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10
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1 '''Filter VCF on GQ parameter.
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2 Created on 24 Sep 2015
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3
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4 @author: alex
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5 '''
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6
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7 import argparse
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8 import logging
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9
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10 from phe.variant_filters import PHEFilterBase
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11
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12
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13 class GQFilter(PHEFilterBase):
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14 '''Filter sites by GQ score.'''
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15
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16 name = "MinGQ"
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17 _default_threshold = 0
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18 parameter = "gq_score"
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19
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20 @classmethod
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21 def customize_parser(self, parser):
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22 arg_name = self.parameter.replace("_", "-")
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23 parser.add_argument("--%s" % arg_name, type=int, default=self._default_threshold,
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24 help="Filter sites below given GQ score (default: %s)" % self._default_threshold)
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25
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26 def __init__(self, args):
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27 """Min Depth constructor."""
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28 # This needs to happen first, because threshold is initialised here.
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29 super(GQFilter, self).__init__(args)
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30
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31 # Change the threshold to custom gq value.
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32 self.threshold = self._default_threshold
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33 if isinstance(args, argparse.Namespace):
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34 self.threshold = args.gq_score
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35 elif isinstance(args, dict):
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36 try:
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37 self.threshold = int(args.get(self.parameter))
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38 except (TypeError, ValueError):
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39 logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
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40 logging.error("This parameter requires to be an integer!")
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41 raise Exception("Could not create GQ filter from parameters: %s" % args)
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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 good_record = self._check_record(record)
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47
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48 if good_record is not True:
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49 return good_record
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50
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51 if len(record.samples) > 1:
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52 logging.warn("More than 1 sample detected. Only first is considered.")
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53
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54 try:
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55 record_gq = record.samples[0].data.GQ
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56 except AttributeError:
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57 logging.warn("Could not retrieve GQ score POS %i", record.POS)
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58 record_gq = None
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59
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60 if record_gq is None or record_gq < self.threshold:
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61 # FIXME: when record_gq is None, i,e, error, what do you do?
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62 return record_gq or False
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63 else:
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64 return None
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65
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66 def short_desc(self):
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67 short_desc = self.__doc__ or ''
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68
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69 if short_desc:
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70 short_desc = "%s (GQ > %s)" % (short_desc, self.threshold)
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71
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72 return short_desc
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