def testCactusRealign(self):
"""Runs cactus realign using the default parameters and checks that the realigned output cigars align
the same subsequences.
"""
for seqFile1, seqFile2 in seqFilePairGenerator():
lastzOutput = getTempFile(rootDir=self.tempDir)
runLastz(seqFile1,
seqFile2,
alignmentsFile=lastzOutput,
lastzArguments=self.defaultLastzArguments,
work_dir=self.tempDir)
realignOutput = getTempFile(rootDir=self.tempDir)
runCactusRealign(seqFile1,
seqFile2,
inputAlignmentsFile=lastzOutput,
outputAlignmentsFile=realignOutput,
realignArguments=self.defaultRealignArguments,
work_dir=self.tempDir)
for realignLine, lastzLine in zip(
[i for i in open(lastzOutput, 'r') if i != ''],
[i for i in open(realignOutput, 'r') if i != '']):
realignCigar = cigarReadFromString(realignLine)
lastzCigar = cigarReadFromString(lastzLine)
self.assertTrue(realignCigar.sameCoordinates(lastzCigar))
def run(self, fileStore):
seqFile1 = fileStore.readGlobalFile(self.seqFileID1)
seqFile2 = fileStore.readGlobalFile(self.seqFileID2)
if self.blastOptions.compressFiles:
seqFile1 = decompressFastaFile(seqFile1,
fileStore.getLocalTempFile())
seqFile2 = decompressFastaFile(seqFile2,
fileStore.getLocalTempFile())
blastResultsFile = fileStore.getLocalTempFile()
runLastz(seqFile1,
seqFile2,
blastResultsFile,
lastzArguments=self.blastOptions.lastzArguments,
gpuLastz=self.blastOptions.gpuLastz)
if self.blastOptions.realign:
realignResultsFile = fileStore.getLocalTempFile()
runCactusRealign(
seqFile1,
seqFile2,
inputAlignmentsFile=blastResultsFile,
outputAlignmentsFile=realignResultsFile,
realignArguments=self.blastOptions.realignArguments)
blastResultsFile = realignResultsFile
resultsFile = fileStore.getLocalTempFile()
cactus_call(parameters=[
"cactus_blast_convertCoordinates", blastResultsFile, resultsFile,
str(self.blastOptions.roundsOfCoordinateConversion)
])
logger.info("Ran the blast okay")
return fileStore.writeGlobalFile(resultsFile)
def testCactusRealignDummy(self):
"""Runs cactus realign using the "rescoreOriginalAlignment" mode
and checks the output is equivalent to what you'd get by just running lastz.
"""
for seqFile1, seqFile2 in seqFilePairGenerator():
lastzOutput = getTempFile(rootDir=self.tempDir)
runLastz(seqFile1,
seqFile2,
alignmentsFile=lastzOutput,
lastzArguments=self.defaultLastzArguments)
realignOutput = getTempFile(rootDir=self.tempDir)
runCactusRealign(seqFile1,
seqFile2,
inputAlignmentsFile=lastzOutput,
outputAlignmentsFile=realignOutput,
realignArguments=self.defaultRealignArguments +
" --rescoreOriginalAlignment")
for realignLine, lastzLine in zip(
[i for i in open(lastzOutput, 'r') if i != ''],
[i for i in open(realignOutput, 'r') if i != '']):
realignCigar = cigarReadFromString(realignLine)
lastzCigar = cigarReadFromString(lastzLine)
self.assertTrue(realignCigar != None)
self.assertTrue(realignCigar == lastzCigar)
def testCactusRealignSplitSequences(self):
"""Runs cactus realign, splitting indels longer than 100bp, and check
that the coverage from the results is the same as the coverage from
realigning with no arguments.."""
for seqFile1, seqFile2 in seqFilePairGenerator():
lastzOutput = getTempFile(rootDir=self.tempDir)
runLastz(seqFile1, seqFile2, alignmentsFile=lastzOutput,
lastzArguments=self.defaultLastzArguments)
realignOutput = getTempFile(rootDir=self.tempDir)
runCactusRealign(seqFile1, seqFile2, inputAlignmentsFile=lastzOutput,
outputAlignmentsFile=realignOutput,
realignArguments=self.defaultRealignArguments)
splitRealignOutput = getTempFile(rootDir=self.tempDir)
runCactusRealign(seqFile1, seqFile2, inputAlignmentsFile=lastzOutput,
outputAlignmentsFile=splitRealignOutput,
realignArguments=self.defaultRealignArguments + " --splitIndelsLongerThanThis 100")
# Check coverage on seqFile1
splitRealignCoverage = runCactusCoverage(seqFile1, splitRealignOutput)
realignCoverage = runCactusCoverage(seqFile1, realignOutput)
self.assertTrue(splitRealignCoverage == realignCoverage)
# Check coverage on seqFile2
splitRealignCoverage = runCactusCoverage(seqFile2, splitRealignOutput)
realignCoverage = runCactusCoverage(seqFile2, realignOutput)
self.assertTrue(splitRealignCoverage == realignCoverage)
os.remove(realignOutput)
os.remove(splitRealignOutput)
def testCactusRealignRescoreByIdentityAndProb(self):
"""Runs cactus realign using the default parameters and checks that the realigned output cigars align
the same subsequences.
