def testSampleNameSelectorWithMaf(self):
input = MafliteInputMutationCreator("testdata/maflite/tiny_maflite.maf.txt")
first_mut = next(input.createMutations())
s = SampleNameSelector(first_mut)
for mut in input.createMutations():
self.assertEqual("Patient0-Normal-Patient0-Tumor", s.getSampleName(mut))
self.assertEqual(s.getAnnotationSource(),"OUTPUT")
self.assertEqual(s.getOutputAnnotationName(), MutUtils.SAMPLE_NAME_ANNOTATION_NAME)
def testSampleNameSelectorWithVCF(self):
input = VcfInputMutationCreator("testdata/vcf/example.1row.vcf")
first_mut = next(input.createMutations())
s = SampleNameSelector(first_mut)
expected = ["NA 00001", "NA 00002", "NA 00003"]
for mut in input.createMutations():
self.assertIn(s.getSampleName(mut), expected)
self.assertEqual(s.getAnnotationSource(), "INPUT")
self.assertEquals(s.getOutputAnnotationName(), "sample_name")
def testSampleNameSelectorWithVCF(self):
input = VcfInputMutationCreator("testdata/vcf/example.1row.vcf")
first_mut = next(input.createMutations())
s = SampleNameSelector(first_mut)
expected = ["NA 00001", "NA 00002", "NA 00003"]
for mut in input.createMutations():
self.assertIn(s.getSampleName(mut), expected)
self.assertEqual(s.getAnnotationSource(), "INPUT")
self.assertEquals(s.getOutputAnnotationName(), "sample_name")
def testSampleNameSelectorWithMaf(self):
input = MafliteInputMutationCreator(
"testdata/maflite/tiny_maflite.maf.txt")
first_mut = next(input.createMutations())
s = SampleNameSelector(first_mut)
for mut in input.createMutations():
self.assertEqual("Patient0-Normal-Patient0-Tumor",
s.getSampleName(mut))
self.assertEqual(s.getAnnotationSource(), "OUTPUT")
self.assertEqual(s.getOutputAnnotationName(),
MutUtils.SAMPLE_NAME_ANNOTATION_NAME)
def _writeMuts2Tsv(self, muts, path):
"""
Given a mutation generator, this methods writes a tab separated file for all mutations in the mutation
generator. In addition, this method computes the appropriate sample name in scenarios where the mutation is
missing sample name annotation. It also computes a list of all chromosomes and sample names contained within
the generator.
:param path: temporary filename
:param muts: generator object with mutations
"""
sampleNames = set()
chroms = set()
writer = None
# create a temporary file to write tab-separated file
tempTsvFile = tempfile.NamedTemporaryFile(dir=path, delete=False)
self.logger.debug("Creating intermediate tsv file at %s" % tempTsvFile.name)
mutAttributeNames = []
sampleNameSelector = SampleNameSelector(self.mutation,
configFile=self.configTable.getConfigFilename(),
section="OTHER")
with open(tempTsvFile.name, 'w') as fptr:
ctr = 0
sampleNameAnnotationName = sampleNameSelector.getOutputAnnotationName()
sampleNameSource = sampleNameSelector.getAnnotationSource()
for mut in muts:
if len(mutAttributeNames) == 0:
mutAttributeNames = mut.getAttributeNames()
sampleName = sampleNameSelector.getSampleName(mut)
if sampleName is not None:
if mut.get(sampleNameAnnotationName, None) is None:
mut.createAnnotation(sampleNameAnnotationName, sampleName, sampleNameSource)
sampleNames.add(sampleName)
# Parse chromosome
chroms.add(mut.chr)
updated_start, updated_ref_allele, updated_alt_allele = MutUtils.retrieveMutCoordinatesForRendering(mut)
mut.ref_allele = updated_ref_allele
mut.alt_allele = updated_alt_allele
mut.start = updated_start
if ctr == 0:
fieldnames2Render = MutUtils.getAllAttributeNames(mut)
if sampleNameAnnotationName is not None:
fieldnames2Render += [sampleNameAnnotationName]
for fieldname in fieldnames2Render: # fieldnames that start "_" aren't rendered
if fieldname.startswith("_"):
fieldnames2Render.remove(fieldname)
writer = csv.DictWriter(fptr, fieldnames2Render, extrasaction='ignore', delimiter=self.delimiter,
lineterminator=self.lineterminator)
writer.writeheader()
writer.writerow(mut)
ctr += 1
if (ctr % 1000) == 0:
self.logger.info("Wrote " + str(ctr) + " mutations to tsv.")
sampleNames = list(sampleNames)
sampleNames.sort()
chroms = list(chroms)
return chroms, sampleNames, tempTsvFile.name
