def test_simple_seg_file_input(self):
"""Test that we can read in a seg file, do no annotation, and output as SIMPLE_TSV"""
inputFilename = "testdata/seg/Patient0.seg.txt"
output_filename = "out/test_simple_seg_file_input.tsv"
if os.path.exists(output_filename):
os.remove(output_filename)
ic = MafliteInputMutationCreator(inputFilename, 'configs/seg_file_input.config')
segs = ic.createMutations()
i = 1
for i,seg in enumerate(segs):
pass
self.assertTrue((i+1) == 27, "Found %d segments when there should have been 27." % (i+1))
ic = MafliteInputMutationCreator(inputFilename, 'configs/seg_file_input.config')
segs = ic.createMutations()
outputRenderer = SimpleOutputRenderer(output_filename, '')
outputRenderer.renderMutations(segs)
# Now check the output
output_reader = GenericTsvReader(output_filename)
required_cols = ["Sample", "Num_Probes", "Segment_Mean"]
headers = output_reader.getFieldNames()
for rcol in required_cols:
self.assertTrue(rcol in headers)
for line_dict in output_reader:
self.assertTrue(line_dict['start'] is not None)
self.assertTrue(line_dict['start'].strip() != "")
self.assertTrue(line_dict['end'] is not None)
self.assertTrue(line_dict['end'].strip() != "")
def test_simple_seg_file_annotations(self):
"""Test that we can read in a seg file, do GENCODE annotation, and output as SIMPLE_TSV"""
inputFilename = "testdata/seg/Patient0.seg.txt"
output_filename = "out/test_simple_seg_file_annotations.tsv"
if os.path.exists(output_filename):
os.remove(output_filename)
ic = MafliteInputMutationCreator(inputFilename, None,
'configs/seg_file_input.config')
segs = ic.createMutations()
i = 1
for i, seg in enumerate(segs):
pass
self.assertTrue(
(i + 1) == 27,
"Found %d segments when there should have been 27." % (i + 1))
ic = MafliteInputMutationCreator(inputFilename, None,
'configs/seg_file_input.config')
segs = ic.createMutations()
gencode_ds = TestUtils._create_test_gencode_v19_ds(
"out/seg_file_gencode_ds")
annotator = Annotator()
segs_annotated = []
for seg in segs:
segs_annotated.append(gencode_ds.annotate_segment(seg))
outputRenderer = SimpleOutputRenderer(output_filename, '')
outputRenderer.renderMutations(segs_annotated.__iter__())
# Now check the output
output_reader = GenericTsvReader(output_filename)
required_cols = ["Sample", "Num_Probes", "Segment_Mean"]
headers = output_reader.getFieldNames()
for rcol in required_cols:
self.assertTrue(rcol in headers)
for line_dict in output_reader:
self.assertTrue(line_dict['start'] is not None)
self.assertTrue(line_dict['start'].strip() != "")
self.assertTrue(line_dict['end'] is not None)
self.assertTrue(line_dict['end'].strip() != "")
self.assertTrue("genes" in line_dict.keys())
def testMulticoreAnnotateFromChunkedFile(self):
#TODO: Add unit test that Mutation data is pickle-able
inputFile = "testdata/maflite/Patient0.snp.maf.txt"
outputFile = "out/testGAFMulticorePatient0.snp.maf.txt"
chunkSize = 200
numChunks = 4
gafDatasource = TestUtils.createGafDatasourceProxy(self.config)
ic = MafliteInputMutationCreator(inputFile)
oc = SimpleOutputRenderer(outputFile)
# createChunks
muts = ic.createMutations()
allAnnotatedChunksFlat = []
are_mutations_remaining = True
p = LoggingPool(processes=numChunks)
while are_mutations_remaining:
chunks = []
for j in xrange(0, numChunks):
chunk = []
for i in xrange(0, chunkSize):
try:
chunk.append(muts.next())
except StopIteration:
are_mutations_remaining = False
break
chunks.append((chunk, gafDatasource))
annotatedChunks = p.map(annotate_mutations_global, chunks)
annotatedChunksFlat = self._flattenChunks(annotatedChunks)
allAnnotatedChunksFlat.append(annotatedChunksFlat)
p.close()
p.join()
annotatedMuts = chain.from_iterable(allAnnotatedChunksFlat)
ctr = 0
oc.renderMutations(annotatedMuts, Metadata())
tsvReader = GenericTsvReader(outputFile)
for line in tsvReader:
ctr += 1
self.assertTrue(ctr == 730, "Should have read 730 variants, but read " + str(ctr))
def testMulticoreAnnotateFromChunkedFile(self):
#TODO: Add unit test that Mutation data is pickle-able
inputFile = "testdata/maflite/Patient0.snp.maf.txt"
outputFile = "out/testGAFMulticorePatient0.snp.maf.txt"
chunkSize = 200
numChunks = 4
gafDatasource = TestUtils.createGafDatasourceProxy(self.config)
ic = MafliteInputMutationCreator(inputFile)
oc = SimpleOutputRenderer(outputFile)
# createChunks
muts = ic.createMutations()
allAnnotatedChunksFlat = []
are_mutations_remaining = True
p = LoggingPool(processes=numChunks)
while are_mutations_remaining:
chunks = []
for j in xrange(0, numChunks):
chunk = []
for i in xrange(0, chunkSize):
try:
chunk.append(muts.next())
except StopIteration:
are_mutations_remaining = False
break
chunks.append((chunk, gafDatasource))
annotatedChunks = p.map(annotate_mutations_global, chunks)
annotatedChunksFlat = self._flattenChunks(annotatedChunks)
allAnnotatedChunksFlat.append(annotatedChunksFlat)
p.close()
p.join()
annotatedMuts = chain.from_iterable(allAnnotatedChunksFlat)
ctr = 0
oc.renderMutations(annotatedMuts, Metadata())
tsvReader = GenericTsvReader(outputFile)
for line in tsvReader:
ctr += 1
self.assertTrue(ctr == 730,
"Should have read 730 variants, but read " + str(ctr))
