10
|
1 '''Filter VCF on MQ filter.
|
|
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 MQ0Filter(PHEFilterBase):
|
|
14 '''Filter sites by MQ0 (Total Mapping Quality Zero Reads) to DP ratio.'''
|
|
15
|
|
16 name = "MinMQ0"
|
|
17 _default_threshold = 0.05
|
|
18 parameter = "mq0_ratio"
|
|
19
|
|
20 @classmethod
|
|
21 def customize_parser(self, parser):
|
|
22 arg_name = self.parameter.replace("_", "-")
|
|
23 parser.add_argument("--%s" % arg_name, type=float, default=self._default_threshold,
|
|
24 help="Filter sites below given MQ score (default: %s)" % self._default_threshold)
|
|
25
|
|
26 def __init__(self, args):
|
|
27 """Min Mapping Quality Zero constructor."""
|
|
28 # This needs to happen first, because threshold is initialised here.
|
|
29 super(MQ0Filter, 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.mq_score
|
|
35 elif isinstance(args, dict):
|
|
36 try:
|
|
37 self.threshold = float(args.get(self.parameter))
|
|
38 except (TypeError, ValueError):
|
|
39 logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
|
|
40 logging.error("This parameter requires to be a float!")
|
|
41 raise Exception("Could not create MQ0 filter from parameters: %s" % args)
|
|
42
|
|
43 def __call__(self, record):
|
|
44 """Filter a :py:class:`vcf.model._Record`."""
|
|
45
|
|
46 good_record = self._check_record(record)
|
|
47
|
|
48 if good_record is not True:
|
|
49 return good_record
|
|
50
|
|
51 record_mq = record.INFO.get("MQ0")
|
|
52
|
|
53 if record_mq:
|
|
54 # We consider DO from INFO not samples because MQ0 is also from INFO.
|
|
55 record_mq /= float(record.INFO.get("DP"))
|
|
56
|
|
57 if record_mq is None or record_mq > self.threshold:
|
|
58 # FIXME: when record_mq is None, i,e, error/missing, what do you do?
|
|
59 return record_mq 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 (MQ0 > %s)" % (short_desc, self.threshold)
|
|
68
|
|
69 return short_desc
|