def verifyGenotypeConversion(self, vcfGenotype, vcfPhaseset, callGenotype, callPhaseset): """ Verifies that the convertGenotype function properly converts the vcf genotype and phaseset values into the desired call genotype and phaseset values. """ self.assertEqual((callGenotype, callPhaseset), variants.convertVCFGenotype(vcfGenotype, vcfPhaseset))
def verifyGenotypeConversion( self, vcfGenotype, vcfPhaseset, callGenotype, callPhaseset): """ Verifies that the convertGenotype function properly converts the vcf genotype and phaseset values into the desired call genotype and phaseset values. """ self.assertEqual( (callGenotype, callPhaseset), variants.convertVCFGenotype(vcfGenotype, vcfPhaseset))
def _verifyVariantCallEqual(self, gaCall, pyvcfCall): genotype, phaseset = variants.convertVCFGenotype( pyvcfCall.data.GT, pyvcfCall.phased) # callSetId information is not available in pyvcf.model._Call self.assertEqual(gaCall.callSetName, pyvcfCall.sample) self.assertEqual(gaCall.genotype, genotype) phaseset = None if pyvcfCall.phased: phaseset = "*" self.assertEqual(gaCall.phaseset, phaseset) if len(gaCall.genotypeLikelihood) > 0: self._compareTwoListFloats( gaCall.genotypeLikelihood, pyvcfCall.data.GL) else: self.assertNotIn("GL", pyvcfCall.data) for key, value in gaCall.info.items(): if key != "GT" and key != "GL": if isinstance(value[0], (list, tuple)): self._compareTwoListFloats(value[0], getattr( pyvcfCall.data, key)) elif isinstance(value[0], float): self._compareTwoFloats(value[0], getattr( pyvcfCall.data, key))
def _verifyVariantCallEqual(self, gaCall, pyvcfCall): genotype, phaseset = variants.convertVCFGenotype( pyvcfCall.data.GT, pyvcfCall.phased) # callSetId information is not available in pyvcf.model._Call self.assertEqual(gaCall.callSetName, pyvcfCall.sample) self.assertEqual(gaCall.genotype, genotype) phaseset = None if pyvcfCall.phased: phaseset = "*" self.assertEqual(gaCall.phaseset, phaseset) if len(gaCall.genotypeLikelihood) > 0: self._compareTwoListFloats(gaCall.genotypeLikelihood, pyvcfCall.data.GL) else: self.assertNotIn("GL", pyvcfCall.data) for key, value in gaCall.info.items(): if key != "GT" and key != "GL": if isinstance(value[0], (list, tuple)): self._compareTwoListFloats(value[0], getattr(pyvcfCall.data, key)) elif isinstance(value[0], float): self._compareTwoFloats(value[0], getattr(pyvcfCall.data, key))