"""Are st and end in capture?
Are st and end in the same exon?"""
import sys, csv, os
import mkSnvBedFile
sys.path.append('/home/evansj/me/projects/diskin/target_indels/code/')
import bed_tools
if __name__ == '__main__':
title, fileToAnnotate, captureBed, outFile = sys.argv[1:]
with open('tmp.bed', 'w') as fout, open(captureBed) as f:
print('chrom\tstart\tend', file=fout)
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'),
"""Are st and end in capture?
Are st and end in the same exon?"""
import sys, csv
import mkSnvBedFile
sys.path.append('/home/evansj/me/projects/diskin/target_indels/code/')
import bed_tools
if __name__ == '__main__':
fileToAnnotate, captureBed, outFile = sys.argv[1:]
captureDataStrict = bed_tools.load_nb222_exome_capture_driver(captureBed, 0)
captureDataRelaxed = bed_tools.load_nb222_exome_capture_driver(captureBed, 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',
'CAPTURE_RELAXED',
]),
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,)
