(batch_size, max_seq_len, hidden_dim)
return output, output_masks
|
[
"def batch_lookup_3D(M, idx):\n batch_size, seq_len, dim = M.size()\n _, sample_size = idx.size()\n M = M.view(batch_size*seq_len, dim)\n offset = long_var_cuda(torch.arange(batch_size).unsqueeze(1))\n idx = idx + offset * seq_len\n idx = idx.view(-1)\n # [batch_size*sample_size, dim]\n features = torch.index_select(M, 0, idx)\n return features.view(batch_size, sample_size, dim)",
"def batch_binary_lookup(M, b_idx, pad_value):\n batch_size = M.size(0)\n seq_len = b_idx.sum(1, keepdim=True)\n max_seq_len = int(seq_len.max())\n output_masks = batch_arange_cuda(batch_size, max_seq_len) >= seq_len\n pad_len = max_seq_len - seq_len\n max_pad_len = int(pad_len.max())\n M = torch.cat([M, fill_var_cuda([batch_size, max_pad_len], pad_value, dtype=M.dtype)], dim=1)\n pad_b_idx = batch_arange_cuda(batch_size, max_pad_len) < pad_len\n b_idx = torch.cat([b_idx, pad_b_idx], dim=1)\n output = M[b_idx].view(batch_size, max_seq_len)\n return output, output_masks",
"def mask_data(token_tensor, mask_inds):\n for i in range(token_tensor.input_ids.shape[0]):\n token_tensor.input_ids[i, mask_inds[i]] = 103",
"def test_permutation_and_input_mask(self):\n seq_length = 4\n batch_size = 1\n memory_length = 0\n\n input_mask = np.array([[1, 1, 0, 0]])\n permutation_mask = np.array([[\n [0, 1, 1, 1],\n [1, 0, 1, 1],\n [1, 1, 0, 1],\n [1, 1, 1, 0],\n ]])\n\n expected_query_mask = np.array([[[\n [0, 1, 0, 0],\n [1, 0, 0, 0],\n [1, 1, 0, 0],\n [1, 1, 0, 0]]]])\n expected_content_mask = np.array([[[\n [1, 1, 0, 0],\n [1, 1, 0, 0],\n [1, 1, 1, 0],\n [1, 1, 0, 1]]]])\n query_mask, content_mask = xlnet_base._compute_attention_mask(\n input_mask=input_mask,\n permutation_mask=permutation_mask,\n attention_type=\"bi\",\n seq_length=seq_length,\n memory_length=memory_length,\n batch_size=batch_size,\n dtype=tf.float32)\n\n self.assertAllClose(query_mask, expected_query_mask)\n self.assertAllClose(content_mask, expected_content_mask)",
"def test_permutation_mask_no_input_mask(self):\n seq_length = 2\n batch_size = 1\n memory_length = 0\n\n input_mask = None\n permutation_mask = np.array([\n [[1, 0],\n [1, 0]],\n ])\n\n expected_query_mask = permutation_mask[:, None, :, :]\n expected_content_mask = np.array([[[\n [1, 0],\n [1, 1]]]])\n\n query_mask, content_mask = xlnet_base._compute_attention_mask(\n input_mask=input_mask,\n permutation_mask=permutation_mask,\n attention_type=\"bi\",\n seq_length=seq_length,\n memory_length=memory_length,\n batch_size=batch_size,\n dtype=tf.float32)\n\n self.assertAllClose(query_mask, expected_query_mask)\n self.assertAllClose(content_mask, expected_content_mask)",
"def test_input_mask_no_permutation(self):\n seq_length = 4\n batch_size = 1\n memory_length = 0\n\n input_mask = np.array([[1, 1, 0, 0]])\n permutation_mask = None\n\n expected_query_mask = input_mask[None, None, :, :]\n expected_content_mask = np.array([[[\n [1, 1, 0, 0],\n [1, 1, 0, 0],\n [1, 1, 1, 0],\n [1, 1, 0, 1]]]])\n\n query_mask, content_mask = xlnet_base._compute_attention_mask(\n input_mask=input_mask,\n permutation_mask=permutation_mask,\n attention_type=\"bi\",\n seq_length=seq_length,\n memory_length=memory_length,\n batch_size=batch_size,\n dtype=tf.float32)\n\n self.assertAllClose(query_mask, expected_query_mask)\n self.assertAllClose(content_mask, expected_content_mask)",
"def apply_mapping(mask, mapping):\n K, F = mapping.shape\n assert K < 20, (K, mapping.shape)\n assert mask.shape[:2] == mapping.shape, (mask.shape, mapping.shape)\n return mask[mapping, range(F)]",
"def batch_mvcnn_voxel_traversal_with_ray_marching(\n M,\n D,\n N,\n F,\n H,\n W,\n padding,\n bbox,\n grid_shape,\n sampling_scheme\n):\n # Set the paths to the files that will be used to construct the cuda kernel\n file_paths = [\n \"ray_tracing.cu\",\n \"utils.cu\",\n \"planes_voxels_mapping.cu\",\n \"feature_similarities.cu\",\n \"sampling_schemes.cu\"\n ]\n\n cu_source_code = parse_cu_files_to_string(file_paths)\n\n tpl = Template(cu_source_code + \"\"\"\n __global__ void batch_mvcnn_planes_voxels_with_ray_marching(\n int n_rays,\n int * ray_idxs,\n float * features,\n float * P,\n float * P_inv,\n float * camera_center,\n float * voxel_grid,\n int * ray_voxel_indices,\n int * ray_voxel_count,\n float * S_new\n ) {\n // Compute the thread\n int r = threadIdx.x + blockDim.x * blockIdx.x;\n if (r >= n_rays)\n return;\n\n // Estimate the ray_start and ray_end for the current pixel\n float ray_start[3], ray_end[3];\n $sampling_scheme(\n ray_idxs[r],\n P_inv,\n camera_center,\n ray_start,\n ray_end\n );\n\n // Compute the similarities between features\n float S[$depth_planes];\n compute_similarities_per_ray(\n features,\n P,\n ray_start,\n ray_end,\n S\n );\n\n // Estimate the ray_voxel_indices and the ray_voxel_count\n voxel_traversal(\n ray_start,\n ray_end,\n ray_voxel_indices + r*$max_voxels*3,\n ray_voxel_count + r\n );\n\n // Map the depth planes to voxel centers\n planes_voxels_mapping(\n voxel_grid,\n ray_voxel_indices + 3*$max_voxels*r,\n ray_voxel_count + r,\n ray_start,\n ray_end,\n S,\n S_new + $max_voxels*r\n );\n }\n \"\"\")\n\n mod = SourceModule(tpl.substitute(\n max_voxels=M,\n depth_planes=D,\n n_views=N,\n padding=padding,\n features_dimensions=F,\n width=W,\n height=H,\n grid_x=grid_shape[0],\n grid_y=grid_shape[1],\n grid_z=grid_shape[2],\n bbox_min_x=bbox[0],\n bbox_min_y=bbox[1],\n bbox_min_z=bbox[2],\n bbox_max_x=bbox[3],\n bbox_max_y=bbox[4],\n bbox_max_z=bbox[5],\n sampling_scheme=sampling_scheme\n ))\n cuda_fp = mod.get_function(\"batch_mvcnn_planes_voxels_with_ray_marching\")\n cuda_fp.prepare(\"i\" + \"P\"*9)\n\n @all_arrays_to_gpu\n def fp(\n ray_idxs,\n features,\n P,\n P_inv,\n camera_center,\n voxel_grid,\n ray_voxel_indices,\n ray_voxel_count,\n S_new,\n threads=2048\n ):\n # Assert everything is the right size, shape and dtype\n assert S_new.shape[1] == M\n assert len(ray_voxel_count.shape) == 1\n assert np.float32 == S_new.dtype\n assert np.int32 == ray_voxel_count.dtype\n\n # Determine the grid and block arguments\n n_rays = len(S_new)\n blocks = n_rays / threads + int(n_rays % threads != 0)\n\n cuda_fp.prepared_call(\n (threads, 1),\n (blocks, 1, 1),\n np.int32(n_rays),\n ray_idxs.gpudata,\n features.gpudata,\n P.gpudata,\n P_inv.gpudata,\n camera_center.gpudata,\n voxel_grid.gpudata,\n ray_voxel_indices.gpudata,\n ray_voxel_count.gpudata,\n S_new.gpudata\n )\n\n return fp",
"def compute_mask_map_over_batch(pixels_with_depth):\n img_wh = 64\n num_vertices = pixels_with_depth.get_shape().as_list()[0] # num_vertices\n indices = tf.expand_dims(tf.range(num_vertices, dtype='float32'), axis=1) # num_vertices x 1\n pixels_with_depth_and_index = tf.concat([pixels_with_depth, indices], axis=1) # num_vertices x 4\n\n i = tf.range(0, img_wh)\n j = tf.range(0, img_wh)\n\n t1, t2 = tf.meshgrid(i, j)\n grid = tf.cast(tf.stack([t1, t2], axis=2), dtype='float32') # img_wh x img_wh x 2\n pixel_coords = tf.reshape(grid, [-1, 2]) # img_wh^2 x 2\n expanded_pixels_with_depth_and_index = tf.tile(tf.expand_dims(pixels_with_depth_and_index,\n axis=0, name='big_tile1'),\n [img_wh*img_wh, 1, 1]) # img_wh^2 x num_vertices x 4\n\n min_depth_verts = tf.map_fn(get_min_depth_vert_index_at_pixel,\n [pixel_coords, expanded_pixels_with_depth_and_index],\n back_prop=False,\n dtype='float32',\n parallel_iterations=128) # img_wh^2 x 1 x 1 x 4\n\n min_depth_verts = tf.squeeze(tf.cast(min_depth_verts, dtype='int32')) # img_wh^2 x 4\n min_indices, _ = tf.unique(min_depth_verts[:, 3]) # (?,), ? is number of visible vertices\n\n mask = K.variable(np.ones(num_vertices) * 500)\n ones = tf.ones_like(min_indices, dtype='float32')\n mask = tf.scatter_update(mask, min_indices, ones) # (num_vertices,)\n\n return mask",
