Mercurial > repos > ulfschaefer > filter_vcf

comparison phe/variant_filters/GQFilter.py @ 0:834a312c0114 draft

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author ulfschaefer
date Thu, 10 Dec 2015 09:22:39 -0500
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-1:000000000000 0:834a312c0114
1 '''Filter VCF on GQ parameter.
2 Created on 24 Sep 2015
3
4 @author: alex
5 '''
6
7 import argparse
8 import logging
9
10 from phe.variant_filters import PHEFilterBase
11
12
13 class GQFilter(PHEFilterBase):
14 '''Filter sites by GQ score.'''
15
16 name = "MinGQ"
17 _default_threshold = 0
18 parameter = "gq_score"
19
20 @classmethod
21 def customize_parser(self, parser):
22 arg_name = self.parameter.replace("_", "-")
23 parser.add_argument("--%s" % arg_name, type=int, default=self._default_threshold,
24 help="Filter sites below given GQ score (default: %s)" % self._default_threshold)
25
26 def __init__(self, args):
27 """Min Depth constructor."""
28 # This needs to happen first, because threshold is initialised here.
29 super(GQFilter, self).__init__(args)
30
31 # Change the threshold to custom gq value.
32 self.threshold = self._default_threshold
33 if isinstance(args, argparse.Namespace):
34 self.threshold = args.gq_score
35 elif isinstance(args, dict):
36 try:
37 self.threshold = int(args.get(self.parameter))
38 except TypeError:
39 logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
40 self.threshold = None
41
42 def __call__(self, record):
43 """Filter a :py:class:`vcf.model._Record`."""
44
45 if not record.is_snp:
46 return None
47
48 if len(record.samples) > 1:
49 logging.warn("More than 1 sample detected. Only first is considered.")
50
51 try:
52 record_gq = record.samples[0].data.GQ
53 except AttributeError:
54 logging.error("Could not retrieve GQ score POS %i", record.POS)
55 record_gq = None
56
57 if record_gq is None or record_gq < self.threshold:
58 # FIXME: when record_gq is None, i,e, error, what do you do?
59 return record_gq or False
60 else:
61 return None
62
63 def short_desc(self):
64 short_desc = self.__doc__ or ''
65
66 if short_desc:
67 short_desc = "%s (GQ > %s)" % (short_desc, self.threshold)
68
69 return short_desc