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10
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1 '''Filter VCF on depth of coverage.
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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 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 DepthFilter(PHEFilterBase):
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14 """Filter sites by depth."""
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15
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16 name = "MinDepth"
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17 _default_threshold = 5
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18 parameter = "min_depth"
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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("--" % arg_name, type=int, default=self._default_threshold,
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24 help="Filter sites below minimum depth (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(DepthFilter, self).__init__(args)
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30
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31 # Change the threshold to custom dp 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.min_depth
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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 integer threshold from %s", args.get(self.parameter))
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40 raise Exception("Could not create depth filter from parameters: %s" % args)
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41
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42 def __call__(self, record):
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43 """Filter a :py:class:`vcf.model._Record`."""
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44
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45 if len(record.samples) > 1:
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46 logging.warn("Currently we only filter VCFs with 1 sample. Only first sample will be used.")
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47 logging.warn("This parameter requires to be an integer!")
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48
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49 try:
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50 record_dp = record.samples[0].data.DP
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51 except AttributeError:
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52 record_dp = None
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53
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54 if record_dp is None:
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55 # logging.debug("Falling back to INFO DP")
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56 record_dp = record.INFO.get("DP")
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57
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58 if record_dp is None or record_dp < self.threshold:
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59 return record_dp or False
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60 else:
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61 return None
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62
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63 def short_desc(self):
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64 short_desc = self.__doc__ or ''
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65
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66 if short_desc:
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67 short_desc = "%s (DP > %i)" % (short_desc, self.threshold)
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68
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69 return short_desc
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