Mercurial > repos > ulfschaefer > filter_vcf
diff phe/variant_filters/MQ0Filter.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/MQ0Filter.py Mon Dec 21 10:50:17 2015 -0500 @@ -0,0 +1,69 @@ +'''Filter VCF on MQ filter. +Created on 24 Sep 2015 + +@author: alex +''' + +import argparse +import logging + +from phe.variant_filters import PHEFilterBase + + +class MQ0Filter(PHEFilterBase): + '''Filter sites by MQ0 (Total Mapping Quality Zero Reads) to DP ratio.''' + + name = "MinMQ0" + _default_threshold = 0.05 + parameter = "mq0_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 given MQ score (default: %s)" % self._default_threshold) + + def __init__(self, args): + """Min Mapping Quality Zero constructor.""" + # This needs to happen first, because threshold is initialised here. + super(MQ0Filter, self).__init__(args) + + # Change the threshold to custom gq value. + self.threshold = self._default_threshold + if isinstance(args, argparse.Namespace): + self.threshold = args.mq_score + 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 MQ0 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 + + record_mq = record.INFO.get("MQ0") + + if record_mq: + # We consider DO from INFO not samples because MQ0 is also from INFO. + record_mq /= float(record.INFO.get("DP")) + + if record_mq is None or record_mq > self.threshold: + # FIXME: when record_mq is None, i,e, error/missing, what do you do? + return record_mq or False + else: + return None + + def short_desc(self): + short_desc = self.__doc__ or '' + + if short_desc: + short_desc = "%s (MQ0 > %s)" % (short_desc, self.threshold) + + return short_desc