'''Filter VCF on GT filter parameter.
:Date: 24 Sep, 2015
:Author: Alex Jironkin
'''
import argparse
import logging
from phe.variant_filters import PHEFilterBase
[docs]class UncallableGTFilter(PHEFilterBase):
'''Filter uncallable genotypes'''
name = "UncallGT"
_default_threshold = None
parameter = "uncall_gt"
[docs] @classmethod
def customize_parser(self, parser):
arg_name = self.parameter.replace("_", "-")
parser.add_argument("--%s" % arg_name, type=str, 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(UncallableGTFilter, 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 = str(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 string!")
self.threshold = None
def __call__(self, record):
"""Filter a :py:class:`vcf.model._Record`."""
if len(record.samples) > 1:
logging.warn("More than 1 sample detected. Only first is considered.")
try:
record_gt = record.samples[0].data.GT
except AttributeError:
logging.warn("Could not retrieve GQ score POS %i", record.POS)
record_gt = None
if record_gt is None:
return "./."
else:
return None
[docs] def short_desc(self):
short_desc = self.__doc__ or ''
if short_desc:
short_desc = "%s (GT != ./. )" % (short_desc)
return short_desc
[docs] def is_gap(self):
return True
[docs] def is_n(self):
return False