"def __apply_input_mask(self):\n with torch.no_grad():\n # apply the input mask\n for tid, in_tensor in enumerate(self.dummy_input):\n if isinstance(in_tensor, torch.Tensor) and self.in_masks[tid] is not None:\n # in_tensor.data = in_tensor.data * \\\n # self.in_masks[tid] + \\\n # (1-self.in_masks[tid]) * self.in_constants[tid]\n # issue-4540 when two tensors are multiplied, the constants part make\n # the propagation weaker, and lead to shape misaligment. Currently, we\n # donnot support the constant folding, so, we just remove the constant here\n in_tensor.data = in_tensor.data * \\\n self.in_masks[tid]",
"def masked_scatter(self, mask, tensor): # real signature unknown; restored from __doc__\n pass",
"def bitmasks2tensor(self, bitmasks, target_sz):\n assert check_argument.is_type_list(bitmasks, BitmapMasks)\n assert isinstance(target_sz, tuple)\n\n batch_size = len(bitmasks)\n num_masks = len(bitmasks[0])\n\n results = []\n\n for level_inx in range(num_masks):\n kernel = []\n for batch_inx in range(batch_size):\n mask = torch.from_numpy(bitmasks[batch_inx].masks[level_inx])\n # hxw\n mask_sz = mask.shape\n # left, right, top, bottom\n pad = [\n 0, target_sz[1] - mask_sz[1], 0, target_sz[0] - mask_sz[0]\n ]\n mask = F.pad(mask, pad, mode='constant', value=0)\n kernel.append(mask)\n kernel = torch.stack(kernel)\n results.append(kernel)\n\n return results",
"def sparse_mask(self, input, mask): # real signature unknown; restored from __doc__\n pass",
"def computeMaskIntersection(gt, gtMask, pred, predMask):\n if gtMask is None or predMask is None:\n return 0\n\n assert gtMask.shape == predMask.shape\n assert len(gtMask.shape) == len(predMask.shape) == 2\n\n xmin, ymin, xmax, ymax = getUnionBox(gt[\"box\"], pred[\"box\"])\n gtMask_crop = gtMask[ymin:ymax, xmin:xmax]\n predMask_crop = predMask[ymin:ymax, xmin:xmax]\n\n # elementwise AND\n intersection = torch.sum(torch.mul(gtMask_crop, predMask_crop)).item()\n return intersection",
"def one_cold_mask(idx, tensor):\n result = np.ones([tensor.get_shape()[-1].value], dtype='bool')\n result[idx] = False\n return tf.tile(tf.expand_dims(result, axis=0), [tf.shape(tensor)[0], 1])",
"def _insert_sparse_mask_ops(cls, main_program, params):\n block = main_program.global_block()\n asp_info = cls._get_program_asp_info(main_program)\n for param in params:\n if param.name in asp_info.mask_vars:\n block.append_op(\n type='elementwise_mul',\n inputs={\"X\": param, 'Y': asp_info.mask_vars[param.name]},\n outputs={'Out': param},\n attrs={\n 'axis': -1,\n 'use_mkldnn': False,\n OP_ROLE_KEY: int(OpRole.Optimize),\n },\n )",
"def _extract_and_mask_tensor(self, multivec, start_pos, end_pos):\n device = multivec.device\n\n # First get the leftmost and rightmost indices, and extract the relevant columns from multivec\n left_lim = torch.min(start_pos)\n right_lim = torch.max(end_pos)\n extracted_segment = multivec[:, left_lim:right_lim]\n\n # modifiers_count represents the batch size, mask_length is the TOTAL amount of relevant columns, but\n # note it may be sparse (we'll make this vector more dense later on).\n # i.e: extracted_segment may contain:\n # [ [1, 2, 3, 0, 0, 0], [0, 0, 0, 3, 4, 5] ].\n # so mask_length is 6, but ultimately we'll want to return: [ [1, 2, 3], [3, 4, 5] ]\n modifiers_count = end_pos.shape[0]\n mask_length = right_lim - left_lim\n\n # Create a mask of: [start_pos, start_pos + 1, .., end_pos] for EACH row.\n tiled_indices = torch.arange(right_lim - left_lim, device=device).repeat(modifiers_count, 1) + left_lim\n\n # Create a mask of [start_pos[i], start_pos[i], .. start_pos[i], for each row. Same goes for end_pos.\n # The binary mask is obtained where the indices are between the start and end positions.\n left_mask_lim = start_pos.unsqueeze(1).repeat(1, mask_length)\n right_mask_lim = end_pos.unsqueeze(1).repeat(1, mask_length)\n mask = torch.mul(tiled_indices >= left_mask_lim, tiled_indices < right_mask_lim)\n\n # -- At this point extracted_segment may contain the result, and mask the actual mask --\n # However, extracted_segment may be sparse, so we wish to \"dilate\" it.\n # ---\n\n # First extract the real length of the dense vector. This is determined by the maximal range: end-start.\n # Then create a mask of dims_per_row: for each row we keep how many \"real\" columns should be extracted\n # Then we obtain a short binary mask, containing a 1 bit for each real value we should extract.\n # So for input: [ [1, 2, 3, 0, 0, 0], [0, 0, 0, 3, 4, 5] ]\n # We get: real_length = 3, and dims_per_row = [ [ 3, 3, 3], [ 3, 3, 3,]],\n # and the short_mask is [ [1, 1, 1], [1, 1, 1] ]\n real_length = torch.max(end_pos - start_pos).item()\n dims_per_row = (right_mask_lim - left_mask_lim)[:, :real_length]\n short_mask = torch.arange(real_length, device=device).repeat(modifiers_count, 1) < dims_per_row\n\n # We pad the original mask with an inverted mask, and the original extracted_segment with empty zero\n # values, to get \"empty dimensions\" we can pick from.\n # Later when we use mask_selection, we'll pick those empty values if this specific row has less columns than\n # other rows.\n # (in other words - for modifiers with less parameters, we append a \"dummy\" mask of ones to make sure all rows\n # contain an equal number of selected columns, but those are empty zero entries)\n inverted_mask = torch.ones_like(short_mask) - short_mask\n padded_mask = torch.cat((mask, inverted_mask), dim=1)\n empty_entries_padding = torch.zeros(modifiers_count, real_length, device=multivec.device)\n padded_segment = torch.cat((extracted_segment, empty_entries_padding), dim=1)\n\n # Finally use mask select to extract the real values and obtain a shorter extracted segment.\n # The real dimensions of this tensor are exactly like the padding we added in the previous stage\n # (think of an empty modifier: it would need the entire padding we've added).\n short_extracted_segment = torch.masked_select(padded_segment, padded_mask).reshape_as(empty_entries_padding)\n\n # This shouldn't be required, but to be on the safe side: zero out elements that fall out of the mask\n short_mask = short_mask.float()\n short_extracted_segment.mul_(short_mask)\n\n return short_extracted_segment, short_mask",
"def mask_mixedlayer(\n ds,\n mld,\n mask=\"outside\",\n z_dim=\"lev\",\n z_bounds=\"lev_bounds\",\n ref_var=None,\n bound_dim=\"bnds\",\n):\n if ref_var is None:\n ref_var = list(ds.data_vars)[0]\n\n # broadcast the mld against a full 3d variable to adjust the chunks...\n mld = xr.ones_like(ds[ref_var]) * mld\n\n crit_name = z_dim\n if z_bounds in ds.coords:\n crit = ds[z_bounds].isel({bound_dim: 1})\n crit_name = z_bounds\n # The proper way to select.\n # This excludes all cells that have an upper bound bound shallower than the mld\n else:\n warnings.warn(\n \"Cell bounds [{z_bounds}] not found in input. Masking is performed with cell centers, which might be less accurate\"\n )\n crit = ds[z_dim]\n # Fallback. Use the center depth of the cell.\n # Could still be influenced by ML, but probably not that bad.\n\n if mask == \"outside\":\n out = ds.where(mld < crit)\n elif mask == \"inside\":\n out = ds.where(mld >= crit)\n else:\n raise ValueError(\"`mask` has to be either `inside` or `outside`\")\n out.attrs.update({\"mixed_layer_values_removed_based_on\": crit_name})\n if z_bounds in ds.coords:\n out = out.assign_coords({z_bounds: ds[z_bounds]})\n return out",
"def landmarks_match_mtcnn(src_im, src_landmarks, tar_landmarks):\n src_size = src_im.shape\n src_tmp = [(int(xy[1]), int(xy[0])) for xy in src_landmarks]\n tar_tmp = [(int(xy[1]), int(xy[0])) for xy in tar_landmarks]\n M = umeyama(np.array(src_tmp), np.array(tar_tmp), True)[0:2]\n result = cv2.warpAffine(src_im, M, (src_size[1], src_size[0]), borderMode=cv2.BORDER_REPLICATE) \n return result"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Pack the hidden state of a BiLSTM s.t. the first dimension equals to the number of layers.
