Mercurial > repos > ulfschaefer > filter_vcf
view phe/variant_filters/ADFilter.py @ 11:cd59be4a7fe3 draft default tip
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author | ulfschaefer |
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date | Mon, 21 Dec 2015 11:12:19 -0500 |
parents | c2f8e7580133 |
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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 ADFilter(PHEFilterBase): '''Filter sites by AD ratio.''' name = "ADRatio" _default_threshold = 0.9 parameter = "ad_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 ad ratio (default: %s)" % self._default_threshold) def __init__(self, args): """AD Ratio constructor.""" # This needs to happen first, because threshold is initialised here. super(ADFilter, 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, ValueError): logging.error("Could not retrieve threshold from %s", args.get(self.parameter)) logging.error("This parameter requires to be a float!") raise Exception("Could not create AD filter from parameters: %s" % args) def __call__(self, record): """Filter a :py:class:`vcf.model._Record`.""" good_record = self._check_record(record) if good_record is not True: return good_record if len(record.samples) > 1: logging.warn("More than 1 sample detected. Only first is considered.") try: record_ad = record.samples[0].data.AD # FIXME: when record length is > 2, what do you do? assert len(record_ad) == 2, "AD data is incomplete POS: %i" % record.POS depth = sum(record.samples[0].data.AD) ratio = float(record_ad[1]) / depth except Exception: logging.warn("Could not calculate AD ratio from %s POS: %s", record, 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 (AD ratio > %s )" % (short_desc, self.threshold) return short_desc