Mercurial > repos > ulfschaefer > filter_vcf
view phe/variant_filters/GTFilter.py @ 0:834a312c0114 draft
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author | ulfschaefer |
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date | Thu, 10 Dec 2015 09:22:39 -0500 |
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'''Filter VCF on GT filter parameter. Created on 24 Sep 2015 @author: alex ''' import argparse import logging from phe.variant_filters import PHEFilterBase class UncallableGTFilter(PHEFilterBase): '''Filter uncallable genotypes''' name = "UncallGT" _default_threshold = None parameter = "uncall_gt" @classmethod def customize_parser(self, parser): arg_name = self.parameter.replace("_", "-") parser.add_argument("--%s" % arg_name, type=str, default=self._default_threshold, help="Filter sites below given GQ score (default: %s)" % self._default_threshold) def __init__(self, args): """Min Depth constructor.""" # This needs to happen first, because threshold is initialised here. super(UncallableGTFilter, self).__init__(args) # Change the threshold to custom gq value. self.threshold = self._default_threshold if isinstance(args, argparse.Namespace): self.threshold = args.gq_score elif isinstance(args, dict): try: self.threshold = str(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 len(record.samples) > 1: logging.warn("More than 1 sample detected. Only first is considered.") try: record_gt = record.samples[0].data.GT except AttributeError: logging.error("Could not retrieve GQ score POS %i", record.POS) record_gt = None if record_gt is None: return "./." else: return None def short_desc(self): short_desc = self.__doc__ or '' if short_desc: short_desc = "%s (GT != ./. )" % (short_desc) return short_desc def is_gap(self): return True def is_n(self): return False