|
def pack_bidirectional_lstm_state(state, num_layers):
assert (len(state) == 2 * num_layers)
_, batch_size, hidden_dim = state.size()
layers = state.view(num_layers, 2, batch_size, hidden_dim).transpose(1, 2).contiguous()
state = layers.view(num_layers, batch_size, -1)
return state
|
[
"def unpack_bidirectional_lstm_state(state, num_directions=2):\n batch_size = state.size(1)\n new_hidden_dim = int(state.size(2) / num_directions)\n return torch.stack(torch.split(state, new_hidden_dim, dim=2), dim=1).view(-1, batch_size, new_hidden_dim)",
"def init_hidden(self):\n weight = next(self.parameters())\n nlayers = self.eta_nlayers\n nhid = self.eta_hidden_size\n return (weight.new_zeros(nlayers, 1, nhid), weight.new_zeros(nlayers, 1, nhid))",
"def init_hidden(self, batch_size):\n if self.bidirectional:\n ##################\n # YOUR CODE HERE\n # A bidirectional RNN has more hidden layers than a regular one-way RNN.\n # For each \"left-to-right\" layer there is one \"right-to-left\" layer.\n ##################\n\n raise NotImplementedError\n\n else:\n rnn_layer_number = self.rnn_layer_number\n\n if self.cell_type == \"RNN_TANH\":\n hidden = torch.randn(rnn_layer_number, batch_size, self.rnn_layer_size)\n self.hidden_layer = hidden\n\n elif self.cell_type == \"LSTM\":\n ##################\n # YOUR CODE HERE\n # LSTM layer uses one more layer tier than basic RNN layer, in which\n # it stores the memory state of the cells. The nn.LSTM class handles the\n # hidden and cell layer in one tuple.\n ##################\n\n raise NotImplementedError",
"def init_state(self, src, memory_bank, encoder_final):\n def _fix_enc_hidden(hidden):\n # The encoder hidden is (layers*directions) x batch x dim.\n # We need to convert it to layers x batch x (directions*dim).\n if self.bidirectional_encoder:\n hidden = torch.cat([hidden[0:hidden.size(0):2],\n hidden[1:hidden.size(0):2]], 2)\n # add by wchen, only use the last \"self.num_layers\" encoder layers' final hidden\n enc_layers = hidden.size(0)\n if enc_layers >= self.num_layers:\n hidden = hidden[enc_layers - self.num_layers:]\n else:\n # broadcast the hidden of the last encoder layer to initialize every layer of the decoder\n hidden = [hidden[-1]] * self.num_layers\n hidden = torch.stack(hidden, dim=0)\n if hidden.dim() == 2:\n hidden = hidden.unsqueeze(0)\n return hidden\n\n if isinstance(encoder_final, tuple): # LSTM\n self.state[\"hidden\"] = tuple([_fix_enc_hidden(enc_hid)\n for enc_hid in encoder_final])\n else: # GRU\n self.state[\"hidden\"] = (_fix_enc_hidden(encoder_final), )\n\n # Init the input feed.\n batch_size = self.state[\"hidden\"][0].size(1)\n h_size = (batch_size, self.hidden_size)\n self.state[\"input_feed\"] = \\\n self.state[\"hidden\"][0].data.new(*h_size).zero_().unsqueeze(0)\n self.state[\"coverage\"] = None\n # add for review mechanism\n self.state[\"previous_hiddens\"] = []\n self.state[\"zero_vec\"] = self.state[\"hidden\"][0].data.new(*h_size).zero_()",
"def init_state(self, src, memory_bank, encoder_final):\n def _fix_enc_hidden(hidden):\n # The encoder hidden is (layers*directions) x batch x dim.\n # We need to convert it to layers x batch x (directions*dim).\n assert self.bidirectional_encoder\n if self.bidirectional_encoder:\n hidden = torch.cat([hidden[0:hidden.size(0):2],\n hidden[1:hidden.size(0):2]], 2)\n # add by wchen, only use the last \"self.num_layers\" encoder layers' final hidden\n enc_layers = hidden.size(0)\n if enc_layers >= self.num_layers:\n hidden = hidden[enc_layers - self.num_layers:]\n else:\n # broadcast the hidden of the last encoder layer to initialize every layer of the decoder\n hidden = [hidden[-1]] * self.num_layers\n hidden = torch.stack(hidden, dim=0)\n if hidden.dim() == 2:\n hidden = hidden.unsqueeze(0)\n return hidden\n\n if isinstance(encoder_final, tuple): # LSTM\n self.state[\"hidden\"] = tuple([_fix_enc_hidden(enc_hid)\n for enc_hid in encoder_final])\n else: # GRU\n self.state[\"hidden\"] = (_fix_enc_hidden(encoder_final), )\n\n # Init the input feed.\n batch_size = self.state[\"hidden\"][0].size(1)\n h_size = (batch_size, self.hidden_size)\n self.state[\"input_feed\"] = \\\n self.state[\"hidden\"][0].data.new(*h_size).zero_().unsqueeze(0)\n self.state[\"coverage\"] = None",
"def mlas_packb(B, K, N, transb_size, transb=True):\n return te.extern(\n (transb_size),\n [B],\n lambda ins, outs: tvm.tir.call_packed(\n \"tvm.contrib.mlas.gemm_packb\",\n N,\n K,\n K if transb else N,\n transb,\n ins[0],\n outs[0],\n ),\n name=\"PackedB\",\n )",
"def lstm_layer(\n input_size: int,\n hidden_size: int,\n num_layers: int = 1,\n batch_first: bool = True,\n forget_bias: float = 1.0,\n kernel_init: Initialization = Initialization.XavierGlorotUniform,\n bias_init: Initialization = Initialization.Zero,\n) -> torch.nn.Module:\n lstm = torch.nn.LSTM(input_size, hidden_size, num_layers, batch_first=batch_first)\n # Add forget_bias to forget gate bias\n for name, param in lstm.named_parameters():\n # Each weight and bias is a concatenation of 4 matrices\n if \"weight\" in name:\n for idx in range(4):\n block_size = param.shape[0] // 4\n _init_methods[kernel_init](\n param.data[idx * block_size : (idx + 1) * block_size]\n )\n if \"bias\" in name:\n for idx in range(4):\n block_size = param.shape[0] // 4\n _init_methods[bias_init](\n param.data[idx * block_size : (idx + 1) * block_size]\n )\n if idx == 1:\n param.data[idx * block_size : (idx + 1) * block_size].add_(\n forget_bias\n )\n return lstm",
"def create_hidden_layers(self):\n RNN_hidden_layers = nn.ModuleList([])\n input_dim = int(self.input_dim - len(self.embedding_dimensions) + np.sum(\n [output_dims[1] for output_dims in self.embedding_dimensions]))\n for layer in self.layers_info[:-1]:\n input_dim = self.create_and_append_layer(input_dim, layer, RNN_hidden_layers)\n self.input_dim_into_final_layer = input_dim\n return RNN_hidden_layers",
"def pack_weights(w_hid, b_hid, w_out, b_out, params):\n\tn_in, n_hid, n_out = params[0], params[1], params[2]\n\tg_j = hstack((reshape(w_hid,(1,n_in*n_hid)), \n\t\t reshape(b_hid,(1,n_hid)),\n\t\t reshape(w_out,(1,n_hid*n_out)),\n\t\t reshape(b_out,(1,n_out))))[0]\n\tg_j = array(g_j[0,:])[0]\n\treturn g_j",
"def head_stack(in_features, out_features, bn=True, p=0., actn=None):\n layers = [nn.BatchNorm1d(in_features)] if bn else []\n if p != 0:\n layers.append(nn.Dropout(p))\n layers.append(nn.Linear(in_features, out_features))\n if actn is not None:\n layers.append(actn)\n return layers",
"def make_lstm_weights_for_keras(\n weight_input_to_hidden, weight_hidden_to_hidden, bias_input_to_hidden, bias_hidden_to_hidden\n):\n return [\n weight_input_to_hidden.T,\n weight_hidden_to_hidden.T,\n bias_input_to_hidden + bias_hidden_to_hidden,\n ]",
"def initialize_hidden_state(self):\n initializer = tf.keras.initializers.Zeros()\n values = initializer(shape=(self.batch, self.units))\n\n return values",
"def __init__(self, input_dim, hidden_dim=20, num_layers=2, output_dim=1):\n super(LSTM, self).__init__()\n self.input_dim = input_dim\n self.hidden_dim = hidden_dim\n self.num_layers = num_layers\n self.output_dim = output_dim\n\n self.lstm = nn.LSTM(self.input_dim, self.hidden_dim, self.num_layers)\n \n self.fc_block = nn.Sequential(\n nn.Linear(self.hidden_dim, self.hidden_dim),\n nn.BatchNorm1d(self.hidden_dim),\n nn.ReLU(inplace=True),\n nn.Linear(self.hidden_dim, self.hidden_dim),\n nn.BatchNorm1d(self.hidden_dim),\n nn.ReLU(inplace=True),\n ) \n self.classifier = nn.Linear(self.hidden_dim, self.output_dim)",
"def Lstm(self, previous_hidden_memory_tuple, x):\n \n previous_hidden_state,c_prev=tf.unstack(previous_hidden_memory_tuple)\n \n #Input Gate\n i= tf.sigmoid(\n tf.matmul(x,self.Wi)+tf.matmul(previous_hidden_state,self.Ui) + self.bi \n )\n \n #Forget Gate\n f= tf.sigmoid(\n tf.matmul(x,self.Wf)+tf.matmul(previous_hidden_state,self.Uf) + self.bf \n )\n \n #Output Gate\n o= tf.sigmoid(\n tf.matmul(x,self.Wog)+tf.matmul(previous_hidden_state,self.Uog) + self.bog\n )\n \n #New Memory Cell\n c_= tf.nn.tanh(\n tf.matmul(x,self.Wc)+tf.matmul(previous_hidden_state,self.Uc) + self.bc \n ) \n \n #Final Memory cell\n c= f*c_prev + i*c_\n \n #Current Hidden state\n current_hidden_state = o*tf.nn.tanh(c)\n\n\n return tf.stack([current_hidden_state,c])",
"def get_hidden(self, layer):",
"def layer_maker(n_layers, n_nodes, activation, model, drop=None, d_rate=.5):\n\n # Creating the specified number of hidden layers with the specified number of nodes\n try:\n\n for x in range(1, n_layers + 1):\n model.add(LSTM(n_nodes, activation=activation, return_sequences=True))\n\n # Adds a Dropout layer after every Nth hidden layer (the 'drop' variable)\n if x % drop == 0:\n model.add(Dropout(d_rate))\n except:\n pass",
