def annotate(options, titleRow, evidence):
'''Annotate variants which appear in a sample of a family member'''
annotateFilename = options.annotations
with open(annotateFilename,'w') as annotateFile:
csvWriter = csv.writer(annotateFile, delimiter='\t', quotechar='|')
if titleRow:
csvWriter.writerow(titleRow)
inFamily = []
notInFamily = []
# sort the variants by coordinate
# XXX does this include the variant multiple times?
# for key,info in sortByCoord(evidence):
# for readCount,depth in info.counts:
# if readCount > 0:
# inFamily.append(info.inputRow)
# else:
# notInFamily.append(info.inputRow)
for key,info in sortByCoord(evidence):
countSum = sum([readCount for (readCount,depth) in info.counts])
if countSum > 0:
inFamily.append(info.inputRow)
else:
notInFamily.append(info.inputRow)
for row in inFamily:
csvWriter.writerow(row + ['IN RELATIVE'])
for row in notInFamily:
csvWriter.writerow(row + ['NOT IN RELATIVE'])
print('Annotated reads saved into file: %s' % annotateFilename)
def filter(options, evidence):
'''Decide which variants to keep and which to bin.'''
binFilename = options.bin
keepFilename = options.keep
logFilename = options.log
with open(logFilename, 'w') as logFile:
with open(binFilename, 'w') as binFile:
with open(keepFilename, 'wb') as keepFile:
csvWriter = csv.writer(keepFile, delimiter='\t', quotechar='|')
# sort the variants by coordinate
for key, info in sortByCoord(evidence):
classification = classify(options, info.counts)
# record the classification of this variant in the logfile
logFile.write(
"%s: %s: %s\n" %
(key, classification.action, classification.reason))
if classification.action == 'bin':
# bin the variant
binFile.write('%s\n' % key)
for readCount, depth in info.counts:
binFile.write(' <vars/coverage: %d/%d>\n' %
(readCount, depth))
elif classification.action == 'keep':
# keep the variant
csvWriter.writerow(info.inputRow)
def filter(options, evidence):
'''Decide which variants to keep and which to bin.'''
binFilename = options.bin
keepFilename = options.keep
logFilename = options.log
with open (logFilename,'w') as logFile:
with open(binFilename,'w') as binFile:
with open(keepFilename,'wb') as keepFile:
csvWriter = csv.writer(keepFile, delimiter='\t', quotechar='|')
# sort the variants by coordinate
for key,info in sortByCoord(evidence):
classification = classify(options, info.counts)
# record the classification of this variant in the logfile
logFile.write("%s: %s: %s\n" % (key, classification.action, classification.reason))
if classification.action == 'bin':
# bin the variant
binFile.write('%s\n' % key)
for readCount,depth in info.counts:
binFile.write(' <vars/coverage: %d/%d>\n' % (readCount,depth))
elif classification.action == 'keep':
# keep the variant
csvWriter.writerow(info.inputRow)
