def testHeaderCreation(self):
"""Test that a tcga vcf header can be generated, even from a blank mutation. """
vcfOR = TcgaVcfOutputRenderer("out/TCGAVCFHeader.out.txt")
m = MutationData()
m.createAnnotation('center', "broad.mit.edu")
hdr = vcfOR.createVcfHeader(m)
self.assertTrue(hdr is not None)
self.assertTrue(hdr <> "")
self.assertTrue(hdr.find("broad.mit.edu") <> -1, "Could not find string that should have been in header.")
def testHeaderCreation(self):
"""Test that a tcga vcf header can be generated, even from a blank mutation. """
vcfOR = TcgaVcfOutputRenderer("out/TCGAVCFHeader.out.txt")
m = MutationData()
m.createAnnotation('center', "broad.mit.edu")
hdr = vcfOR.createVcfHeader(m)
self.assertTrue(hdr is not None)
self.assertTrue(hdr <> "")
self.assertTrue(hdr.find("broad.mit.edu") <> -1, "Could not find string that should have been in header.")
def testChromRendering(self):
"""Make sure that the chromosome rendering in TCGA VCF is correct: "1" --> "1", "GLXXXX.Y" --> GLXXXX.Y, not <GLXXXX.Y>"""
vcfOR = TcgaVcfOutputRenderer("out/TCGAVCF.empty.out.txt")
testChrs = ["21", "MT", "GL1234.4", "1"]
gt = ["21", "MT", "GL1234.4", "1"]
ctr = 0
for t in testChrs:
val = vcfOR._renderChrom(t)
self.assertTrue(val == gt[ctr], "Chrom value did not match ground truth: " + t + " --> " + val + " GT: " + gt[ctr])
ctr += 1
def testChromRendering(self):
"""Make sure that the chromosome rendering in TCGA VCF is correct: "1" --> "1" , "GLXXXX.Y" --> <GLXXXX.Y>"""
vcfOR = TcgaVcfOutputRenderer("out/TCGAVCF.empty.out.txt")
testChrs = ["21", "MT", "GL1234.4", "1"]
gt = ["21", "MT", "<GL1234.4>", "1"]
ctr = 0
for t in testChrs:
val = vcfOR._renderChrom(t)
self.assertTrue(val == gt[ctr], "Chrom value did not match ground truth: " + t + " --> " + val + " GT: " + gt[ctr])
ctr += 1
def testFullIndelVcf(self):
""" Perform test of a Indel maflite all the way through TCGA VCF creation
"""
outputFilename = "out/TCGAVCFTest.indel.vcf"
callStatsIn = MafliteInputMutationCreator("testdata/maflite/Patient0.indel.maf.txt")
vcfOR = TcgaVcfOutputRenderer(outputFilename)
datasources = self._createDatasourcesForTesting()
annotator = Annotator()
annotator.setInputCreator(callStatsIn)
annotator.setOutputRenderer(vcfOR)
annotator.setManualAnnotations(self._createManualAnnotations())
for ds in datasources:
annotator.addDatasource(ds)
annotator.annotate()
self.assertTrue(os.path.exists(outputFilename))
# Check that the deletions have position decremented by one from what is present in the maflite
# Checking that 1 36643701 in the maflite (a deletion) becomes 1 36643700 in the vcf, but that the others are
# the same.
maflite_ic = MafliteInputMutationCreator("testdata/maflite/Patient0.indel.maf.txt")
muts = maflite_ic.createMutations()
vcf_reader = vcf.Reader(open(outputFilename, 'r'))
vcf_pos = [int(rec.POS) for rec in vcf_reader]
for m in muts:
# If the variant is a deletion, then the vcf position should be the same as maflite minus one. Otherwise, the same.
is_variant_deletion = (m.alt_allele == "") or (m.alt_allele == "-") or (m.alt_allele == ".")
if is_variant_deletion:
self.assertTrue((int(m.start) - 1) in vcf_pos, "Deletion was not correct for " + m.chr + ":" + m.start)
else:
self.assertTrue(int(m.start) in vcf_pos, "Insertion was not correct for " + m.chr + ":" + m.start)
def testFullSnpVcf(self):
""" Perform test of a SNP call stats (maflite) all the way through TCGA VCF creation. Only checks that a file was created.
