CSV with allele frequencies from GoNL VCF

gonl_freqs.py

#!/usr/bin/env python
#
# CSV with allele frequencies from GoNL VCF.
#
# https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5/


import sys
from vcf import Reader


def main(filenames):
    print '%s\t%s\t%s\t%s\t%s\t%s\t%s' % (
        'CHROM', 'POS', 'REF', 'ALT', 'TOTAL_ALLELES', 'ALT_ALLELES', 'ALT_FREQ')

    for filename in filenames:
        reader = Reader(filename=filename)

        for record in reader:
            if record.var_type != 'snp':
                continue
            for alt, ac, af in zip(record.ALT,
                                   record.INFO['AC'],
                                   record.INFO['AF']):
                print '%s\t%d\t%s\t%s\t%d\t%d\t%f' % (record.CHROM,
                                                      record.POS,
                                                      record.REF,
                                                      alt,
                                                      record.INFO['AN'],
                                                      ac,
                                                      af)


if __name__ == '__main__':
    main(sys.argv[1:])