diff phe/variant_filters/DP4Filter.py @ 0:834a312c0114 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/DP4Filter.py	Thu Dec 10 09:22:39 2015 -0500
@@ -0,0 +1,76 @@
+'''Filter VCFs on AD ratio.
+
+Created on 24 Sep 2015
+
+@author: alex
+'''
+
+import argparse
+import logging
+
+from phe.variant_filters import PHEFilterBase
+
+
+class DP4Filter(PHEFilterBase):
+    '''Filter sites by AD ratio.'''
+
+
+    name = "DP4"
+    _default_threshold = 0.9
+    parameter = "dp4_ratio"
+
+    @classmethod
+    def customize_parser(self, parser):
+        arg_name = self.parameter.replace("_", "-")
+        parser.add_argument("--%s" % arg_name, type=float, default=self._default_threshold,
+                help="Filter sites below minimum dp4 ratio (default: %s)" % self._default_threshold)
+
+    def __init__(self, args):
+        """AD Ratio constructor."""
+        # This needs to happen first, because threshold is initialised here.
+        super(DP4Filter, self).__init__(args)
+
+        # Change the threshold to custom dp value.
+        self.threshold = self._default_threshold
+        if isinstance(args, argparse.Namespace):
+            self.threshold = args.ad_ratio
+        elif isinstance(args, dict):
+            try:
+                self.threshold = float(args.get(self.parameter))
+            except TypeError:
+                logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
+                self.threshold = None
+
+
+    def __call__(self, record):
+        """Filter a :py:class:`vcf.model._Record`."""
+
+        if not record.is_snp:
+            return None
+
+        try:
+            record_dp = record.INFO.get("DP4")
+
+            # FIXME: when record length is > 2, what do you do?
+            assert len(record_dp) == 4, "DP4 data should have 4 datum POS: %i" % record.POS
+
+            depth = sum(record_dp)
+
+            ratio = float(sum(record_dp[2:])) / depth
+        except Exception:
+            logging.error("Could not calculate DP4 ratio from %s POS: %s", record_dp, record.POS)
+            ratio = None
+
+        if ratio is None or ratio < self.threshold:
+            # FIXME: When ratio is None, i.e. error, what do you do?
+            return ratio or False
+        else:
+            return None
+
+    def short_desc(self):
+        short_desc = self.__doc__ or ''
+
+        if short_desc:
+            short_desc = "%s (DP4 ratio > %s )" % (short_desc, self.threshold)
+
+        return short_desc