"def reshape_data(self):\n \n # In general, the arrays have dimensions of [batch_size, seq_len, feature_size]\n # to comply with the LSTM dimension handle\n # Initialize the tensor arrays:\n # inputs_swl: dim[batch_size, 1, 1]\n # contains the SWL values at only the initial time step as\n # initial input to the LSTM\n # inputs: dim[batch_size, forecast_horizon, input_size]\n # contains the input values with the order of: precipitation,\n # precipitation forecast, air temperature, air temperature\n # forecast, sunshine duration, sunshine duration forecast, relative humidity,\n # relative humidity forecast, wind velocity, wind velocity forecast,\n # forecast, well 5 pumping rate, well 5 pumping rate forecast,\n # well 6 pumping rate, well 6 pumping rate forecast\n # target: dim[batch_size, forecast_horizon, 1]\n # contains the target SWL values until time step t = t_init + forecast_horizon\n \n self.inputs_swl = torch.zeros(self.batch_size, 1, 1)\n self.inputs = torch.zeros(self.batch_size,self.cfg.forecast_horizon, self.cfg.input_size)\n self.target = torch.zeros(self.batch_size, self.cfg.forecast_horizon, 1)\n \n for i in range(self.batch_size):\n # Assign values to the inputs_swl tensor array using data from\n # tensor inp_swl at the same corresponding batch/sample index\n self.inputs_swl[i,0] = self.inp_swl[i]\n \n # Assign values to the inputs tensor array using data from tensors\n # inp_p, inp_t, inp_w5, and inp_w6, each at the corresponding batch/\n # sample index, and also the forecast at index + 1\n \n # The time steps covered range from t0 = 0 to t_end = t0 + forecast horizon\n for t in range(self.cfg.forecast_horizon):\n self.inputs[i,t] = torch.cat(\n (self.inp_p[i + t : i + self.cfg.in_p + self.cfg.in_p_forecast + t],\n self.inp_t[i + t : i + self.cfg.in_t + self.cfg.in_t_forecast + t],\n self.inp_sd[i + t : i + self.cfg.in_sd + self.cfg.in_sd_forecast + t],\n self.inp_rh[i + t : i + self.cfg.in_rh + self.cfg.in_rh_forecast + t],\n self.inp_wv[i + t : i + self.cfg.in_wv + self.cfg.in_wv_forecast + t])).squeeze()\n # Assign values to the target tensor array using data from tensor\n # inp_swl, offset by 1 time step\n self.target[i] = self.tar_swl[i + 1 : i + 1 + self.cfg.forecast_horizon]",
"def layer_maker(n_layers, n_nodes, activation, drop=None, d_rate=.5):\r\n \r\n # Creating the specified number of hidden layers with the specified number of nodes\r\n for x in range(1,n_layers+1):\r\n model.add(LSTM(n_nodes, activation=activation, return_sequences=True))\r\n\r\n # Adds a Dropout layer after every Nth hidden layer (the 'drop' variable)\r\n try:\r\n if x % drop == 0:\r\n model.add(Dropout(d_rate))\r\n except:\r\n pass",
"def _build_bidirectional_encoder(self, inputs, src_seq_lens):\n num_bi_layers = self._num_encoder_layers // 2\n num_bi_res_layers = self._num_encoder_res_layers // 2\n cell_fw = self._build_encoder_cell(num_bi_layers, num_bi_res_layers)\n cell_bw = self._build_encoder_cell(num_bi_layers, num_bi_res_layers)\n # bi_outputs.shape: \n # ([batch, max_time_src, num_units], [batch, max_time_src, num_units]) or \n # ([max_time_src, batch, num_units], [max_time_src, batch, num_units])\n # bi_states.shape: (\n # [state_tuple(c=[batch, num_units], h=[batch, num_units])]\n # * num_bi_layers ==> forward direction ,\n # [state_tuple(c=[batch, num_units], h=[batch, num_units])]\n # * num_bi_layers ==> backward direction\n # )\n bi_outputs, bi_states = tf.nn.bidirectional_dynamic_rnn(\n cell_fw,\n cell_bw,\n inputs,\n sequence_length=src_seq_lens,\n time_major=self._time_major,\n dtype=tf.float32,\n swap_memory=True)\n outputs = tf.concat(bi_outputs, -1)\n\n if num_bi_layers == 1:\n states = bi_states\n else:\n states = []\n # interleave forward and backward state_tuples, but total num of \n # state_tuples is still `num_encoder_layers`, the same as output of \n # `_unidirectional_encode`.\n for l in range(num_bi_layers):\n states.append(bi_states[0][l])\n states.append(bi_states[1][l])\n states = tuple(states)\n return outputs, states"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Unpack the packed hidden state of a BiLSTM s.t. the first dimension equals to the number of layers multiplied by the number of directions.
|
def unpack_bidirectional_lstm_state(state, num_directions=2):
batch_size = state.size(1)
new_hidden_dim = int(state.size(2) / num_directions)
return torch.stack(torch.split(state, new_hidden_dim, dim=2), dim=1).view(-1, batch_size, new_hidden_dim)
|
[
"def pack_bidirectional_lstm_state(state, num_layers):\n assert (len(state) == 2 * num_layers)\n _, batch_size, hidden_dim = state.size()\n layers = state.view(num_layers, 2, batch_size, hidden_dim).transpose(1, 2).contiguous()\n state = layers.view(num_layers, batch_size, -1)\n return state",
"def decode_step(self, prev_state, prev_tokens, **flags):\n \n prev_gru0_state, enc_seq, enc_mask, _ = prev_state\n attn, attn_prob = self.attn(enc_seq, prev_gru0_state, enc_mask)\n \n x = self.emb_out(prev_tokens)\n assert len(x.shape) == 2 and len(attn.shape) == 2\n \n x = torch.cat([attn, x], dim=-1)\n x = self.dec0(x, prev_gru0_state)\n \n new_dec_state = [x, enc_seq, enc_mask, attn_prob]\n output_logits = self.logits(x)\n \n return new_dec_state, output_logits",
"def decode_step(self, prev_state, prev_tokens, **flags):\n \n x = self.emb_out(prev_tokens)\n x = self.dec0(x, prev_state[0])\n return [x], self.logits(x)",
"def layered_state_tuple(num_layers: int, batch_size: int, hidden_size: int) -> tuple:\r\n hidden_state_shape = [num_layers, batch_size, hidden_size]\r\n hidden_state_placeholder = tf.placeholder(\r\n dtype=tf.float32,\r\n shape=[num_layers, batch_size, hidden_size],\r\n name=\"hidden_state_placeholder\")\r\n unpacked_hidden_state = tf.unstack(hidden_state_placeholder, axis=0, name=\"unpack_hidden_state\")\r\n hidden_state = tuple(unpacked_hidden_state)\r\n return hidden_state, hidden_state_placeholder, hidden_state_shape",
"def _unpack_batch_channel(data, old_shape, unpack_transpose=False):\n if unpack_transpose:\n data = op.transpose(data, axes=(0, 4, 1, 5, 2, 3))\n data = op.reshape(data, newshape=old_shape)\n return data",
"def init_hidden(self):\n weight = next(self.parameters())\n nlayers = self.eta_nlayers\n nhid = self.eta_hidden_size\n return (weight.new_zeros(nlayers, 1, nhid), weight.new_zeros(nlayers, 1, nhid))",
"def get_output(self, input_, mask_, hidden_init):\n # input_ are (n_batch, n_timesteps, n_features)\n # change to (n_timesteps, n_batch, n_features)\n input_ = input_.dimshuffle(1, 0, 2)\n # mask_ are (n_batch, n_timesteps)\n masks = masks.dimshuffle(1, 0, 'x')\n sequence_length = input_.shape[0]\n batch_num = input_.shape[1]\n\n # precompute input\n if self.precompute:\n additional_dims = tuple(input.shape[k] for k in range(2, input.ndim)) # (output_dim,)\n input = T.reshape(input, (sequence_length*batch_num,) + additional_dims)\n input = T.dot(input, self.W)\n additional_dims = tuple(input.shape[k] for k in range(1, input.ndim)) # (output_dim,)\n input = T.reshape(input, (sequence_length, batch_num,) + additional_dims)\n\n # step function\n def step(input_, hidden):\n if self.precompute:\n return self.out_activation.get_output(input_ + T.dot(hidden, self.U) + self.b)\n else:\n return self.out_activation.get_output(T.dot(input_, self.W) + T.dot(hidden, self.U) + self.b)\n\n # step function, with mask\n def step_masked(input_, mask_, hidden):\n hidden_computed = step(input_, hidden)\n return T.switch(mask_, hidden_computed, hidden)\n\n # main operation\n if self.unroll:\n counter = range(self.gradient_steps)\n if self.backward:\n counter = counter[::-1] # reversed index\n iter_output = []\n outputs_info = [hidden_init]\n for index in counter:\n step_input = [input_[index], mask_[index]] + outputs_info\n step_output = step_masked(*step_input)\n iter_output.append(step_output)\n outputs_info = [iter_output[-1]]\n hidden_output = T.stack(iter_output, axis=0)\n\n else:\n hidden_output = theano.scan(fn=step_masked,\n sequences=[input_, mask_],\n outputs_info=[hidden_init],\n go_backwards=self.backward,\n n_steps = None,\n truncate_gradient=self.gradient_steps)[0] # only need outputs, not updates\n\n # computed output are (n_timesteps, n_batch, n_features)\n # select only required\n if self.output_return_index is None:\n hidden_output_return = hidden_output\n else:\n hidden_output_return = hidden_output[self.output_return_index]\n # change to (n_batch, n_timesteps, n_features)\n hidden_output_return = hidden_output_return.dimshuffle(1, 0, *range(2, hidden_output_return.ndim))\n\n # backward order straight\n if self.backward:\n hidden_output_return = hidden_output_return[:, ::-1]\n\n return hidden_output_return",
"def unroll_state_transitions(self):\n\n states = ()\n actions = ()\n next_states = ()\n rewards = ()\n dones = ()\n Q_sa = ()\n\n for episode in self.rollout_memory:\n ep_states, ep_actions, ep_next_states, ep_rewards, ep_dones, ep_Q_s_a = zip(\n *episode)\n\n states += ep_states\n actions += ep_actions\n next_states += ep_next_states\n rewards += ep_rewards\n dones += ep_dones\n Q_sa += ep_Q_s_a\n\n states = np.asarray(states)\n actions = np.asarray(actions)\n next_states = np.asarray(next_states)\n rewards = np.asarray(rewards)\n dones = np.asarray(dones, dtype=int)\n Q_sa = np.asarray(Q_sa).reshape(-1, 1)\n\n return states, actions, next_states, rewards, dones, Q_sa",
