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10
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1 '''Filter VCFs on AD ratio.
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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 ADFilter(PHEFilterBase):
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15 '''Filter sites by AD ratio.'''
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16
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17
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18 name = "ADRatio"
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19 _default_threshold = 0.9
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20 parameter = "ad_ratio"
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21
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22 @classmethod
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23 def customize_parser(self, parser):
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24 arg_name = self.parameter.replace("_", "-")
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25 parser.add_argument("--%s" % arg_name, type=float, default=self._default_threshold,
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26 help="Filter sites below minimum ad ratio (default: %s)" % self._default_threshold)
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27
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28 def __init__(self, args):
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29 """AD Ratio constructor."""
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30 # This needs to happen first, because threshold is initialised here.
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31 super(ADFilter, self).__init__(args)
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32
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33 # Change the threshold to custom dp value.
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34 self.threshold = self._default_threshold
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35 if isinstance(args, argparse.Namespace):
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36 self.threshold = args.ad_ratio
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37 elif isinstance(args, dict):
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38 try:
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39 self.threshold = float(args.get(self.parameter))
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40 except (TypeError, ValueError):
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41 logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
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42 logging.error("This parameter requires to be a float!")
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43 raise Exception("Could not create AD filter from parameters: %s" % args)
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44
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45
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46 def __call__(self, record):
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47 """Filter a :py:class:`vcf.model._Record`."""
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48
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49 good_record = self._check_record(record)
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50
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51 if good_record is not True:
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52 return good_record
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53
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54 if len(record.samples) > 1:
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55 logging.warn("More than 1 sample detected. Only first is considered.")
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56
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57 try:
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58 record_ad = record.samples[0].data.AD
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59
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60 # FIXME: when record length is > 2, what do you do?
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61 assert len(record_ad) == 2, "AD data is incomplete POS: %i" % record.POS
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62
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63 depth = sum(record.samples[0].data.AD)
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64
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65 ratio = float(record_ad[1]) / depth
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66 except Exception:
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67 logging.warn("Could not calculate AD ratio from %s POS: %s", record, record.POS)
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68 ratio = None
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69
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70 if ratio is None or ratio < self.threshold:
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71 # FIXME: When ratio is None, i.e. error, what do you do?
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72 return ratio or False
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73 else:
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74 return None
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75
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76 def short_desc(self):
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77 short_desc = self.__doc__ or ''
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78
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79 if short_desc:
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80 short_desc = "%s (AD ratio > %s )" % (short_desc, self.threshold)
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81
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82 return short_desc
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