Datasets:
thisisanshgupta
/
Pycode

Dataset card Data Studio Files Community
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return files"
58,"def _parse(self):
""""""Parses file contents
:return: Tree hierarchy of file
""""""
with open(self.path, ""rt"") as reader:
return ast.parse(reader.read(), filename=self.path)"
59,"def _find_package(self, root_package):
""""""Finds package name of file
:param root_package: root package
:return: package name
""""""
package = self.path.replace(root_package, """")
if package.endswith("".py""):
package = package[:-3]
package = package.replace(os.path.sep, MODULE_SEP)
root_package = get_folder_name(root_package)
package = root_package + package # add root
return package"
60,"def _get_instances(self, instance):
""""""Finds all instances of instance in tree
:param instance: type of object
:return: list of objects in tree of same instance
""""""
return [
x
for x in self.tree.body
if isinstance(x, instance)
]"
61,"def get_classes(self):
""""""Finds classes in file
:return: list of top-level classes
""""""
instances = self._get_instances(ast.ClassDef)
instances = [
PyClass(instance, self.package)
for instance in instances
]
return instances"
62,"def get_functions(self):
""""""Finds top-level functions in file
:return: list of top-level functions
""""""
instances = self._get_instances(ast.FunctionDef)
instances = [
PyFunction(instance, self.package)
for instance in instances
]
return instances"
63,"def get_functions(self, include_meta=False):
""""""Finds top-level functions in file
:param include_meta: whether include meta functions like (__init__)
:return: list of top-level functions
""""""
instances = self._get_instances(ast.FunctionDef)
instances = [
PyFunction(instance, self.full_package) # fix package name
for instance in instances
]
if not include_meta:
instances = [
instance # fix package name
for instance in instances
if not instance.get_name().startswith(""__"")
]
return instances"
64,"def skesa_assemble(self):
""""""
Run skesa to assemble genomes
""""""
with progressbar(self.metadata) as bar:
for sample in bar:
# Initialise the assembly command
sample.commands.assemble = str()
try:
if sample.general.trimmedcorrectedfastqfiles:
# If the sample is a pure isolate, assemble it. Otherwise, run the pre-metagenome pipeline
try:
status = sample.run.Description
except AttributeError:
status = 'unknown'
if status == 'metagenome':
self.merge(sample)
else:
# Set the output directory
sample.general.assembly_output = os.path.join(sample.general.outputdirectory,
'assembly_output')