"""
outputFilename = "out/TCGAVCFTest.snp.vcf"
callStatsIn = MafliteInputMutationCreator(
"testdata/Test.call_stats.trim.txt")
vcfOR = TcgaVcfOutputRenderer(outputFilename)
datasources = self._createDatasourcesForTesting()
annotator = Annotator()
annotator.setInputCreator(callStatsIn)
annotator.setOutputRenderer(vcfOR)
annotator.setManualAnnotations(self._createManualAnnotations())
for ds in datasources:
annotator.addDatasource(ds)
annotator.annotate()
self.assertTrue(os.path.exists(outputFilename))
maflite_ic = MafliteInputMutationCreator(
"testdata/maflite/Patient0.indel.maf.txt")
muts = maflite_ic.createMutations()
vcf_reader = vcf.Reader(open(outputFilename, 'r'))
for i, m in enumerate(muts):
rec = vcf_reader.next()
qual = rec.QUAL
# All records should have QUAL with a value (i.e. NOT ".")
self.assertIsNotNone(qual)
def _testInfoField(self, filter):
outputFilename = "out/TCGAVCFTest.indel.vcf.dummy"
vcfOR = TcgaVcfOutputRenderer(outputFilename)
mq0 = "0"
ss = "Somatic"
m = MutationData()
m.createAnnotation('t_ref_count', '20')
m.createAnnotation('t_alt_count', '25')
m.createAnnotation('n_ref_count', '100')
m.createAnnotation('n_alt_count', '150')
m.createAnnotation('dbSNP_RS', '')
m.createAnnotation('gene', 'FAKE')
m.createAnnotation('variant_type', 'SNP')
m.createAnnotation('variant_classification', 'Missense')
m.createAnnotation('transcript_id', 'tid001')
infoData = vcfOR._generateInfoField(m, filter, mq0, ss)
return infoData
def _testInfoField(self, filter):
outputFilename = "out/TCGAVCFTest.indel.vcf.dummy"
vcfOR = TcgaVcfOutputRenderer(outputFilename)
mq0 = "0"
ss = "Somatic"
m = MutationData()
m.createAnnotation('t_ref_count', '20')
m.createAnnotation('t_alt_count', '25')
m.createAnnotation('n_ref_count', '100')
m.createAnnotation('n_alt_count', '150')
m.createAnnotation('dbSNP_RS', '')
m.createAnnotation('gene', 'FAKE')
m.createAnnotation('variant_type', 'SNP')
m.createAnnotation('variant_classification', 'Missense')
m.createAnnotation('transcript_id', 'tid001')
infoData = vcfOR._generateInfoField(m, filter, mq0, ss)
return infoData
def testMafInput(self):
"""Make sure that we can render a TCGA VCF from a TCGA MAF -- using no datasources"""
inputFile = "testdata/maf/Patient1.snp.maf.annotated"
outputFilename = "out/maf2tcgavcf.vcf"
mafIn = MafliteInputMutationCreator(inputFile)
vcfOR = TcgaVcfOutputRenderer(outputFilename)
annotator = Annotator()
annotator.setInputCreator(mafIn)
annotator.setOutputRenderer(vcfOR)
annotator.setManualAnnotations(self._createManualAnnotations())
annotator.annotate()
self.assertTrue(os.path.exists(outputFilename))
statinfo = os.stat(outputFilename)
self.assertTrue(statinfo.st_size > 0, "Generated VCF file (" + outputFilename + ") is empty.")
def testFullSnpVcf(self):
""" Perform test of a SNP call stats (maflite) all the way through TCGA VCF creation. Only checks that a file was created.
"""
outputFilename = "out/TCGAVCFTest.snp.vcf"
callStatsIn = MafliteInputMutationCreator("testdata/Test.call_stats.trim.txt")
vcfOR = TcgaVcfOutputRenderer(outputFilename)
datasources = self._createDatasourcesForTesting()
annotator = Annotator()
annotator.setInputCreator(callStatsIn)
annotator.setOutputRenderer(vcfOR)
annotator.setManualAnnotations(self._createManualAnnotations())
for ds in datasources:
annotator.addDatasource(ds)
annotator.annotate()
self.assertTrue(os.path.exists(outputFilename))
def testEmptyInput(self):
"""Make sure that we can generate an empty vcf from an empty maflite"""
inputFile = "testdata/maflite/empty.maflite"
outputFilename = "out/empty.vcf"
callStatsIn = MafliteInputMutationCreator(inputFile)
vcfOR = TcgaVcfOutputRenderer(outputFilename)
datasources = self._createDatasourcesForTesting()
annotator = Annotator()
annotator.setInputCreator(callStatsIn)
annotator.setOutputRenderer(vcfOR)
annotator.setManualAnnotations(self._createManualAnnotations())
for ds in datasources:
annotator.addDatasource(ds)
annotator.annotate()
self.assertTrue(os.path.exists(outputFilename))
statinfo = os.stat(outputFilename)
self.assertTrue(statinfo.st_size > 0, "Generated VCF file (" + outputFilename + ") is empty.")