"def _unpack_rnn_state_into_tuples(self, rnn_state):\n rnn_state_tuples = []\n cur_state_pos = 0\n for cell in self.component_cells:\n total_state_size = sum(cell.state_size)\n cur_state = tf.slice(rnn_state, [0, cur_state_pos],\n [-1, total_state_size])\n cur_state_tuple = tf.split(value=cur_state, num_or_size_splits=2,\n axis=1)\n rnn_state_tuples.append(cur_state_tuple)\n cur_state_pos += total_state_size\n return rnn_state_tuples",
"def init_hidden(self, batch_size):\n if self.bidirectional:\n ##################\n # YOUR CODE HERE\n # A bidirectional RNN has more hidden layers than a regular one-way RNN.\n # For each \"left-to-right\" layer there is one \"right-to-left\" layer.\n ##################\n\n raise NotImplementedError\n\n else:\n rnn_layer_number = self.rnn_layer_number\n\n if self.cell_type == \"RNN_TANH\":\n hidden = torch.randn(rnn_layer_number, batch_size, self.rnn_layer_size)\n self.hidden_layer = hidden\n\n elif self.cell_type == \"LSTM\":\n ##################\n # YOUR CODE HERE\n # LSTM layer uses one more layer tier than basic RNN layer, in which\n # it stores the memory state of the cells. The nn.LSTM class handles the\n # hidden and cell layer in one tuple.\n ##################\n\n raise NotImplementedError",
"def reset_hidden(self, hidden_state, done):\n if hidden_state.dim() != done.dim():\n if done.dim() == 2:\n done = done.unsqueeze(0)\n elif done.dim() == 1:\n done = done.unsqueeze(0).unsqueeze(2)\n hidden_state = hidden_state * (1 - done)\n return hidden_state",
"def init_state(self, src, memory_bank, encoder_final):\n def _fix_enc_hidden(hidden):\n # The encoder hidden is (layers*directions) x batch x dim.\n # We need to convert it to layers x batch x (directions*dim).\n if self.bidirectional_encoder:\n hidden = torch.cat([hidden[0:hidden.size(0):2],\n hidden[1:hidden.size(0):2]], 2)\n # add by wchen, only use the last \"self.num_layers\" encoder layers' final hidden\n enc_layers = hidden.size(0)\n if enc_layers >= self.num_layers:\n hidden = hidden[enc_layers - self.num_layers:]\n else:\n # broadcast the hidden of the last encoder layer to initialize every layer of the decoder\n hidden = [hidden[-1]] * self.num_layers\n hidden = torch.stack(hidden, dim=0)\n if hidden.dim() == 2:\n hidden = hidden.unsqueeze(0)\n return hidden\n\n if isinstance(encoder_final, tuple): # LSTM\n self.state[\"hidden\"] = tuple([_fix_enc_hidden(enc_hid)\n for enc_hid in encoder_final])\n else: # GRU\n self.state[\"hidden\"] = (_fix_enc_hidden(encoder_final), )\n\n # Init the input feed.\n batch_size = self.state[\"hidden\"][0].size(1)\n h_size = (batch_size, self.hidden_size)\n self.state[\"input_feed\"] = \\\n self.state[\"hidden\"][0].data.new(*h_size).zero_().unsqueeze(0)\n self.state[\"coverage\"] = None\n # add for review mechanism\n self.state[\"previous_hiddens\"] = []\n self.state[\"zero_vec\"] = self.state[\"hidden\"][0].data.new(*h_size).zero_()",
"def unpack(self, layer_tars, last_layer=None):\n if (last_layer is None):\n last_layer = sys.maxsize\n INFO(\"flattening image\")\n self.unpack_clear()\n self.unpack_layers(layer_tars, last_layer)\n self.unpack_init()",
"def reshape_data(self):\n \n # In general, the arrays have dimensions of [batch_size, seq_len, feature_size]\n # to comply with the LSTM dimension handle\n # Initialize the tensor arrays:\n # inputs_swl: dim[batch_size, 1, 1]\n # contains the SWL values at only the initial time step as\n # initial input to the LSTM\n # inputs: dim[batch_size, forecast_horizon, input_size]\n # contains the input values with the order of: precipitation,\n # precipitation forecast, air temperature, air temperature\n # forecast, sunshine duration, sunshine duration forecast, relative humidity,\n # relative humidity forecast, wind velocity, wind velocity forecast,\n # forecast, well 5 pumping rate, well 5 pumping rate forecast,\n # well 6 pumping rate, well 6 pumping rate forecast\n # target: dim[batch_size, forecast_horizon, 1]\n # contains the target SWL values until time step t = t_init + forecast_horizon\n \n self.inputs_swl = torch.zeros(self.batch_size, 1, 1)\n self.inputs = torch.zeros(self.batch_size,self.cfg.forecast_horizon, self.cfg.input_size)\n self.target = torch.zeros(self.batch_size, self.cfg.forecast_horizon, 1)\n \n for i in range(self.batch_size):\n # Assign values to the inputs_swl tensor array using data from\n # tensor inp_swl at the same corresponding batch/sample index\n self.inputs_swl[i,0] = self.inp_swl[i]\n \n # Assign values to the inputs tensor array using data from tensors\n # inp_p, inp_t, inp_w5, and inp_w6, each at the corresponding batch/\n # sample index, and also the forecast at index + 1\n \n # The time steps covered range from t0 = 0 to t_end = t0 + forecast horizon\n for t in range(self.cfg.forecast_horizon):\n self.inputs[i,t] = torch.cat(\n (self.inp_p[i + t : i + self.cfg.in_p + self.cfg.in_p_forecast + t],\n self.inp_t[i + t : i + self.cfg.in_t + self.cfg.in_t_forecast + t],\n self.inp_sd[i + t : i + self.cfg.in_sd + self.cfg.in_sd_forecast + t],\n self.inp_rh[i + t : i + self.cfg.in_rh + self.cfg.in_rh_forecast + t],\n self.inp_wv[i + t : i + self.cfg.in_wv + self.cfg.in_wv_forecast + t])).squeeze()\n # Assign values to the target tensor array using data from tensor\n # inp_swl, offset by 1 time step\n self.target[i] = self.tar_swl[i + 1 : i + 1 + self.cfg.forecast_horizon]",
"def init_state(self, src, memory_bank, encoder_final):\n def _fix_enc_hidden(hidden):\n # The encoder hidden is (layers*directions) x batch x dim.\n # We need to convert it to layers x batch x (directions*dim).\n assert self.bidirectional_encoder\n if self.bidirectional_encoder:\n hidden = torch.cat([hidden[0:hidden.size(0):2],\n hidden[1:hidden.size(0):2]], 2)\n # add by wchen, only use the last \"self.num_layers\" encoder layers' final hidden\n enc_layers = hidden.size(0)\n if enc_layers >= self.num_layers:\n hidden = hidden[enc_layers - self.num_layers:]\n else:\n # broadcast the hidden of the last encoder layer to initialize every layer of the decoder\n hidden = [hidden[-1]] * self.num_layers\n hidden = torch.stack(hidden, dim=0)\n if hidden.dim() == 2:\n hidden = hidden.unsqueeze(0)\n return hidden\n\n if isinstance(encoder_final, tuple): # LSTM\n self.state[\"hidden\"] = tuple([_fix_enc_hidden(enc_hid)\n for enc_hid in encoder_final])\n else: # GRU\n self.state[\"hidden\"] = (_fix_enc_hidden(encoder_final), )\n\n # Init the input feed.\n batch_size = self.state[\"hidden\"][0].size(1)\n h_size = (batch_size, self.hidden_size)\n self.state[\"input_feed\"] = \\\n self.state[\"hidden\"][0].data.new(*h_size).zero_().unsqueeze(0)\n self.state[\"coverage\"] = None",
"def decoder_state(self, z):\r\n\r\n batch_size = z.size(0)\r\n\r\n state_shape = (batch_size, self.hidden_size)\r\n \r\n #raise NotImplementedError()\r\n c0 = variable(torch.zeros(state_shape))\r\n c0 = cuda(c0)\r\n \r\n return z, c0",
"def unpak(self, w):\n\n # Check arguments for consistency\n errstring = self.consist('mlp')\n if errstring != None:\n raise Exception(errstring)\n \n if self.nwts != len(w):\n raise Exception('Invalid weight vector length')\n\n nin = self.nin\n nhidden = self.nhidden\n nout = self.nout\n\n mark1 = nin*nhidden\n self.w1 = np.reshape(w[0:mark1], (nin, nhidden), order='F')\n mark2 = mark1 + nhidden\n self.b1 = np.reshape(w[mark1:mark2], (1, nhidden), order='F')\n mark3 = mark2 + nhidden*nout\n self.w2 = np.reshape(w[mark2:mark3], (nhidden, nout), order='F')\n mark4 = mark3 + nout\n self.b2 = np.reshape(w[mark3:mark4], (1, nout), order='F')",
"def Lstm(self, previous_hidden_memory_tuple, x):\n \n previous_hidden_state,c_prev=tf.unstack(previous_hidden_memory_tuple)\n \n #Input Gate\n i= tf.sigmoid(\n tf.matmul(x,self.Wi)+tf.matmul(previous_hidden_state,self.Ui) + self.bi \n )\n \n #Forget Gate\n f= tf.sigmoid(\n tf.matmul(x,self.Wf)+tf.matmul(previous_hidden_state,self.Uf) + self.bf \n )\n \n #Output Gate\n o= tf.sigmoid(\n tf.matmul(x,self.Wog)+tf.matmul(previous_hidden_state,self.Uog) + self.bog\n )\n \n #New Memory Cell\n c_= tf.nn.tanh(\n tf.matmul(x,self.Wc)+tf.matmul(previous_hidden_state,self.Uc) + self.bc \n ) \n \n #Final Memory cell\n c= f*c_prev + i*c_\n \n #Current Hidden state\n current_hidden_state = o*tf.nn.tanh(c)\n\n\n return tf.stack([current_hidden_state,c])",
"def _decode_step(self, states: List[ModelState]) -> Tuple[mx.nd.NDArray, mx.nd.NDArray, List[ModelState]]:\n model_probs, model_attention_scores = [], []\n for m, s in zip(self.models, states):\n probs, attention_scores, s.source_dynamic, s.decoder_hidden, s.decoder_states = m.run_decoder(\n s.source_encoded,\n s.source_dynamic,\n s.source_length,\n s.prev_target_word_id,\n s.decoder_hidden,\n s.decoder_states,\n s.bucket_key)\n model_probs.append(probs)\n model_attention_scores.append(attention_scores)\n probs, attention_scores = self._combine_predictions(model_probs, model_attention_scores)\n return probs, attention_scores, states"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Perform list or list_details action with given params and validates result.
