def execute(self, executable):
"""The method execute checks which program has to be executed and executes this program
:param executable: the argument of the commandline which determines which program has to be executed
:type executable: str
"""
if executable == "haplotyping":
if Grid.useGrid == True:
Haplotyper.executeBeagleCluster(self.pool)
else:
Haplotyper.executeBeagleMultiThread(self.pool)
elif executable == "snvCalling":
if Program.config.snvCaller == "samtools": # @UndefinedVariable
SamtoolsMpileup.executeSamtoolsMultiThreaded(self.pool)
elif Program.config.snvCaller == "GATK": # @UndefinedVariable
Gatk.Gatk(self.pool).callSnvs()
elif executable == "mapping":
mapper = Mapper.Mapper()
for sample in self.samples:
mapper.map(sample)
elif executable == "allelicDiversity":
if Program.config.gffFile == None: # @UndefinedVariable
print("When calculating the allelic diversity, a gff file is needed, this option can be set with the option --gff <file>")
exit()
allelicDiverityCalculator = AllelicDiversity.AllelicDiversity(self.pool, Program.config.gffFile) # @UndefinedVariable
allelicDiverityCalculator.getAllelicDiversity()
elif executable == "findLoci":
if Program.config.phenoData == None: # @UndefinedVariable
print("When finding loci, a csv file is needed with the phenotype data, this option can be set with the option --phen <file>")
exit()
if Program.config.gffFile == None: # @UndefinedVariable
print("When finding loci, a file with phenotype data is needed, this option can be set with the option --gff <file>")
exit()
lociFinder = LociFinder.LociFinder()
lociFinder.findLoci(self.pool)
def testSamtoolsMpileupMultiThread(self):
expOutFile = "../testFiles/output/testPool/testPool_SL2.40ch11_22900-24100.vcf"
SamtoolsMpileup.executeSamtoolsMultiThreaded(TestSnvCaller.testPool)
outputFile = TestSnvCaller.testPool.vcf["SL2.40ch11_22900-24100"].fileName
self.assertEqual(
os.path.abspath(outputFile),
os.path.abspath(expOutFile),
os.path.abspath(outputFile) + " not is " + os.path.abspath(expOutFile),
)
# Check if the file contains exactly one snp
self.checkNoOfSnps(expOutFile)
def testSamtoolsMpileupMultiThread(self):
expOutFile = "../testFiles/output/testPool/testPool_SL2.40ch11_22900-24100.vcf"
SamtoolsMpileup.executeSamtoolsMultiThreaded(TestSnvCaller.testPool)
outputFile = TestSnvCaller.testPool.vcf[
"SL2.40ch11_22900-24100"].fileName
self.assertEqual(
os.path.abspath(outputFile), os.path.abspath(expOutFile),
os.path.abspath(outputFile) + " not is " +
os.path.abspath(expOutFile))
#Check if the file contains exactly one snp
self.checkNoOfSnps(expOutFile)
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 execute(self, executable):
"""The method execute checks which program has to be executed and executes this program
:param executable: the argument of the commandline which determines which program has to be executed
:type executable: str
"""
if executable == "haplotyping":
if Grid.useGrid == True:
Haplotyper.executeBeagleCluster(self.pool)
else:
Haplotyper.executeBeagleMultiThread(self.pool)
elif executable == "snvCalling":
if Program.config.snvCaller == "samtools": # @UndefinedVariable
SamtoolsMpileup.executeSamtoolsMultiThreaded(self.pool)
elif Program.config.snvCaller == "GATK": # @UndefinedVariable
Gatk.Gatk(self.pool).callSnvs()
elif executable == "mapping":
mapper = Mapper.Mapper()
for sample in self.samples:
mapper.map(sample)
elif executable == "allelicDiversity":
if Program.config.gffFile == None: # @UndefinedVariable
print(
"When calculating the allelic diversity, a gff file is needed, this option can be set with the option --gff <file>"
)
exit()
allelicDiverityCalculator = AllelicDiversity.AllelicDiversity(
self.pool, Program.config.gffFile) # @UndefinedVariable
allelicDiverityCalculator.getAllelicDiversity()
elif executable == "findLoci":
if Program.config.phenoData == None: # @UndefinedVariable
print(
"When finding loci, a csv file is needed with the phenotype data, this option can be set with the option --phen <file>"
)
exit()
if Program.config.gffFile == None: # @UndefinedVariable
print(
"When finding loci, a file with phenotype data is needed, this option can be set with the option --gff <file>"
)
exit()
lociFinder = LociFinder.LociFinder()
lociFinder.findLoci(self.pool)
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)
