'''Filter VCFs on AD ratio.
:Date: 24 Sep, 2015
:Author: Alex Jironkin
'''
import argparse
import logging
from phe.variant_filters import PHEFilterBase
[docs]class DP4Filter(PHEFilterBase):
'''Filter sites by DP4 ratio.'''
name = "DP4"
_default_threshold = 0.9
parameter = "dp4_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 minimum dp4 ratio (default: %s)" % self._default_threshold)
def __init__(self, args):
"""AD Ratio constructor."""
# This needs to happen first, because threshold is initialised here.
super(DP4Filter, self).__init__(args)
# Change the threshold to custom dp value.
self.threshold = self._default_threshold
if isinstance(args, argparse.Namespace):
self.threshold = args.ad_ratio
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 DP4 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
try:
record_dp = record.INFO.get("DP4")
# FIXME: when record length is > 2, what do you do?
assert len(record_dp) == 4, "DP4 data should have 4 datum POS: %i" % record.POS
depth = sum(record_dp)
ratio = float(sum(record_dp[2:])) / depth
except Exception:
logging.warn("Could not calculate DP4 ratio from %s POS: %s", record_dp, record.POS)
ratio = None
if ratio is None or ratio < self.threshold:
# FIXME: When ratio is None, i.e. error, what do you do?
return ratio or False
else:
return None
[docs] def short_desc(self):
short_desc = self.__doc__ or ''
if short_desc:
short_desc = "%s (DP4 ratio > %s )" % (short_desc, self.threshold)
return short_desc