def test_onp_ignore_indels(self): """make sure indels aren't being combined with onps""" file = 'testdata/maflite/onp.indel.maf.txt' input = OnpCombiner(MafliteInputMutationCreator(file)) expected = list(MafliteInputMutationCreator(file).createMutations()) onp_muts = [mut for mut in input.createMutations()] self.assert_mutations_match_expected(expected=expected, result=onp_muts)
def test_multi_sample_maflite(self): """Tests a multi sample maf with several unaligned onps""" input = OnpCombiner(MafliteInputMutationCreator('testdata/maflite/onp_combination.maf.txt')) onp_muts =list(input.createMutations()) expected = self._tuples_to_MutationData([(1, 1, 1, "G", "A", "hg19"), (1, 1, 4, "GTTT", "CGAA", "hg19"), (1, 2, 3, "TT", "CC", "hg19"), (1, 12, 12, "T", "G", "hg19"), (2, 13, 13, "A", "G", "hg19")]) expected_pair_names = ['P2','P1','P3','P1','P1'] self._assert_mutation_lists_equal(onp_muts, expected) for mut, pair in zip(onp_muts, expected_pair_names): self.assertEqual(mut["Pair_Name"], pair)
def create_input_creator(inputFilename, inputFormat, genome_build="hg19", input_creator_options=None): inputCreatorDict = OncotatorCLIUtils.createInputFormatNameToClassDict() if inputFormat not in inputCreatorDict.keys(): raise NotImplementedError("The inputFormat specified: " + inputFormat + " is not supported.") else: inputConfig = inputCreatorDict[inputFormat][1] inputCreator = inputCreatorDict[inputFormat][0]( inputFilename, inputConfig, genome_build, input_creator_options) if input_creator_options.get( OptionConstants.INFER_ONPS ): #If we're combinging ONPs, wrap the input creater inputCreator = OnpCombiner(inputCreator) return inputCreator