def testSamtoolsMpileupSingleThread(self):
Grid.useGrid = False
SamtoolsMpileup.SamtoolsMpileup(TestSnvCaller.testPool).callSnvs()
outputFile = TestSnvCaller.testPool.vcf[None].fileName
self.assertEqual(
os.path.abspath(outputFile),
os.path.abspath(TestSnvCaller.expVcfFile),
os.path.abspath(outputFile) + " not is " +
os.path.abspath(TestSnvCaller.expVcfFile))
#Check if the file contains exactly one snp
self.checkNoOfSnps(TestSnvCaller.expVcfFile)
def testSamtoolsPath(self):
SnvCaller.converting = "not done"
gzFile = "../testFiles/input/test.fq.gz"
refGzFile = "../testFiles/input/revTest.fq.gz"
TestSnvCaller.sample.bam = None
TestSnvCaller.sample.setForwardFq(gzFile)
TestSnvCaller.sample.setReversedFq(refGzFile)
TestSnvCaller.sample.reversedFq.forward = False
samt = SamtoolsMpileup.SamtoolsMpileup(TestSnvCaller.testPool)
samt.callSnvs()
outputFile = TestSnvCaller.testPool.vcf[None].fileName
self.assertEqual(
os.path.abspath(outputFile),
os.path.abspath(TestSnvCaller.expVcfFile),
os.path.abspath(outputFile) + " not is " +
os.path.abspath(TestSnvCaller.expVcfFile))
#Check if the file contains exactly one snp
self.checkNoOfSnps(TestSnvCaller.expVcfFile)
def testSamtoolsMultiple(self):
#add an extra sample to the pool
TestSnvCaller.sample2 = Sample.Sample(TestSnvCaller.testPool,
"testLib2")
TestSnvCaller.sample2.bam = BamFile.BamFile(TestSnvCaller.testPool,
TestSnvCaller.sample2,
TestSnvCaller.inputBam)
TestSnvCaller.testPool.addSample(TestSnvCaller.sample2)
#Execute and check execution output
SamtoolsMpileup.SamtoolsMpileup(TestSnvCaller.testPool).callSnvs()
outputFile = TestSnvCaller.testPool.vcf[None].fileName
self.assertEqual(
os.path.abspath(outputFile),
os.path.abspath(TestSnvCaller.expVcfFile),
os.path.abspath(outputFile) + " not is " +
os.path.abspath(TestSnvCaller.expVcfFile))
#Check if the file contains exactly one snp
self.checkNoOfSnps(TestSnvCaller.expVcfFile)