def testAnotherFullSNP(self):
"""Test SNP call stats . Just make sure no exception is thrown."""
inputFile = "testdata/maflite/Another.call_stats.txt"
outputFilename = "out/Another.call_stats.out.vcf"
callStatsIn = MafliteInputMutationCreator(inputFile)
vcfOR = TcgaVcfOutputRenderer(outputFilename)
datasources = self._createDatasourcesForTesting()
annotator = Annotator()
annotator.setInputCreator(callStatsIn)
annotator.setOutputRenderer(vcfOR)
annotator.setManualAnnotations(self._createManualAnnotations())
for ds in datasources:
annotator.addDatasource(ds)
annotator.annotate()
self.assertTrue(os.path.exists(outputFilename))
statinfo = os.stat(outputFilename)
self.assertTrue(statinfo.st_size > 0, "Generated VCF file (" + outputFilename + ") is empty.")
def testPopulatedButNullValuesInInitNLod(self):
"""Test that if init_n_lod is "." or "", there is no error """
m = MutationData()
m.createAnnotation("init_n_lod", "")
outputFilename = "out/blank.vcf"
vcfOR = TcgaVcfOutputRenderer(outputFilename)
lod = vcfOR._extract_lod(m,"init_n_lod")
self.assertEqual(lod, 50)
m["init_n_lod"] = '.'
lod = vcfOR._extract_lod(m, "init_n_lod")
self.assertEqual(lod, 50)
m["init_n_lod"] = '6'
lod = vcfOR._extract_lod(m, "init_n_lod")
self.assertEqual(lod, 6)
m["init_n_lod"] = '6.8'
lod = vcfOR._extract_lod(m, "init_n_lod")
self.assertEqual(lod, 6)
m["init_n_lod"] = '-12.8'
lod = vcfOR._extract_lod(m, "init_n_lod")
self.assertEqual(lod, -12)
m.createAnnotation("t_lod_fstar", "")
lod = vcfOR._extract_lod(m, "t_lod_fstar")
self.assertEqual(lod, 50)
m["t_lod_fstar"] = '.'
lod = vcfOR._extract_lod(m, "t_lod_fstar")
self.assertEqual(lod, 50)
m["t_lod_fstar"] = '6'
lod = vcfOR._extract_lod(m, "t_lod_fstar")
self.assertEqual(lod, 6)
m["t_lod_fstar"] = '6.8'
lod = vcfOR._extract_lod(m, "t_lod_fstar")
self.assertEqual(lod, 6)
m["t_lod_fstar"] = '-12.8'
lod = vcfOR._extract_lod(m, "t_lod_fstar")
self.assertEqual(lod, -12)
def testPopulatedButNullValuesInInitNLod(self):
"""Test that if init_n_lod is "." or "", there is no error """
m = MutationData()
m.createAnnotation("init_n_lod", "")
outputFilename = "out/blank.vcf"
vcfOR = TcgaVcfOutputRenderer(outputFilename)
lod = vcfOR._extract_lod(m,"init_n_lod")
self.assertEqual(lod, 50)
m["init_n_lod"] = '.'
lod = vcfOR._extract_lod(m, "init_n_lod")
self.assertEqual(lod, 50)
m["init_n_lod"] = '6'
lod = vcfOR._extract_lod(m, "init_n_lod")
self.assertEqual(lod, 6)
m["init_n_lod"] = '6.8'
lod = vcfOR._extract_lod(m, "init_n_lod")
self.assertEqual(lod, 6)
m["init_n_lod"] = '-12.8'
lod = vcfOR._extract_lod(m, "init_n_lod")
self.assertEqual(lod, -12)
m.createAnnotation("t_lod_fstar", "")
lod = vcfOR._extract_lod(m, "t_lod_fstar")
self.assertEqual(lod, 50)
m["t_lod_fstar"] = '.'
lod = vcfOR._extract_lod(m, "t_lod_fstar")
self.assertEqual(lod, 50)
m["t_lod_fstar"] = '6'
lod = vcfOR._extract_lod(m, "t_lod_fstar")
self.assertEqual(lod, 6)
m["t_lod_fstar"] = '6.8'
lod = vcfOR._extract_lod(m, "t_lod_fstar")
self.assertEqual(lod, 6)
m["t_lod_fstar"] = '-12.8'
lod = vcfOR._extract_lod(m, "t_lod_fstar")
self.assertEqual(lod, -12)