"""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,)