Mercurial > repos > artbio > varscan_vaf
comparison varscan_vaf.py @ 0:0b6ec297a6bc draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf commit ff9426700b78da43ad64bf4905d358ee4986127b
| author | artbio |
|---|---|
| date | Mon, 28 Nov 2022 21:59:34 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:0b6ec297a6bc |
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| 1 #!/usr/bin/python3 | |
| 2 | |
| 3 import argparse | |
| 4 | |
| 5 | |
| 6 def Parser(): | |
| 7 the_parser = argparse.ArgumentParser() | |
| 8 the_parser.add_argument( | |
| 9 '--input', action="store", type=str, | |
| 10 help="varscan vcf file with normal and tumor genotypes \ | |
| 11 (columns 10 and 11)") | |
| 12 the_parser.add_argument( | |
| 13 '--output', action="store", type=str, | |
| 14 help="vcf with computed VAFs") | |
| 15 args = the_parser.parse_args() | |
| 16 return args | |
| 17 | |
| 18 | |
| 19 def main(input, output): | |
| 20 with open(input, 'r') as f: | |
| 21 myinput = f.read() | |
| 22 mylines = myinput.split('\n') | |
| 23 entete = [i for i in mylines[:-1] if i[0] == '#'] | |
| 24 variant = [i for i in mylines[:-1] if i[0] != '#'] | |
| 25 out = open(output, 'w') | |
| 26 out.write('\n'.join(entete[:-1]) + '\n') | |
| 27 out.write('##FORMAT=<ID=VAF,Number=R,Type=float,Description="Variant' | |
| 28 'Allele Frequency">\n') | |
| 29 out.write(entete[-1] + '\n') | |
| 30 for i in variant: | |
| 31 fields = i.split('\t')[9:11] | |
| 32 af_normal = fields[0].split(':')[3] | |
| 33 vac_normal = af_normal.split(',') | |
| 34 af_tumor = fields[1].split(':')[3] | |
| 35 vac_tumor = af_tumor.split(',') | |
| 36 vaf_normal = int( | |
| 37 vac_normal[1]) / (int(vac_normal[0]) + int(vac_normal[1])) | |
| 38 vaf_tumor = int( | |
| 39 vac_tumor[1]) / (int(vac_tumor[0]) + int(vac_tumor[1])) | |
| 40 normal_list = fields[0].split(':') | |
| 41 normal_list.append(f'{vaf_normal:.3f}') | |
| 42 tumor_list = fields[1].split(':') | |
| 43 tumor_list.append(f'{vaf_tumor:.3f}') | |
| 44 normal_string = ':'.join(normal_list) | |
| 45 tumor_string = ':'.join(tumor_list) | |
| 46 fields = i.split('\t')[0:9] | |
| 47 fields[8] += ':VAF' | |
| 48 fields.append(normal_string) | |
| 49 fields.append(tumor_string) | |
| 50 out.write('\t'.join(fields) + '\n') | |
| 51 out.close() | |
| 52 | |
| 53 | |
| 54 if __name__ == "__main__": | |
| 55 args = Parser() | |
| 56 main(args.input, args.output) |