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1 #!/usr/bin/env python
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2 '''Simple VCF parser using custom filters.
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3
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4 Created on 6 Oct 2015
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5
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6 @author: alex
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7 '''
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8 import argparse
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9
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10 from phe.variant import VariantSet
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11
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12
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13 def get_args():
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14
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15 args = argparse.ArgumentParser()
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16
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17 args.add_argument("--vcf", "-v", required=True, help="VCF file to (re)filter.")
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18 args.add_argument("--filters", "-f", required=True, help="Filter(s) to apply as key:threshold pairs, separated by comma.")
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19 args.add_argument("--output", "-o", required=True, help="Location for filtered VCF to be written.")
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20
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21 return args.parse_args()
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22
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23
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24 def main():
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25 args = get_args()
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26
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27 var_set = VariantSet(args.vcf, filters=args.filters)
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28
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29 var_set.filter_variants()
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30
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31 var_set.serialise(args.output)
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32
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33 if __name__ == '__main__':
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34 exit(main())
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