'''Filter VCF on MQ filter.
:Date: 24 Sep, 2015
:Author: Alex Jironkin
'''
import argparse
import logging
from phe.variant_filters import PHEFilterBase
[docs]class MQ0Filter(PHEFilterBase):
'''Filter sites by MQ0 (Total Mapping Quality Zero Reads) to DP ratio.'''
name = "MinMQ0"
_default_threshold = 0.05
parameter = "mq0_ratio"
[docs] @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:
# print "%s\tthis happened" % (record.POS)
# 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"))
# print "%s\t%s\t%s\t%s" % (record.POS,record.INFO.get("MQ0"),record.INFO.get("DP"),record_mq)
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
[docs] def short_desc(self):
short_desc = self.__doc__ or ''
if short_desc:
short_desc = "%s (MQ0 > %s)" % (short_desc, self.threshold)
return short_desc