def run(self, fileStore):
blastResultsFile = fileStore.getLocalTempFile()
seqFile = fileStore.readGlobalFile(self.seqFileID)
runSelfLastz(seqFile,
blastResultsFile,
lastzArguments=self.blastOptions.lastzArguments,
gpuLastz=self.blastOptions.gpuLastz)
if self.blastOptions.realign:
realignResultsFile = fileStore.getLocalTempFile()
runCactusSelfRealign(
seqFile,
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)
])
if self.blastOptions.compressFiles:
#TODO: This throws away the compressed file
seqFile = compressFastaFile(seqFile)
logger.info("Ran the self blast okay")
return fileStore.writeGlobalFile(resultsFile)
def alignAndRunPipeline(self, concatenatedSequenceFile):
# Run lastz
startTime = time.time()
runSelfLastz(concatenatedSequenceFile, self.simpleInputCigarPath, "")
print "It took %s seconds to run lastz" % (time.time() - startTime)
with open(self.simpleInputCigarPath, 'r') as fh:
inputCigars = [ cigar[:-1] for cigar in fh.readlines() ] # Remove new lines
print "There are %s cigars from lastz" % len(inputCigars)
# Run toil pipeline
startTime = time.time()
outputCigars = self.runToilPipeline(self.simpleInputCigarPath)
print "It took %s seconds to run unique mapping pipeline" % (time.time() - startTime)
# Check output
print "Total input cigars:", len(inputCigars), "total output cigars", len(outputCigars)
def alignAndRunPipeline(self, concatenatedSequenceFile):
# Run lastz
startTime = time.time()
runSelfLastz(concatenatedSequenceFile, self.simpleInputCigarPath, "")
print "It took %s seconds to run lastz" % (time.time() - startTime)
with open(self.simpleInputCigarPath, 'r') as fh:
inputCigars = [cigar[:-1]
for cigar in fh.readlines()] # Remove new lines
print "There are %s cigars from lastz" % len(inputCigars)
# Run toil pipeline
startTime = time.time()
outputCigars = self.runToilPipeline(self.simpleInputCigarPath)
print "It took %s seconds to run unique mapping pipeline" % (
time.time() - startTime)
# Check output
print "Total input cigars:", len(
inputCigars), "total output cigars", len(outputCigars)
def run(self, fileStore):
blastResultsFile = fileStore.getLocalTempFile()
seqFile = fileStore.readGlobalFile(self.seqFileID)
runSelfLastz(seqFile, blastResultsFile, lastzArguments=self.blastOptions.lastzArguments)
if self.blastOptions.realign:
realignResultsFile = fileStore.getLocalTempFile()
runCactusSelfRealign(seqFile, 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)])
if self.blastOptions.compressFiles:
#TODO: This throws away the compressed file
seqFile = compressFastaFile(seqFile)
logger.info("Ran the self blast okay")
return fileStore.writeGlobalFile(resultsFile)