yaml-to-vcf.py

import argparse as ap
import sys
import vcf
import yaml

VERSION = 0.1

def filter_variants(yaml_variants):
    variants = []
    for v in yaml_variants:
        if v['type'] != 'deletion' and v['type'] != 'insertion':
            variants.append(v)
    return variants

def go(args):
    vcf_reader = vcf.Reader('template.vcf')
    vcf_writer = vcf.Writer(open(args.output, 'w'), vcf_reader)

    y = yaml.safe_load(open(args.yaml))
    variants = filter_variants(y['variants'])

    for row in variants:
        record = vcf.model._Record('NC_045512',
                                   int(row['one-based-reference-position']),
                                   '.',
                                   row['reference-base'],
                                   [vcf.model._Substitution(row['variant-base'])],
                                   '.',
                                   'PASS',
                                   {},
                                   '.', sample_indexes=[])
        vcf_writer.write_record(record)


if __name__ == '__main__':
    parser = ap.ArgumentParser(
        prog='csv-to-vcf.py',
        conflict_handler='resolve',
        description=("Produce basic VCF file from a CSV file.")
    )
    parser.add_argument('yaml', metavar="YAML_FILE", type=str,
                        help='variant definition file')
    parser.add_argument('--output', metavar="STRING", type=str,
                        default='/dev/stdout',
                        help='File to write VCF output to (Default STDOUT).')
    parser.add_argument('--version', action='version',
                        version='%(prog)s {0}'.format(VERSION))

    if len(sys.argv) == 1:
        parser.print_help()
        sys.exit(0)

    args = parser.parse_args()

    vars = go(args)