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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 DP4Filter(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 = "DP4"
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19 _default_threshold = 0.9
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20 parameter = "dp4_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 dp4 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(DP4Filter, 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:
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41 logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
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42 self.threshold = None
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43
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44
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45 def __call__(self, record):
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46 """Filter a :py:class:`vcf.model._Record`."""
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47
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48 if not record.is_snp:
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49 return None
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50
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51 try:
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52 record_dp = record.INFO.get("DP4")
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53
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54 # FIXME: when record length is > 2, what do you do?
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55 assert len(record_dp) == 4, "DP4 data should have 4 datum POS: %i" % record.POS
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56
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57 depth = sum(record_dp)
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58
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59 ratio = float(sum(record_dp[2:])) / depth
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60 except Exception:
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61 logging.error("Could not calculate DP4 ratio from %s POS: %s", record_dp, record.POS)
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62 ratio = None
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63
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64 if ratio is None or ratio < self.threshold:
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65 # FIXME: When ratio is None, i.e. error, what do you do?
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66 return ratio or False
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67 else:
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68 return None
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69
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70 def short_desc(self):
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71 short_desc = self.__doc__ or ''
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72
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73 if short_desc:
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74 short_desc = "%s (DP4 ratio > %s )" % (short_desc, self.threshold)
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75
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76 return short_desc
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