|
def _list_by_param_value_and_assert(self, params, with_detail=False):
if with_detail:
fetched_vol_list = \
self.client.list_volumes(detail=True, params=params)
else:
fetched_vol_list = self.client.list_volumes(params=params)
# Validating params of fetched volumes
# In v2, only list detail view includes items in params.
# In v1, list view and list detail view are same. So the
# following check should be run when 'with_detail' is True
# or v1 tests.
if with_detail or self._api_version == 1:
for volume in fetched_vol_list:
for key in params:
msg = "Failed to list volumes %s by %s" % \
('details' if with_detail else '', key)
if key == 'metadata':
self.assertThat(
volume[key].items(),
matchers.ContainsAll(params[key].items()),
msg)
else:
self.assertEqual(params[key], volume[key], msg)
|
[
"def _get_list(self, list_title, list_id, action_result):\n endpoint = 'list/'\n params = {}\n if not list_id:\n params['name'] = list_title\n ret_val, found_list_info = self._make_rest_call(endpoint, action_result, method='get', params=params)\n\n if phantom.is_fail(ret_val):\n logout_error = self._logout(action_result)\n if logout_error:\n self.debug_print(logout_error)\n return RetVal(action_result.get_status(), None)\n\n list_id = found_list_info.get('feed', {}).get('entry', {}).get('id')\n\n if not list_id:\n self._logout(action_result)\n return RetVal(action_result.set_status(phantom.APP_ERROR, 'Could not find list by title'), None)\n\n endpoint = f'{endpoint}{list_id}'\n\n ret_val, found_list_data = self._make_rest_call(endpoint, action_result, method='get', params=params)\n\n if phantom.is_fail(ret_val):\n logout_error = self._logout(action_result)\n if logout_error:\n self.debug_print(logout_error)\n return RetVal(action_result.get_status(), None)\n\n return RetVal(phantom.APP_SUCCESS, found_list_data)",
"def do_list(self, args):\n r = requests.get(self.api_url + \"rs\")\n self.print_result(r)\n if r.status_code == 200:\n self.rs = json.loads(r.text)\n for n, item in enumerate(self.rs, 1):\n print(\"{0} {1}\".format(n, item))",
"def list_detail(self, request, *args, **kwargs):\n queryset = self.filter_queryset(self.get_queryset())\n serializer = ProductDetailSerializer(queryset, many=True)\n page = self.paginate_queryset(queryset)\n if page is not None:\n return self.get_paginated_response(serializer.data)\n return Response(serializer.data)",
"def test_ok_list_result(self):\n process_result = process_response(self.resp_ok_list, is_detail=False)\n self.assertEqual(process_result[\"result\"], 0)",
"def admin_find_action_list(\n x_additional_headers: Optional[Dict[str, str]] = None, **kwargs\n):\n request = AdminFindActionList.create()\n return run_request(request, additional_headers=x_additional_headers, **kwargs)",
"def list_detail(self, request, *args, **kwargs):\n queryset = self.filter_queryset(self.get_queryset())\n serializer = SupplierDetailSerializer(queryset, many=True)\n page = self.paginate_queryset(queryset)\n if page is not None:\n return self.get_paginated_response(serializer.data)\n return Response(serializer.data)",
"async def admin_find_action_list_async(\n x_additional_headers: Optional[Dict[str, str]] = None, **kwargs\n):\n request = AdminFindActionList.create()\n return await run_request_async(\n request, additional_headers=x_additional_headers, **kwargs\n )",
"def do_list(self, _):\n self._print_list()",
"def list_details(list_id):\n try:\n details = db.lists.find_one({'_id': list_id})\n\n if not details:\n return util.response.error(\n status_code=404,\n message='The specified list ID does not exist.',\n failure='failure_nonexistent_list',\n )\n\n return util.response.success({\n 'list': details,\n })\n except:\n return util.response.undefined_error()",
"def tasks(list_id):\n db_connection = connect_to_database() # connect to db\n\n # check if requested list belongs to the user\n cursor = db_connection.cursor()\n cursor.callproc('getListUserId', [list_id, ])\n rtn = cursor.fetchall()\n cursor.close()\n if rtn[0][0] != current_user.id:\n print(rtn)\n db_connection.close() # close connection before returning\n webapp.logger.warning(\"Invalid access to view list. userid: %s\", current_user.id)\n return redirect(url_for('invalid_access'))\n\n context = {} # create context dictionary\n\n cursor = db_connection.cursor()\n cursor.callproc('getTasks', [list_id, ])\n rtn = cursor.fetchall() # run query\n cursor.close()\n context = {'list_name': rtn[0][0], 'list_desc': rtn[0][1], 'list_id': list_id}\n\n cursor = db_connection.cursor()\n cursor.callproc('returnTasks', [list_id, ])\n rtn = cursor.fetchall()\n cursor.close()\n context['rows'] = rtn # rtn = tasks data\n\n query = \"SELECT * from dataTypes\" # get list of all types of tasks\n cursor = execute_query(db_connection, query)\n rtn = cursor.fetchall()\n cursor.close()\n context['taskTypes'] = rtn\n\n db_connection.close() # close connection before returning\n webapp.logger.info(\"View list. User_id: %s\", current_user.id)\n return render_template('tasks.html', context=context)",
"def rest_get_list(cls, query_params):\n\n def apply_search(query):\n search_columns = getattr(cls, '_rest_search_columns', None)\n if not search_columns or not 'search' in query_params:\n return query\n\n search = query_params['search'].lower()\n\n if len(search_columns) == 1:\n col = search_columns[0]\n search_filter = func.lower(col).like('%' + search + '%')\n else: # > 1\n clauses = [func.lower(col).like('%' + search + '%') for col in search_columns]\n search_filter = or_(*clauses)\n\n return query.filter(search_filter)\n\n def apply_filters(query):\n if 'filters' not in query_params:\n return query\n\n filters = query_params['filters']\n\n for key, val in filters.items():\n op, field_name = key.split('_', 1)\n\n try:\n field = getattr(cls, field_name)\n except AttributeError:\n log.warn('RestMixin.rest_get_list(): filter \"%s=%s\": unknown attribute %s',\n key, val, field_name)\n continue\n\n if op == 'e':\n query = query.filter(field == val)\n elif op == 'n':\n query = query.filter(or_(field == val, field == None))\n elif op == 'l':\n query = query.filter(func.lower(field).like('%' + val.lower() + '%'))\n elif op == 's':\n query = query.filter(func.lower(field).like(val.lower() + '%'))\n else:\n log.error('get_for_rest_grid: filter \"%s=%s\": unknown op: %s' % (key, val, op))\n\n return query\n\n def apply_order(query):\n if 'order' not in query_params:\n return query\n\n order = query_params['order']\n order_split = order['col'].split('.')\n\n try:\n order_attr = getattr(cls, order_split[0])\n except AttributeError:\n log.error('get_for_rest_grid: sort key %s: unknown attribute %s.%s' % (order['col'], cls.__name__, order['col']))\n return query\n\n for el in order_split[1:]:\n if not isinstance(order_attr.property, RelationshipProperty):\n log.error('get_for_rest_grid: sort key %s: not a RelationshipProperty: %s' % (order['col'], str(order_attr.property)))\n return query\n\n entity = order_attr.property.mapper.entity\n\n try:\n order_attr = getattr(entity, el)\n except AttributeError:\n log.error('get_for_rest_grid: sort key %s: unknown attribute %s.%s' % (order['col'], entity.__name__, el))\n return query\n\n if not isinstance(order_attr.property, ColumnProperty):\n log.error('get_for_rest_grid: sort key %s: not a ColumnProperty: %s' % (order['col'], str(order_attr.property)))\n return query\n\n return query.order_by(desc(order_attr) if order['dir'] == 'desc' else order_attr)\n\n def apply_limit(query):\n if 'limit' in query_params:\n query = query.limit(query_params['limit'])\n\n if 'start' in query_params:\n query = query.offset(query_params['start'])\n\n return query\n\n # select * from (select * from users limit 10 offset 10) as u left join files f on u.id = f.user_id\n # http://docs.sqlalchemy.org/en/rel_1_0/orm/tutorial.html#using-subqueries\n\n session = config.sqlalchemy_session\n\n q_inner = session().query(cls)\n q_inner = cls._rest_get_inner_query(session, q_inner, query_params)\n q_inner = apply_search(q_inner)\n q_inner = apply_filters(q_inner)\n q_count = q_inner # count() query should not have ORDER BY\n q_inner = apply_order(q_inner)\n q_inner = apply_limit(q_inner)\n\n q_joined = q_inner.from_self()\n q_joined = cls._rest_get_joined_query(session, q_joined, query_params)\n q_joined = apply_order(q_joined)\n\n return q_count.count(), q_joined.all()",
