Mercurial > repos > ulfschaefer > filter_vcf
diff phe/variant_filters/GQFilter.py @ 10:c2f8e7580133 draft
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author | ulfschaefer |
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date | Mon, 21 Dec 2015 10:50:17 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phe/variant_filters/GQFilter.py Mon Dec 21 10:50:17 2015 -0500 @@ -0,0 +1,72 @@ +'''Filter VCF on GQ parameter. +Created on 24 Sep 2015 + +@author: alex +''' + +import argparse +import logging + +from phe.variant_filters import PHEFilterBase + + +class GQFilter(PHEFilterBase): + '''Filter sites by GQ score.''' + + name = "MinGQ" + _default_threshold = 0 + parameter = "gq_score" + + @classmethod + def customize_parser(self, parser): + arg_name = self.parameter.replace("_", "-") + parser.add_argument("--%s" % arg_name, type=int, 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(GQFilter, 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 = int(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 an integer!") + raise Exception("Could not create GQ 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_gq = record.samples[0].data.GQ + except AttributeError: + logging.warn("Could not retrieve GQ score POS %i", record.POS) + record_gq = None + + if record_gq is None or record_gq < self.threshold: + # FIXME: when record_gq is None, i,e, error, what do you do? + return record_gq or False + else: + return None + + def short_desc(self): + short_desc = self.__doc__ or '' + + if short_desc: + short_desc = "%s (GQ > %s)" % (short_desc, self.threshold) + + return short_desc