def addContext(indelFile, indelSeqFileIns, outFile):
seqs = loadSeqs((indelSeqFileIns,))
with open(outFile, 'w') as fout, open(indelFile) as f:
reader = csv.DictReader(f, delimiter='\t')
header = reader.fieldnames
print('\t'.join(header + ['st_seq-1', 'st_seq', 'st_seq+1',
]),
file=fout)
for row in reader:
st, end = mkSnvBedFile.fixCoords(row)
indelKeySt = ':'.join([row['chrom'], st])
newData = list(seqs[indelKeySt])
print('\t'.join( ([row[x] for x in header]
+ newData)),
file=fout)
def annotateWithMasterVarCall(indelFile, indelCovFile,
indelTumorCovFile, annOut):
indelToCov = getIndelCov(indelCovFile)
indelToCov_tumor = getIndelCov(indelTumorCovFile)
with open(annOut, 'w') as fout, open(indelFile) as f:
reader = csv.DictReader(f, delimiter='\t')
header = reader.fieldnames
print('\t'.join(header + ['sampleCov', 'tumorSampleCov']),
file=fout)
for row in reader:
st, end = mkSnvBedFile.fixCoords(row)
indelKey = ':'.join([row['chrom'], str(st),
str(end)])
if indelKey in indelToCov and indelKey in indelToCov_tumor:
print('\t'.join( ([row[x] for x in header]
+ [indelToCov[indelKey],
indelToCov_tumor[indelKey]])
),
file=fout)
else:
print(indelKey)
for line in f:
if line.split('\t')[1] != 'chromStart':
print(line[3:].strip(), file=fout)
captureDataStrict = bed_tools.load_nb222_exome_capture_driver('tmp.bed', 0)
captureDataRelaxed = bed_tools.load_nb222_exome_capture_driver('tmp.bed', 100)
with open(fileToAnnotate) as f, open(outFile, 'w') as fout:
reader = csv.DictReader(f, delimiter='\t')
print('\t'.join(reader.fieldnames) + '\t'
+ '\t'.join(['CAPTURE_STRICT_' + title,
'CAPTURE_RELAXED_' + title,
]),
file=fout)
for row in reader:
chrom = row['chrom']
st,end = mkSnvBedFile.fixCoords(row)
st = int(st)
status = {}
for captureData, label in ( (captureDataStrict, 'STRICT'),
(captureDataRelaxed, 'RELAXED') ):
captureStatusSt = bed_tools.find_location_in_bed("chr" + chrom, st, captureData[1], captureData[0])
if captureStatusSt:
status[label] = 'CAP_%s_TRUE' % (label,)
else:
status[label] = 'CAP_%s_FALSE' % (label,)
print('\t'.join([row[x] for x in reader.fieldnames]
+ [status['STRICT'],
status['RELAXED'],
]),