"def showList():\n params = request.args\n required_param = ['searchType', 'email']\n for r in required_param:\n if r not in params.keys():\n flash('A parameter is missing.')\n return redirect('/')\n type = request.args.get('searchType')\n email = request.args.get('email')\n logging.info('Parameters: {}, {}'.format(type, email))\n\n qry = Search.query((ndb.AND(Search.email == email,\n Search.type == type))).fetch()\n mydata = []\n for each in qry:\n datadic = {}\n datadic['value'] = each.value\n datadic['plot'] = each.plot\n datadic['counter'] = each.counter\n mydata.append(datadic)\n\n # set response\n json_response = {}\n json_response['user'] = email\n json_response['search type'] = type\n json_response['data'] = mydata\n json_response['status'] = 'OK'\n json_response['message'] = 'Successfully retourned the resource'\n risp = make_response(json.dumps(json_response, ensure_ascii=True), 200)\n risp.headers['content-type'] = 'application/json'\n return risp",
"def test_investigation_result_list_command(requests_mock, mocker):\n MOCK_RESULT_LIST = load_test_data('./test_data/result_list_command_mock.json')\n from TrendMicroApex import investigation_result_list_command\n\n requests_mock.put(f'{MOCK_URL}/WebApp/OSCE_iES/OsceIes/ApiEntry', json=MOCK_RESULT_LIST)\n mocker.patch.object(client, 'create_jwt_token', return_value=\"fake_token\")\n args = {\n 'scan_type': 'YARA rule file'\n }\n response = investigation_result_list_command(client, args)\n\n outputs = response.outputs\n assert outputs\n assert len(outputs) == 2\n assert 'Meta' not in outputs # check that unnecessary fields was removed from the response\n assert 'Investigation result list' in response.readable_output\n assert outputs[0].get('status') == 'Complete'\n assert outputs[0].get('submitTime') == '2020-07-26T17:02:03+00:00' # check that time values were parsed\n assert response.outputs_prefix == 'TrendMicroApex.InvestigationResult'",
"def test_list_operations(self):\n pass",
"def query():\n if request.method == 'GET':\n print(\"**************************query**************************\")\n args = request.args\n forms = request.form\n #print(\"forms: \" + str(forms.to_dict()))\n #print(\"getlist('HousingType')\" + str(args.getlist('HousingType')))\n for k, v in args.items():\n #print(f\"{k}: {v} (if there is a list, you will only see first item)\")\n print(f\"{k}: \" + str(args.getlist(k)))\n args['search_string']\n # access as a dictionary and key = 'search_string'\n # but now because there can be multiple checkboxes, need to use args.getlist('param_name')\n\n # package data to send for backend seaarch and\n # also persistent search and filters in saved_options\n saved_options = {}\n search = query_helper(args, saved_options, 'search_string', '', take_first_element=True)\n housingType = query_helper(args, saved_options, 'HousingType', [])\n sellOrRent = query_helper(args, saved_options, 'sellOrRent', [])\n petsAllowed = query_helper(args, saved_options, 'petsAllowed', [])\n\n #if they type nothing and choose no filters, show all listings\n if not (search or housingType or sellOrRent or petsAllowed):\n all_listings = db.session.query(Listings)\n all_listings = all_listings.filter(Listings.adminAppr == 1)\n results_list_of_dicts = postMaker(all_listings)\n else:\n results = backendSearch(search_string=search, housingType=housingType, sellOrRent=sellOrRent, petsAllowed=petsAllowed)\n # returns a list of dictionaries matching images with associated posts\n results_list_of_dicts = postMaker(results)\n #pretty_print_results_dictionaries_list(results_list_of_dicts)\n\n return results_list_of_dicts, saved_options",
"def _call_api(amazon, params):\n return amazon.ItemLookup(**params)",
"def _validate_list_params(self, params):\n if 'workspace' not in params and 'workspaces' not in params:\n raise ValueError('One of \"workspace\" or \"workspaces\" field required to list sets')\n\n if params.get('include_set_item_info', 0) not in [0, 1]:\n raise ValueError('\"include_set_item_info\" field must be set to 0 or 1')",
"def list(ctx, debug, remote) -> None:\n if ctx.obj is None:\n ctx.obj = {}\n ctx.obj['DEBUG'] = debug\n ctx.obj['REMOTE'] = remote\n _current_args = \" \".join(sys.argv)\n if not (\"data-products\" in _current_args or \"code-runs\" in _current_args):\n ctx.invoke(data_products)\n ctx.invoke(code_runs)",
"def get_queryset(self):\n queryset = Parliament1.objects.all()\n id = self.request.query_params.get(\"mp\")\n pp = self.request.query_params.get(\"pp\")\n dob = self.request.query_params.get(\"dob\")\n if id is not None:\n # endpoint: ?mp=21\n queryset = queryset.filter(id=id) # return filtered by id\n return queryset\n if pp is not None:\n # endpoint: ?mp=21\n queryset = queryset.filter(pp=pp) # return filtered by pp\n return queryset\n if dob is not None:\n queryset = queryset.filter(dob=dob) # return filtered by dob\n return queryset\n return queryset # return whole list"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Computes HPDI (Highest Posterior Density Interval), which is the inteval of minimum width that includes the given `probability` (or proportion of the numbers) The following code is based on from `hpd` function from
|
def hpdi(values, probability):
values = np.sort(values)
n = len(values)
interval_idx_inc = int(np.floor(probability * n))
n_intervals = n - interval_idx_inc
interval_width = values[interval_idx_inc:] - values[:n_intervals]
if len(interval_width) == 0:
raise ValueError("Too few elements for interval calculation. ")
min_idx = np.argmin(interval_width)
hdi_min = values[min_idx]
hdi_max = values[min_idx + interval_idx_inc]
return (hdi_min, hdi_max)
|
[
"def highest_density_interval(samples, mass=.95):\n _samples = np.asarray(sorted(samples))\n n = len(_samples)\n\n interval_idx_inc = int(np.floor(mass * n))\n n_intervals = n - interval_idx_inc\n interval_width = _samples[interval_idx_inc:] - _samples[:n_intervals]\n\n if len(interval_width) == 0:\n raise ValueError('Too few elements for interval calculation')\n\n min_idx = np.argmin(interval_width)\n hdi_min = _samples[min_idx]\n hdi_max = _samples[min_idx + interval_idx_inc]\n return hdi_min, hdi_max",
"def hdi(self, alpha=.05):\n credible_mass = 1 - alpha\n try:\n _hdi = highest_density_interval(self.data, credible_mass)\n return (round(_hdi[0], 4), round(_hdi[1], 4))\n except Exception as e:\n logger.warn(e)\n return (None, None)",
"def EntropyFromProbabilityDistribution(distribution):\n\n if not isinstance(distribution, collections.Iterable):\n HX = -1\n\n # Check the sum of probabilities is 1.0\n elif (round(sum(distribution), 2) != 1.0):\n HX = -1\n\n # Check for negative probabilities\n elif (min(distribution) < 0.0):\n HX = -1\n\n else:\n HX = 0\n\n for i in range(0, len(distribution)):\n Px = distribution[i]\n\n if (Px > 0):\n HX = HX - Px * math.log(Px, 2)\n\n return (HX)",
"def d_hsi(d):\n if 0.05 <= d <= 0.1:\n return (d-0.05)*1/0.05\n elif 0.1 < d <= 0.3:\n return 1\n elif 0.3 < d <= 0.35:\n return 1 - (d-0.3)*0.6/0.05\n elif 0.35 < d <= 0.66:\n return 0.4\n elif 0.66 <= d <= 0.71:\n return 0.4 - (d-0.66)*0.4/0.05\n else:\n return 0",
"def EntropyFromSampleDistribution(distribution):\n\n if not isinstance(distribution, collections.Iterable):\n HX = -1\n\n elif len(distribution) < 1:\n HX = -1\n\n else:\n sampleSize = len(distribution)\n\n HX = 0\n\n for frequency in collections.Counter(sorted(distribution)).values():\n Px = float(frequency) / sampleSize\n\n if (Px > 0.0):\n HX = HX - Px * math.log(Px, 2)\n\n return (HX)",
"def entropy1d(x, binrule):\n p, be = np.histogram(x, bins=binrule, density=True)\n r = be[1:] - be[:-1]\n P = p * r\n H = -(P * np.log2(P)).sum()\n\n return H, be",
"def EntropyFromFrequencyDistribution(distribution):\n\n if not isinstance(distribution, collections.Iterable):\n HX = -1\n\n elif len(distribution) < 1:\n HX = -1\n\n elif (min(distribution) < 0.0):\n HX = -1\n\n else:\n\n HX = 0\n\n totalFrequency = sum(distribution)\n\n for i in range(0, len(distribution)):\n Px = float(distribution[i]) / totalFrequency\n\n if (Px > 0.0):\n HX = HX - Px * math.log(Px, 2)\n\n return (HX)",
"def pH_H():\n Hydrogen_ion_concentration = float(app.question('Hydrogen Ion Concentration',\"Please enter as a number (e.g '1.890') the hydrogen ion concentration\"))\n pH = -1* (math.log10(Hydrogen_ion_concentration))\n print(\"pH\",pH)\n return pH",
"def pdf_entropy(density_df, input_density_df,\n pseudocount, input_pseudocount,\n min_density_threshold=0):\n\n df_indices = density_df.index\n dfi_indices = input_density_df.index\n missing = set(df_indices) - set(dfi_indices)\n\n input_density_df = input_density_df.append(input_density_df.ix[missing])\n\n pdf = calculate_pdf(density_df, pseudocount, min_density_threshold)\n input_pdf = calculate_pdf(\n input_density_df, input_pseudocount, min_density_threshold\n )\n\n en = pdf.multiply(np.log2(pdf.div(input_pdf)))\n return en",
