'''Filter VCF on GQ parameter.
:Date: 24 Sep, 2015
:Author: Alex Jironkin
'''
import argparse
import logging
from phe.variant_filters import PHEFilterBase
[docs]class QualFilter(PHEFilterBase):
'''Filter sites by QUAL score.'''
name = "LowSNPQual"
_default_threshold = 40.0
parameter = "qual_score"
[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 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(QualFilter, 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 = 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 QUAL filter from parameters: %s" % args)
def __call__(self, record):
"""Filter a :py:class:`vcf.model._Record`."""
record_qual = record.QUAL
if record_qual is None or record_qual < self.threshold:
# FIXME: when record_gq is None, i,e, error, what do you do?
return record_qual or False
else:
return None
[docs] def short_desc(self):
short_desc = self.__doc__ or ''
if short_desc:
short_desc = "%s (QUAL > %s)" % (short_desc, self.threshold)
return short_desc