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thisisanshgupta
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Pycode

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INSERT OR IGNORE INTO {}
(sample_id) VALUES (""{}"")
'''.format(table, sampleid))
# Add the data to the table
try:
# Find the data for each table/column
for item in sorted(sample[table].datastore.items()):
# Clean the names
cleanedcolumn = self.columnclean(str(item[0]))
# Add the data to the column of the appropriate table,
# where the sample_id matches the current strain
cursor.execute('''
UPDATE {}
SET {} = ?
WHERE sample_id = {}
'''.format(table, cleanedcolumn, sampleid), (str(item[1]), ))
except KeyError:
pass
# Commit the changes to the database
db.commit()"
20,"def columnclean(column):
""""""
Modifies column header format to be importable into a database
:param column: raw column header
:return: cleanedcolumn: reformatted column header
""""""
cleanedcolumn = str(column) \
.replace('%', 'percent') \
.replace('(', '_') \
.replace(')', '') \
.replace('As', 'Adenosines') \
.replace('Cs', 'Cytosines') \
.replace('Gs', 'Guanines') \
.replace('Ts', 'Thymines') \
.replace('Ns', 'Unknowns') \
.replace('index', 'adapterIndex')
return cleanedcolumn"
21,"def getLabel(self, key):
""""""Gets the label assigned to an axes
:param key:???
:type key: str
""""""
axisItem = self.getPlotItem().axes[key]['item']
return axisItem.label.toPlainText()"
22,"def updateData(self, axeskey, x, y):
""""""Replaces the currently displayed data
:param axeskey: name of data plot to update. Valid options are 'stim' or 'response'
:type axeskey: str
:param x: index values associated with y to plot
:type x: numpy.ndarray
:param y: values to plot at x
:type y: numpy.ndarray
""""""
if axeskey == 'stim':
self.stimPlot.setData(x,y)
# call manually to ajust placement of signal
ranges = self.viewRange()
self.rangeChange(self, ranges)
if axeskey == 'response':
self.clearTraces()
if self._traceUnit == 'A':
y = y * self._ampScalar
if self.zeroAction.isChecked():
start_avg = np.mean(y[5:25])
y = y - start_avg
self.tracePlot.setData(x,y*self._polarity)"
23,"def appendData(self, axeskey, bins, ypoints):
""""""Appends data to existing plotted data
:param axeskey: name of data plot to update. Valid options are 'stim' or 'response'
:type axeskey: str
:param bins: bins to plot a point for
:type bin: numpy.ndarray
:param ypoints: iteration number of raster, *should* match bins dimension, but really takes the first value in array for iteration number and plot row at proper place for included bins
:type ypoints: numpy.ndarray
""""""
if axeskey == 'raster' and len(bins) > 0:
x, y = self.rasterPlot.getData()
# don't plot overlapping points
bins = np.unique(bins)
# adjust repetition number to response scale
ypoints = np.ones_like(bins)*self.rasterYslots[ypoints[0]]
x = np.append(x, bins)
y = np.append(y, ypoints)
self.rasterPlot.setData(x, y)"
24,"def setThreshold(self, threshold):
""""""Sets the current threshold
:param threshold: the y value to set the threshold line at
:type threshold: float
""""""
self.threshLine.setValue(threshold)
self.threshold_field.setValue(threshold)"
25,"def setRasterBounds(self, lims):
""""""Sets the raster plot y-axis bounds, where in the plot the raster will appear between
:param lims: the (min, max) y-values for the raster plot to be placed between
:type lims: (float, float)