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