def testSimpleRead(self):
""" Read a good maflite file and make sure that each mutation validates """
tmp = MafliteInputMutationCreator("testdata/maflite/Patient0.indel.maf.txt", 'configs/maflite_input.config')
muts = tmp.createMutations()
# If no exception is thrown, then this test passes.
for m in muts:
MutUtils.validateMutation(m)
def testSimpleRead(self):
""" Read a good maflite file and make sure that each mutation validates """
tmp = MafliteInputMutationCreator(
"testdata/maflite/Patient0.indel.maf.txt", None,
'configs/maflite_input.config')
muts = tmp.createMutations()
# If no exception is thrown, then this test passes.
for m in muts:
MutUtils.validateMutation(m)
def testNoUnknownAnnotations(self):
""" Make sure that the gaf 3.0 datasource does not annotate anything with source set to Unknown """
inputCreator = MafliteInputMutationCreator('testdata/maflite/Patient0.snp.maf.txt')
gafDatasource = TestUtils.createTranscriptProviderDatasource(self.config)
mutations = inputCreator.createMutations()
for m in mutations:
m = gafDatasource.annotate_mutation(m)
MutUtils.validateMutation(m)
unknownAnnotations = MutUtils.getUnknownAnnotations(m)
self.assertTrue(len(unknownAnnotations) == 0, "Unknown annotations exist in mutation: " + str(unknownAnnotations))
def testChrGLs(self):
""" Test that mutations on unaligned transcripts can be annotated properly. I.e. when chromosome = GL....."""
inputCreator = MafliteInputMutationCreator('testdata/maflite/chrGLs.maf.tsv', "configs/maflite_input.config")
gafDatasource = TestUtils.createTranscriptProviderDatasource(self.config)
mutations = inputCreator.createMutations()
for m in mutations:
try:
m = gafDatasource.annotate_mutation(m)
MutUtils.validateMutation(m)
except Exception as e:
# Fail this test because an exception was thrown
self.assertTrue(False, "Erroneous exception was thrown: " + str(e) + "\n" + traceback.format_exc())
self.assertTrue(m['gene'] != '')
def testNoLostMutations(self):
""" Does a simple gaf datasource annotation run and makes sure that no mutations were lost """
inputFilename = 'testdata/maflite/Patient0.snp.maf.txt'
inputCreator = MafliteInputMutationCreator(inputFilename, "configs/maflite_input.config")
gafDatasource = TestUtils.createTranscriptProviderDatasource(self.config)
numMutsInput = len(file(inputFilename, 'r').readlines()) - 1
mutations = inputCreator.createMutations()
ctr = 0
for m in mutations:
m = gafDatasource.annotate_mutation(m)
MutUtils.validateMutation(m)
ctr += 1
self.assertEqual(ctr, numMutsInput, "Gaf data source altered mutation count.")
def testNoUnknownAnnotations(self):
""" Make sure that the gaf 3.0 datasource does not annotate anything with source set to Unknown """
inputCreator = MafliteInputMutationCreator(
'testdata/maflite/Patient0.snp.maf.txt')
gafDatasource = TestUtils.createTranscriptProviderDatasource(
self.config)
mutations = inputCreator.createMutations()
for m in mutations:
m = gafDatasource.annotate_mutation(m)
MutUtils.validateMutation(m)
unknownAnnotations = MutUtils.getUnknownAnnotations(m)
self.assertTrue(
len(unknownAnnotations) == 0,
"Unknown annotations exist in mutation: " +
str(unknownAnnotations))
def testChrGLs(self):
""" Test that mutations on unaligned transcripts can be annotated properly. I.e. when chromosome = GL....."""
inputCreator = MafliteInputMutationCreator(
'testdata/maflite/chrGLs.maf.tsv', "configs/maflite_input.config")
gafDatasource = TestUtils.createTranscriptProviderDatasource(
self.config)
mutations = inputCreator.createMutations()
for m in mutations:
try:
m = gafDatasource.annotate_mutation(m)
MutUtils.validateMutation(m)
except Exception as e:
# Fail this test because an exception was thrown
self.assertTrue(
False, "Erroneous exception was thrown: " + str(e) + "\n" +
traceback.format_exc())
self.assertTrue(m['gene'] != '')
def testNoLostMutations(self):
""" Does a simple gaf datasource annotation run and makes sure that no mutations were lost """
inputFilename = 'testdata/maflite/Patient0.snp.maf.txt'
inputCreator = MafliteInputMutationCreator(
inputFilename, "configs/maflite_input.config")
gafDatasource = TestUtils.createTranscriptProviderDatasource(
self.config)
numMutsInput = len(file(inputFilename, 'r').readlines()) - 1
mutations = inputCreator.createMutations()
ctr = 0
for m in mutations:
m = gafDatasource.annotate_mutation(m)
MutUtils.validateMutation(m)
ctr += 1
self.assertEqual(ctr, numMutsInput,
"Gaf data source altered mutation count.")