"def thickness_halsey(pressure):\n return 0.354 * ((-5) / numpy.log(pressure))**0.333",
"def hpdLocalOffset( hpd, counterdict ):\n algstr = 'RichHPDImageSummary/RICH_HPD_' + str(hpd)\n xarr = counterFromDict(algstr+'_XOffset',counterdict)\n yarr = counterFromDict(algstr+'_YOffset',counterdict)\n if xarr[0] and yarr[0]:\n return ( True, xarr[1]/xarr[2],yarr[1]/yarr[2] )\n else:\n return ( False,0,0 )",
"def get_probs(state, std):\n\n # Get the index of the state next to 3*std\n # Check if it\n top_border = state + 3 * std\n if top_border[0] > np.pi:\n top_border -= 2 * np.pi\n\n bot_border = state - 3 * std\n if bot_border[0] < -np.pi:\n bot_border += 2 * np.pi\n\n max_index = discretize_index(top_border)[0]\n min_index = discretize_index(bot_border)[0]\n\n # if we go from 3.1 to -3.1 its only a small step\n # so we have to go from top index to bot index\n if top_border[0] < bot_border[0]:\n interval_1 = np.arange(min_index, len(state_space[0]))\n interval_2 = np.arange(0, max_index)\n i_interval = np.concatenate((interval_1, interval_2))\n else:\n i_interval = np.arange(min_index,max_index+1)\n\n probs_list = []\n\n for i in i_interval:\n s = state_space[0][i]\n if s < 0:\n s_hat = s + 2*np.pi\n if (s_hat - state[0]) < (s - state[0]):\n s = s_hat\n else:\n s_hat = s - 2*np.pi\n if (s_hat - state[0]) < (s - state[0]):\n s = s_hat\n\n gaus = gaussian(s, state[0], std)\n # print(gaus)\n\n probs_list.append(gaus)\n\n probs_list = [x * (1/np.sum(probs_list)) for x in probs_list]\n return i_interval, probs_list",
"def __minowski_low_negative_integer_p(h1, h2, p = 2): # 14..46 us for p = -1..-24 \\w 100 bins\n mult = scipy.absolute(h1 - h2)\n dif = mult\n for _ in range(-p + 1): dif = scipy.multiply(dif, mult)\n return math.pow(scipy.sum(1./dif), 1./p)",
"def relative_deviation(h1, h2): # 18 us @array, 42 us @list \\w 100 bins\n h1, h2 = __prepare_histogram(h1, h2)\n numerator = math.sqrt(scipy.sum(scipy.square(h1 - h2)))\n denominator = (math.sqrt(scipy.sum(scipy.square(h1))) + math.sqrt(scipy.sum(scipy.square(h2)))) / 2.\n return numerator / denominator",
"def calculate_pdf(density_df, pseudocount=None, min_density_threshold=0):\n\n df = clean(density_df)\n df = df[df.sum(axis=1) >= min_density_threshold]\n min_read = pseudocount if pseudocount else min(\n [item for item in df.unstack().values if item > 0]\n )\n\n df = df + min_read\n pdf = df.div(df.sum(axis=1), axis=0)\n return pdf # , mean, sem",
"def histogramPrune(HT, beam_size):\n sorted_HT = sorted(HT, key=lambda ht: ht[1], reverse=True) # Order by scores (index 1), descending.\n pruned_HT = sorted_HT[0:beam_size] # Select the beam_size number of highest scored hypothesis.\n\n return pruned_HT",
"def density_estimation(sample, X, h, kernel=\"epanechnikov\"):\n kde = KernelDensity(kernel=kernel, bandwidth=h).fit(sample.reshape(-1, 1))\n log_dens = kde.score_samples(X.reshape(-1, 1))\n density = np.exp(log_dens)\n return density",
"def Intensity(spl):\n return np.power(10.0,(spl-96.0)/10.0) # intensity value from SPL",
"def FWHM(X,Y):\n HM = Y.max() / 2.0 # Half Max\n imax = smart_argmax(Y)\n right_edge = False\n left_edge = False\n if imax == 0:\n print('NOTE: Max of hist is at left edge')\n HMi_L = 0\n left_edge = True\n else:\n mask = (Y[:imax] <= HM)\n HMi_L = imax-np.flip(mask).argmax()-1 # index of HM on left\n if mask.sum() == 0: HMi_L=0 # No bin is lower than HM\n if imax >= Y.shape[0]-1:\n print('NOTE: Max of hist is at right edge')\n HMi_R = Y.shape[0] - 1\n right_edge = True\n else:\n mask = Y[imax+1:] <= HM\n HMi_R = (mask).argmax()+imax # index of HM on right\n if mask.sum() == 0: HMi_R = Y.shape[0] - 1\n try:\n FWHM = X[HMi_R] - X[HMi_L]\n except:\n pdb.set_trace()\n if FWHM == 0:\n print('NOTE: FWHM compuated as zero. \\nArtificially making FWHM 1 bin unit long')\n if left_edge:\n HMi_R = 1\n elif right_edge: \n HMi_L == HMi_R - 1\n else:\n HMi_R += 1\n FWHM = X[HMi_R] - X[HMi_L]\n \n #plt.close('all') # Debug plotting\n #plt.plot(X,Y)\n #plt.plot([X[HMi_L],X[HMi_R]],[HM,HM])\n #plt.plot([X[HMi_L],X[HMi_L]],[0,HM])\n #plt.plot([X[HMi_R],X[HMi_R]],[0,HM])\n #plt.show()\n #pdb.set_trace()\n return FWHM, X[HMi_R], X[HMi_L]"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
Build the cache key for a particular type of cached value
|
def cache_key(type, user_pk):
return CACHE_TYPES[type] % user_pk
|
[
"def _build_cache_key(self, *args):\n return self.key if not self.key_mod else self.key % tuple(args)",
"def gen_cache(self, key, value=None, type=Cache):\n if type == MultiHeadAttention.StaticCache: # static_kv\n k, v = self.compute_kv(key, value)\n return self.StaticCache(k, v)\n elif value is None: # incremental_state\n fill_shape = [-1, self.num_heads, 0, self.head_dim]\n fill_shape[0] = paddle.shape(key)[0].item()\n k = paddle.full(fill_shape, 0, key.dtype)\n v = paddle.full(fill_shape, 0, key.dtype)\n return self.Cache(k, v)\n else:\n # incremental_state with initial value, mainly for usage like UniLM\n return self.Cache(key, value)",
"def make_cache_key(pattern, flags):\n return '{}_{}'.format(pattern, flags)",
"def __cache_key__(*args, **kwargs):\n return args_to_key(base, args, kwargs, False)",
"def get_cache_key(class_name, settings=()):\n return '#{0}:{1}'.format(class_name, hash(tuple(settings)))",
"def _get_cache_key(self, **kwargs):\n key = 'cartodb_%s_' % _geohash.encode(\n kwargs.pop('lat'), kwargs.pop('lon'))[:8]\n key += '_'.join([\n '%s=%s' % (k, kwargs[k]) for k in sorted(kwargs.iterkeys())])\n return key",
"def _get_cache_key(self, **kwargs):\n m = md5()\n for significant_kwarg in self.significant_kwargs:\n key, to_str = significant_kwarg\n m.update(to_str(kwargs[key]))\n\n if hasattr(self, 'cache_prefix'):\n cache_prefix = self.cache_prefix\n else:\n cache_prefix = '%s.%s' % (self.__module__, self.__name__)\n return '%s:%s' % (cache_prefix, m.hexdigest())",
"def as_cache_key(self, ireq):\n extras = tuple(sorted(ireq.extras))\n if not extras:\n extras_string = \"\"\n else:\n extras_string = \"[{}]\".format(\",\".join(extras))\n name = _key_from_req(ireq.req)\n version = get_pinned_version(ireq)\n return name, \"{}{}\".format(version, extras_string)",
"def build_key(cls, user_id):\n key = ndb.Key(cls, user_id)\n return key",
"def get_cache_key(instance, extra=None):\n return '%s.%s.%s' % (instance.__class__.__name__, instance.short_url, extra) if extra else '%s.%s' % (instance.__class__.__name__, instance.short_url)",
"def _make_widget_key(widgets: list[tuple[str, Any]], cache_type: CacheType) -> str:\n func_hasher = hashlib.new(\"md5\")\n for widget_id_val in widgets:\n update_hash(widget_id_val, func_hasher, cache_type)\n\n return func_hasher.hexdigest()",
"def _make_cache_key(url, permanent=False):\n return \"WebTemplate:%s:%s\" % (url, {True: \"p\", False: \"t\"}[permanent])",
"def _build_key(tenant_it, obj):\n\n str_list = []\n\n if tenant_it:\n str_list.append(str(tenant_it))\n\n if obj:\n if 'application_type' in obj and obj['application_type']:\n str_list += obj['application_type']\n\n if 'dimensions' in obj and obj['dimensions']:\n dims = obj['dimensions']\n sorted_dims = sorted(dims)\n for name in sorted_dims:\n str_list += name\n str_list += str(dims[name])\n\n return ''.join(str_list)",
"def _build_key(self, observable):\n return str(observable)",
"def cachekey_static(func, *args, **kwargs):\n return prefix(func) + kwargs.get('cachekey', '')",
"def make(cls, args: Tuple[Any, ...], kwds: Dict[str, Any]) -> \"CacheKey\":\n key = []\n # positional arguments\n for argument in args:\n if cls.is_primitive(argument):\n key.append(argument)\n # keyword arguments\n for pair in sorted(kwds.items()):\n if cls.is_primitive(pair[1]):\n key.append(pair)\n return CacheKey(tuple(key))",
"def cache_key(self):\n return \" \".join([\n str(self.query._Query__kind),\n str(self.query._Query__ancestor),\n str(self.query._Query__filters),\n str(self.query._Query__orders),\n str(self.query._Query__app),\n str(self.query._Query__namespace)\n ]).replace(\" \", \"_\")",
"def cache_key(self, url):\n\n return f\"IXF-CACHE-{url}\"",
"def _tuple_to_cache_key(t):\n key_data = '(%(s_data)s)' % {\n 's_data': ','.join(t)\n }\n if six.PY3:\n key_data = key_data.encode('utf-8')\n\n key = hashlib.sha1()\n key.update(key_data)\n return key.hexdigest()",
"def build(self, key):\n if key == \"?\":\n return key\n if key.startswith(\"-\"):\n prefix = \"-\"\n key = key[1:]\n else:\n prefix = \"\"\n if key.startswith(self.shared_fields):\n return '%smaster__%s' % (prefix, key)\n else:\n return '%s%s' % (prefix, key)"
] |
{
"objective": {
"paired": [],
"self": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
}
|
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