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 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)