"""
for seqFile1, seqFile2 in seqFilePairGenerator():
lastzOutput = getTempFile(rootDir=self.tempDir)
runLastz(seqFile1,
seqFile2,
alignmentsFile=lastzOutput,
lastzArguments=self.defaultLastzArguments,
work_dir=self.tempDir)
realignByIdentityOutput = getTempFile(rootDir=self.tempDir)
runCactusRealign(seqFile1,
seqFile2,
inputAlignmentsFile=lastzOutput,
outputAlignmentsFile=realignByIdentityOutput,
realignArguments=self.defaultRealignArguments +
" --rescoreByIdentity",
work_dir=self.tempDir)
realignByPosteriorProbOutput = getTempFile(rootDir=self.tempDir)
runCactusRealign(seqFile1,
seqFile2,
inputAlignmentsFile=lastzOutput,
outputAlignmentsFile=realignByPosteriorProbOutput,
realignArguments=self.defaultRealignArguments +
" --rescoreByPosteriorProb",
work_dir=self.tempDir)
realignByIdentityIgnoringGapsOutput = getTempFile(
rootDir=self.tempDir)
runCactusRealign(
seqFile1,
seqFile2,
inputAlignmentsFile=lastzOutput,
outputAlignmentsFile=realignByIdentityIgnoringGapsOutput,
realignArguments=self.defaultRealignArguments +
" --rescoreByIdentityIgnoringGaps",
work_dir=self.tempDir)
for realignLineByIdentity, realignLineByPosteriorProb, realignLineByIdentityIgnoringGaps, lastzLine in \
zip([ i for i in open(realignByIdentityOutput, 'r') if i != '' ], \
[ i for i in open(realignByPosteriorProbOutput, 'r') if i != '' ], \
[ i for i in open(realignByIdentityIgnoringGapsOutput, 'r') if i != '' ], \
[ i for i in open(lastzOutput, 'r') if i != '' ]):
realignCigarByIdentity = cigarReadFromString(
realignLineByIdentity)
realignCigarByPosteriorProb = cigarReadFromString(
realignLineByPosteriorProb)
realignCigarByIdentityIgnoringGaps = cigarReadFromString(
realignLineByIdentityIgnoringGaps)
lastzCigar = cigarReadFromString(lastzLine)
#Check scores are as expected
self.assertTrue(realignCigarByIdentity.score >= 0)
self.assertTrue(realignCigarByIdentity.score <= 100.0)
self.assertTrue(realignCigarByPosteriorProb.score >= 0)
self.assertTrue(realignCigarByPosteriorProb.score <= 100.0)
self.assertTrue(realignCigarByIdentityIgnoringGaps.score >= 0)
self.assertTrue(
realignCigarByIdentityIgnoringGaps.score <= 100.0)
def runNaiveBlast(seqFile1, seqFile2, outputFile, tempDir, lastzArguments=""):
"""Runs the blast command in a very naive way (not splitting things up).
"""
startTime = time.time()
tmpSeqFile1 = os.path.join(tempDir, "seq1.fa")
tmpSeqFile2 = os.path.join(tempDir, "seq2.fa")
shutil.copyfile(seqFile1, tmpSeqFile1)
shutil.copyfile(seqFile2, tmpSeqFile2)
runLastz(tmpSeqFile1, tmpSeqFile2, alignmentsFile=outputFile, lastzArguments=lastzArguments)
return time.time()-startTime
def runNaiveBlast(seqFile1, seqFile2, outputFile, tempDir, lastzArguments=""):
"""Runs the blast command in a very naive way (not splitting things up).
"""
startTime = time.time()
tmpSeqFile1 = os.path.join(tempDir, "seq1.fa")
tmpSeqFile2 = os.path.join(tempDir, "seq2.fa")
shutil.copyfile(seqFile1, tmpSeqFile1)
shutil.copyfile(seqFile2, tmpSeqFile2)
runLastz(tmpSeqFile1, tmpSeqFile2, alignmentsFile=outputFile, lastzArguments=lastzArguments)
return time.time()-startTime
def testCactusRealign(self):
"""Runs cactus realign using the default parameters and checks that the realigned output cigars align
the same subsequences.
"""
for seqFile1, seqFile2 in seqFilePairGenerator():
lastzOutput = getTempFile(rootDir=self.tempDir)
runLastz(seqFile1, seqFile2, alignmentsFile=lastzOutput,
lastzArguments=self.defaultLastzArguments)
realignOutput = getTempFile(rootDir=self.tempDir)
runCactusRealign(seqFile1, seqFile2, inputAlignmentsFile = lastzOutput,
outputAlignmentsFile = realignOutput,
realignArguments=self.defaultRealignArguments)
for realignLine, lastzLine in zip([ i for i in open(lastzOutput, 'r') if i != '' ],
[ i for i in open(realignOutput, 'r') if i != '' ]):
realignCigar = cigarReadFromString(realignLine)
lastzCigar = cigarReadFromString(lastzLine)
self.assertTrue(realignCigar.sameCoordinates(lastzCigar))
def testCactusRealignDummy(self):
"""Runs cactus realign using the "rescoreOriginalAlignment" mode
and checks the output is equivalent to what you'd get by just running lastz.
