Mercurial > repos > ulfschaefer > filter_vcf

comparison phe/variant_filters/GTFilter.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 GT filter parameter.
2
3 Created on 24 Sep 2015
4
5 @author: alex
6 '''
7
8 import argparse
9 import logging
10
11 from phe.variant_filters import PHEFilterBase
12
13
14 class UncallableGTFilter(PHEFilterBase):
15 '''Filter uncallable genotypes'''
16
17 name = "UncallGT"
18 _default_threshold = None
19 parameter = "uncall_gt"
20
21 @classmethod
22 def customize_parser(self, parser):
23 arg_name = self.parameter.replace("_", "-")
24 parser.add_argument("--%s" % arg_name, type=str, default=self._default_threshold,
25 help="Filter sites below given GQ score (default: %s)" % self._default_threshold)
26
27 def __init__(self, args):
28 """Min Depth constructor."""
29 # This needs to happen first, because threshold is initialised here.
30 super(UncallableGTFilter, self).__init__(args)
31
32 # Change the threshold to custom gq value.
33 self.threshold = self._default_threshold
34 if isinstance(args, argparse.Namespace):
35 self.threshold = args.gq_score
36 elif isinstance(args, dict):
37 try:
38 self.threshold = str(args.get(self.parameter))
39 except TypeError:
40 logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
41 self.threshold = None
42
43 def __call__(self, record):
44 """Filter a :py:class:`vcf.model._Record`."""
45
46 if len(record.samples) > 1:
47 logging.warn("More than 1 sample detected. Only first is considered.")
48
49 try:
50 record_gt = record.samples[0].data.GT
51 except AttributeError:
52 logging.error("Could not retrieve GQ score POS %i", record.POS)
53 record_gt = None
54
55 if record_gt is None:
56 return "./."
57 else:
58 return None
59
60 def short_desc(self):
61 short_desc = self.__doc__ or ''
62
63 if short_desc:
64 short_desc = "%s (GT != ./. )" % (short_desc)
65
66 return short_desc
67
68 def is_gap(self):
69 return True
70
71 def is_n(self):
72 return False