def testHaplotyperPath(self):
Grid.useGrid = False
expOutFile = "../testFiles/output/testPool/out.testPoolSL2.40ch11_22900-24100.BEAGLE.PL.phased.gz"
TestHaplotyper.testPool.vcf = {}
TestHaplotyper.sample = Sample.Sample(TestHaplotyper.testPool,
"testLib")
TestHaplotyper.testPool.addSample(TestHaplotyper.sample)
TestHaplotyper.sample.bam = BamFile.BamFile(TestHaplotyper.testPool,
TestHaplotyper.sample,
TestHaplotyper.inputBam,
sortedBam=True,
headerLine=True,
duplicates=False,
mdTag=True,
index=True)
TestHaplotyper.haplotyper.callHaplotypes()
createdOutFile = TestHaplotyper.testPool.beagleFiles.values(
)[0].phasedFile
self.assertEqual(
os.path.abspath(createdOutFile), os.path.abspath(expOutFile),
os.path.abspath(createdOutFile) + " not is " +
os.path.abspath(expOutFile))
self.checkNoOfSnps(expOutFile)
def _executeBwa(self, forwardFq, reversedFq=None):
"""The method executeBwa executes the mapping with BWA.
:param forwardFq: The forward fastq file to map against the reference genome
:type forwardFq: an instance of :py:class:`FastqFile.FastqFile`
:param reversedFq: The reversed fastq file to map against the reference genome
:type reversedFq: an instance of :py:class:`FastqFile.FastqFile`, None if the data has no paired end reads.
"""
if os.path.exists(Program.config.getPath("refGenome") +
".pac") == False:
exitStatus = subprocess.call("bwa index " +
Program.config.getPath("refGenome"))
if exitStatus == 1:
print(
"ERROR: Failed to create a bwa index file for the reference genome, do I have permissions to write in the directory of the reference genome?"
)
exit(1)
##Build the command
cmd = Program.config.getPath("bwa") # @UndefinedVariable
if reversedFq == None:
cmd = cmd + " samse "
else:
cmd = cmd + " sampe " + self.getProgramArguments("BWA")
cmd = cmd + Program.config.getPath("refGenome")
#add the .sai files to the command
forwardMapped = self._bwaAlign(forwardFq)
cmd = cmd + " " + forwardMapped
if reversedFq != None:
reversedMapped = self._bwaAlign(reversedFq)
cmd = cmd + " " + reversedMapped
#add the high quality reads to the command
cmd = cmd + " " + forwardFq.fileName
if reversedFq != None:
cmd = cmd + " " + reversedFq.fileName
#add the output file to the command
forwardFq.sample.bam = BamFile.BamFile(forwardFq.pool,
forwardFq.sample,
sam=True)
cmd = cmd + " > " + forwardFq.sample.bam.getFile()
##Execute the command
self.execute(cmd, "BWA", forwardFq.sample.bam)
##Cleanup the mess
self.execute("rm " + forwardMapped, "rm", forwardFq)
if reversedFq != None:
self.execute("rm " + reversedMapped, "rm", reversedFq)
def testAddMdTag(self):
TestConversionTools.sample.bam = BamFile.BamFile(
TestConversionTools.testPool, TestConversionTools.sample,
TestConversionTools.bamFile)
self.convTools.addMdTag(TestConversionTools.sample)
self.assertTrue(os.path.exists(TestConversionTools.expBamOutFile),
"output file not created...")
output, error = Popen(Program.config.getPath("samtools") +
" view -h " + TestConversionTools.expBamOutFile +
" | wc -l",
shell=True,
stdout=PIPE,
stderr=PIPE).communicate()
self.assertEqual(
output.rstrip(), "1283",
"number of lines: " + output.rstrip() + " is not " + str(1283))
def testHaplotyperPathGrid(self):
TestHaplotyper.testPool.vcf = {}
TestHaplotyper.sample = Sample.Sample(TestHaplotyper.testPool,
"testLib")
TestHaplotyper.testPool.addSample(TestHaplotyper.sample)
TestHaplotyper.sample.bam = BamFile.BamFile(TestHaplotyper.testPool,
TestHaplotyper.sample,
TestHaplotyper.inputBam,
sortedBam=True,
headerLine=True,
duplicates=False,
mdTag=True,
index=True)
Haplotyper.executeBeagleCluster(TestHaplotyper.testPool)
# self.assertEqual(os.path.abspath(createdOutFile),os.path.abspath(expOutFile) , os.path.abspath(createdOutFile) + " not is " + os.path.abspath(expOutFile))
self.checkNoOfSnps(
"../testFiles/output/testPool/SL2.40ch11_22900-24100_testPool_SL2.40ch11_22900-24100.vcf"
)
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)
def setUp(self):
for handler in logging.getLogger().handlers:
handler.close()
for delFile in os.listdir("../testFiles/output/"):
file_path = os.path.join("../testFiles/output/", delFile)
if os.path.isdir(file_path):
shutil.rmtree(file_path)
else:
os.unlink(file_path)
TestSnvCaller.testPool = Pool.Pool("testPool", "../testFiles/output/")
Program.config.setPath("refGenome",
"../testFiles/input/smallRefGenome.fa")
TestSnvCaller.sample = Sample.Sample(TestSnvCaller.testPool, "testLib")
