Mercurial > repos > ulfschaefer > filter_vcf
diff filter_vcf.py @ 0:834a312c0114 draft
Uploaded
author | ulfschaefer |
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date | Thu, 10 Dec 2015 09:22:39 -0500 |
parents | |
children | cd59be4a7fe3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_vcf.py Thu Dec 10 09:22:39 2015 -0500 @@ -0,0 +1,34 @@ +#!/usr/bin/env python +'''Simple VCF parser using custom filters. + +Created on 6 Oct 2015 + +@author: alex +''' +import argparse + +from phe.variant import VariantSet + + +def get_args(): + + args = argparse.ArgumentParser() + + args.add_argument("--vcf", "-v", required=True, help="VCF file to (re)filter.") + args.add_argument("--filters", "-f", required=True, help="Filter(s) to apply as key:threshold pairs, separated by comma.") + args.add_argument("--output", "-o", required=True, help="Location for filtered VCF to be written.") + + return args.parse_args() + + +def main(): + args = get_args() + + var_set = VariantSet(args.vcf, filters=args.filters) + + var_set.filter_variants() + + var_set.serialise(args.output) + +if __name__ == '__main__': + exit(main())