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_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 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