TestSnvCaller.testPool.addSample(TestSnvCaller.sample)
TestSnvCaller.sample.bam = BamFile.BamFile(TestSnvCaller.testPool,
TestSnvCaller.sample,
TestSnvCaller.inputBam,
sortedBam=True,
headerLine=True,
duplicates=False,
mdTag=True,
index=True)
def testCreateBamIndex(self):
indexFilesize = 96
TestConversionTools.sample.bam = BamFile.BamFile(
TestConversionTools.testPool, TestConversionTools.sample,
TestConversionTools.bamFile)
self.convTools.sortBam(TestConversionTools.sample)
self.convTools.createBamIndex(TestConversionTools.sample)
outputFile = TestConversionTools.sample.bam.fileName
self.assertEqual(
os.path.abspath(outputFile),
os.path.abspath(TestConversionTools.expBamOutFile),
os.path.abspath(outputFile) + " not is " +
os.path.abspath(TestConversionTools.expBamOutFile))
self.assertTrue(
os.path.isfile(TestConversionTools.expBamOutFile + ".bai"),
os.path.abspath(TestConversionTools.expBamOutFile + ".bai") +
" is not created")
self.assertEqual(
indexFilesize,
os.path.getsize(TestConversionTools.expBamOutFile + ".bai"),
"filesize: " +
str(os.path.getsize(TestConversionTools.expBamOutFile + ".bai")) +
" is not " + str(indexFilesize))
def setbam(self, fileName):
"""Setter for setting the bam file as a :py:class:`FastqFile.FastqFile`
"""
self.bam = BamFile.BamFile(self.pool, self, fileName)
def findFastqFiles(self, directory, inFormat):
"""The method findFastqFiles finds all fastq files recursively in a directory, from each directory with fastq files a sample is created.
:param directory: the directory where the user hid his fastq files
:type directory: str -- path to the directory
"""
fastqFiles = []
for fileName in os.listdir(directory):
fileName = directory + "/" + fileName
if os.path.isdir(fileName):
self.findFastqFiles(fileName, inFormat)
else:
if inFormat == "bam":
if fileName.endswith(".bam") or fileName.endswith(
".bam.gz"):
newSamp = Sample.Sample(
self.pool,
os.path.basename(os.path.splitext(fileName)[0]))
self.samples.append(newSamp)
newSamp.bam = BamFile.BamFile(self.pool,
newSamp,
fileName,
sortedBam=True,
headerLine=True,
duplicates=False,
mdTag=True,
index=True)
self.pool.addSample(newSamp)
elif inFormat == "fq":
if fileName.endswith(".fq") or fileName.endswith(".fq.gz"):
fastqFiles.append(fileName)
elif inFormat == "vcf":
if fileName.endswith(".vcf") or fileName.endswith(
".vcf.gz"):
if len(os.listdir(directory)) == 1:
chrom = None
else:
chrom = self.getChromosomeFromVcf(fileName)
self.pool.vcf[chrom] = VcfFile.VcfFile(self.pool,
fileName,
bcf=False,
filtered=True,
phased=True,
chrom=chrom)
elif fileName.endswith(".bcf") or fileName.endswith(
".bcf.gz"):
chrom = Tools.getChromosomeOfFile(
Program.config.getPath("refGenome"), fileName)
self.pool.vcf[chrom] = VcfFile.VcfFile(self.pool,
fileName,
bcf=True,
filtered=True,
phased=True,
chrom=chrom)
if inFormat == "bam" or inFormat == "vcf":
return
if len(fastqFiles) > 0:
#create a library name from the file name
libName = os.path.basename(fastqFiles[0])
if libName.endswith("_1.fq") or libName.endswith("_2.fq"):
libName = libName[:-5]
if libName.endswith("_1.fq.gz") or libName.endswith("_2.fq.gz"):
libName = libName[:-8]
else:
libName = libName[:-3]
#create the sample
sample = Sample.Sample(self.pool, libName)
self.pool.addSample(sample)
#add the fastq files to the sample
if len(fastqFiles) == 1:
sample.setForwardFq(fastqFiles[0])
elif len(fastqFiles) == 2:
sample.setForwardFq(fastqFiles[0])
sample.setReversedFq(fastqFiles[1])
elif len(fastqFiles) > 2:
if fastqFiles[0].endswith("_1.fq"):
suffix = "_1.fq"
elif fastqFiles[0].endswith("_1.fq.gz"):
suffix = "_1.fq.gz"
else:
print(
"WARNING: files do not end with _1.fq or _1.fq.gz or _2.fq or _2.fq.gz, using all files in one directory as 1 sample with only forward reads"
)
suffix = fastqFiles[0][-3:]
#create a list of forward fastq files and one of reversed fastq files
forward = []
reversedFastq = []
for fastqFile in fastqFiles:
if fastqFile.endswith(suffix):
forward.append(fastqFile)
else:
reversedFastq.append(fastqFile)
#Convert files to fastqFile objects
for i in range(len(forward)):
forward[i] = FastqFile.FastqFile(
self.pool, sample, forward[i])
for i in range(len(reversedFastq)):
reversedFastq[i] = FastqFile.FastqFile(
self.pool, sample, reversedFastq[i], forward=False)
#add the fastq files to the sample
sample.forwardFq = forward
sample.reversedFq = reversedFastq