diff 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan_vaf.py	Mon Nov 28 21:59:34 2022 +0000
@@ -0,0 +1,56 @@
+#!/usr/bin/python3
+
+import argparse
+
+
+def Parser():
+    the_parser = argparse.ArgumentParser()
+    the_parser.add_argument(
+        '--input', action="store", type=str,
+        help="varscan vcf file with normal and tumor genotypes \
+              (columns 10 and 11)")
+    the_parser.add_argument(
+        '--output', action="store", type=str,
+        help="vcf with computed VAFs")
+    args = the_parser.parse_args()
+    return args
+
+
+def main(input, output):
+    with open(input, 'r') as f:
+        myinput = f.read()
+    mylines = myinput.split('\n')
+    entete = [i for i in mylines[:-1] if i[0] == '#']
+    variant = [i for i in mylines[:-1] if i[0] != '#']
+    out = open(output, 'w')
+    out.write('\n'.join(entete[:-1]) + '\n')
+    out.write('##FORMAT=<ID=VAF,Number=R,Type=float,Description="Variant'
+              'Allele Frequency">\n')
+    out.write(entete[-1] + '\n')
+    for i in variant:
+        fields = i.split('\t')[9:11]
+        af_normal = fields[0].split(':')[3]
+        vac_normal = af_normal.split(',')
+        af_tumor = fields[1].split(':')[3]
+        vac_tumor = af_tumor.split(',')
+        vaf_normal = int(
+            vac_normal[1]) / (int(vac_normal[0]) + int(vac_normal[1]))
+        vaf_tumor = int(
+            vac_tumor[1]) / (int(vac_tumor[0]) + int(vac_tumor[1]))
+        normal_list = fields[0].split(':')
+        normal_list.append(f'{vaf_normal:.3f}')
+        tumor_list = fields[1].split(':')
+        tumor_list.append(f'{vaf_tumor:.3f}')
+        normal_string = ':'.join(normal_list)
+        tumor_string = ':'.join(tumor_list)
+        fields = i.split('\t')[0:9]
+        fields[8] += ':VAF'
+        fields.append(normal_string)
+        fields.append(tumor_string)
+        out.write('\t'.join(fields) + '\n')
+    out.close()
+
+
+if __name__ == "__main__":
+    args = Parser()
+    main(args.input, args.output)