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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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11
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9 import logging
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10 import yaml
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11
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12 from phe.variant import VariantSet
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13
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14
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15 def get_args():
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16
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17 args = argparse.ArgumentParser()
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18
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19 args.add_argument("--vcf", "-v", required=True, help="VCF file to (re)filter.")
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11
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20
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21 group = args.add_mutually_exclusive_group()
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22
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23 group.add_argument("--filters", "-f", help="Filter(s) to apply as key:threshold pairs, separated by comma.")
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24 group.add_argument("--config", "-c", help="Config with filters in YAML format. E.g.filters:-key:value")
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25
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26 args.add_argument("--output", "-o", required=True, help="Location for filtered VCF to be written.")
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27
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28 args.add_argument("--only-good", action="store_true", default=False, help="Write only variants that PASS all filters (default all variants are written).")
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29
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30 args.add_argument("--debug", action="store_true", default=False, help="Make output more verbose.")
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31
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32 return args.parse_args()
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33
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34 def load_config(config_path):
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35 with open(config_path) as fp:
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36 config = yaml.load(fp)
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37
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38 return config.get("filters", {})
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39
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40 def main():
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41 args = get_args()
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42
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43 log_level = logging.DEBUG if args.debug else logging.INFO
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44 logging.basicConfig(format="[%(asctime)s] %(levelname)s: %(message)s",
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45 level=log_level)
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46
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47 if args.config is not None:
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48 args.filters = load_config(args.config)
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49 elif args.filters is None:
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50 logging.error("Either --config or --filters needs to be specified.")
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51 return 1
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52
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53 var_set = VariantSet(args.vcf, filters=args.filters)
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54
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55 if args.filters:
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56 var_set.filter_variants()
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57
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58 var_set.write_variants(args.output, only_good=args.only_good)
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59
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60
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61
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62 if __name__ == '__main__':
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63 exit(main())
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