"""
for seqFile1, seqFile2 in seqFilePairGenerator():
lastzOutput = getTempFile(rootDir=self.tempDir)
runLastz(seqFile1, seqFile2, alignmentsFile=lastzOutput,
lastzArguments=self.defaultLastzArguments)
realignOutput = getTempFile(rootDir=self.tempDir)
runCactusRealign(seqFile1, seqFile2, inputAlignmentsFile = lastzOutput,
outputAlignmentsFile = realignOutput,
realignArguments=self.defaultRealignArguments + " --rescoreOriginalAlignment")
for realignLine, lastzLine in zip([ i for i in open(lastzOutput, 'r') if i != '' ],
[ i for i in open(realignOutput, 'r') if i != '' ]):
realignCigar = cigarReadFromString(realignLine)
lastzCigar = cigarReadFromString(lastzLine)
self.assertTrue(realignCigar != None)
self.assertTrue(realignCigar == lastzCigar)
def testCactusRealignRescoreByIdentityAndProb(self):
"""Runs cactus realign using the default parameters and checks that the realigned output cigars align
the same subsequences.
"""
for seqFile1, seqFile2 in seqFilePairGenerator():
lastzOutput = getTempFile(rootDir=self.tempDir)
runLastz(seqFile1, seqFile2, alignmentsFile=lastzOutput,
lastzArguments=self.defaultLastzArguments)
realignByIdentityOutput = getTempFile(rootDir=self.tempDir)
runCactusRealign(seqFile1, seqFile2, inputAlignmentsFile=lastzOutput,
outputAlignmentsFile=realignByIdentityOutput,
realignArguments=self.defaultRealignArguments + " --rescoreByIdentity")
realignByPosteriorProbOutput = getTempFile(rootDir=self.tempDir)
runCactusRealign(seqFile1, seqFile2, inputAlignmentsFile=lastzOutput,
outputAlignmentsFile=realignByPosteriorProbOutput,
realignArguments=self.defaultRealignArguments + " --rescoreByPosteriorProb")
realignByIdentityIgnoringGapsOutput = getTempFile(rootDir=self.tempDir)
runCactusRealign(seqFile1, seqFile2, inputAlignmentsFile=lastzOutput,
outputAlignmentsFile=realignByIdentityIgnoringGapsOutput,
realignArguments=self.defaultRealignArguments + " --rescoreByIdentityIgnoringGaps")
for realignLineByIdentity, realignLineByPosteriorProb, realignLineByIdentityIgnoringGaps, lastzLine in \
zip([ i for i in open(realignByIdentityOutput, 'r') if i != '' ], \
[ i for i in open(realignByPosteriorProbOutput, 'r') if i != '' ], \
[ i for i in open(realignByIdentityIgnoringGapsOutput, 'r') if i != '' ], \
[ i for i in open(lastzOutput, 'r') if i != '' ]):
realignCigarByIdentity = cigarReadFromString(realignLineByIdentity)
realignCigarByPosteriorProb = cigarReadFromString(realignLineByPosteriorProb)
realignCigarByIdentityIgnoringGaps = cigarReadFromString(realignLineByIdentityIgnoringGaps)
lastzCigar = cigarReadFromString(lastzLine)
#Check scores are as expected
self.assertTrue(realignCigarByIdentity.score >= 0)
self.assertTrue(realignCigarByIdentity.score <= 100.0)
self.assertTrue(realignCigarByPosteriorProb.score >= 0)
self.assertTrue(realignCigarByPosteriorProb.score <= 100.0)
self.assertTrue(realignCigarByIdentityIgnoringGaps.score >= 0)
self.assertTrue(realignCigarByIdentityIgnoringGaps.score <= 100.0)
def run(self, fileStore):
seqFile1 = fileStore.readGlobalFile(self.seqFileID1)
seqFile2 = fileStore.readGlobalFile(self.seqFileID2)
if self.blastOptions.compressFiles:
seqFile1 = decompressFastaFile(seqFile1, fileStore.getLocalTempFile())
seqFile2 = decompressFastaFile(seqFile2, fileStore.getLocalTempFile())
blastResultsFile = fileStore.getLocalTempFile()
runLastz(seqFile1, seqFile2, blastResultsFile, lastzArguments = self.blastOptions.lastzArguments)
if self.blastOptions.realign:
realignResultsFile = fileStore.getLocalTempFile()
runCactusRealign(seqFile1, seqFile2, inputAlignmentsFile=blastResultsFile,
outputAlignmentsFile=realignResultsFile,
realignArguments=self.blastOptions.realignArguments)
blastResultsFile = realignResultsFile
resultsFile = fileStore.getLocalTempFile()
cactus_call(parameters=["cactus_blast_convertCoordinates",
blastResultsFile,
resultsFile,
str(self.blastOptions.roundsOfCoordinateConversion)])
logger.info("Ran the blast okay")
return fileStore.writeGlobalFile(resultsFile)
