'''Filter VCF on depth of coverage.
:Date: 24 Sep, 2015
:Author: Alex Jironkin
'''
import argparse
import logging
from phe.variant_filters import PHEFilterBase
[docs]class DepthFilter(PHEFilterBase):
"""Filter sites by depth."""
name = "MinDepth"
_default_threshold = 5
parameter = "min_depth"
[docs] @classmethod
def customize_parser(self, parser):
arg_name = self.parameter.replace("_", "-")
parser.add_argument("--" % arg_name, type=int, default=self._default_threshold,
help="Filter sites below minimum depth (default: %s)" % self._default_threshold)
def __init__(self, args):
"""Min Depth constructor."""
# This needs to happen first, because threshold is initialised here.
super(DepthFilter, self).__init__(args)
# Change the threshold to custom dp value.
self.threshold = self._default_threshold
if isinstance(args, argparse.Namespace):
self.threshold = args.min_depth
elif isinstance(args, dict):
try:
self.threshold = int(args.get(self.parameter))
except (TypeError, ValueError):
logging.error("Could not retrieve integer threshold from %s", args.get(self.parameter))
raise Exception("Could not create depth filter from parameters: %s" % args)
def __call__(self, record):
"""Filter a :py:class:`vcf.model._Record`."""
if len(record.samples) > 1:
logging.warn("Currently we only filter VCFs with 1 sample. Only first sample will be used.")
logging.warn("This parameter requires to be an integer!")
try:
record_dp = record.samples[0].data.DP
except AttributeError:
logging.debug("Falling back to INFO DP")
record_dp = record.INFO.get("DP")
if record_dp is None or record_dp < self.threshold:
return record_dp or False
else:
return None
[docs] def short_desc(self):
short_desc = self.__doc__ or ''
if short_desc:
short_desc = "%s (DP > %i)" % (short_desc, self.threshold)
return short_desc