Mercurial > repos > ulfschaefer > filter_vcf
view phe/variant_filters/DP4Filter.py @ 1:b3fe10e4b93f draft
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author | ulfschaefer |
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date | Fri, 11 Dec 2015 09:40:42 -0500 |
parents | 834a312c0114 |
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'''Filter VCFs on AD ratio. Created on 24 Sep 2015 @author: alex ''' import argparse import logging from phe.variant_filters import PHEFilterBase class DP4Filter(PHEFilterBase): '''Filter sites by AD ratio.''' name = "DP4" _default_threshold = 0.9 parameter = "dp4_ratio" @classmethod def customize_parser(self, parser): arg_name = self.parameter.replace("_", "-") parser.add_argument("--%s" % arg_name, type=float, default=self._default_threshold, help="Filter sites below minimum dp4 ratio (default: %s)" % self._default_threshold) def __init__(self, args): """AD Ratio constructor.""" # This needs to happen first, because threshold is initialised here. super(DP4Filter, self).__init__(args) # Change the threshold to custom dp value. self.threshold = self._default_threshold if isinstance(args, argparse.Namespace): self.threshold = args.ad_ratio elif isinstance(args, dict): try: self.threshold = float(args.get(self.parameter)) except TypeError: logging.error("Could not retrieve threshold from %s", args.get(self.parameter)) self.threshold = None def __call__(self, record): """Filter a :py:class:`vcf.model._Record`.""" if not record.is_snp: return None try: record_dp = record.INFO.get("DP4") # FIXME: when record length is > 2, what do you do? assert len(record_dp) == 4, "DP4 data should have 4 datum POS: %i" % record.POS depth = sum(record_dp) ratio = float(sum(record_dp[2:])) / depth except Exception: logging.error("Could not calculate DP4 ratio from %s POS: %s", record_dp, record.POS) ratio = None if ratio is None or ratio < self.threshold: # FIXME: When ratio is None, i.e. error, what do you do? return ratio or False else: return None def short_desc(self): short_desc = self.__doc__ or '' if short_desc: short_desc = "%s (DP4 ratio > %s )" % (short_desc, self.threshold) return short_desc