def doScaffolding(self, outputDir, assembly, pool):
for lib in pool.libs:
lib.mergedFile = outputDir + lib.libName + "Merged.fastq"
if os.path.exists(lib.mergedFile) == False or Configuration.instance.getGlobalOption("overwrite") == 1:
FastqUtils.mergeFastqFiles(lib.forward, lib.reversed, lib.mergedFile)
scarpaProcesser = ScarpaProcess(outputDir, contigs=assembly, libs=pool.libs)
scarpaContigs = scarpaProcesser.execute()
libInfo = scarpaProcesser.libInfo
mergedFiles = []
for lib in pool.libs:
mergedFiles.append(lib.mergedFile)
samFile = BowtieOne(outputDir, contigs=scarpaContigs, mergedFiles=mergedFiles).execute()
mapFile = ScarpaParser(outputDir, samFile=samFile).execute()
self.scaffolds = ScarpaCommand(outputDir, libInfo = libInfo, contigs = scarpaContigs, mappedFile=mapFile).execute()
return self.scaffolds
def setCommand(self):
self.outputFile = os.path.splitext(self.contigs)[0] + ".sam"
self.addArg("bowtie -p " + Configuration.instance.getGlobalOption("maxThreads"))
self.addArg("--sam")
if FastqUtils.determineQuality(self.mergedFiles[0]) == 64:
self.addArg("--phred64-quals")
self.addArg(self.bowtieIndex)
self.addArg(",".join(self.mergedFiles))
self.addArg(self.outputFile)
def setCommand(self):
self.outputFile = self.outputDir + "jump_reads_orig.fastb"
self.addArg("PrepareAllPathsInputs.pl")
self.addArg("DATA_DIR=" + self.outputDir)
self.addArg("IN_GROUPS_CSV=" + self.groupsCsv)
self.addArg("IN_LIBS_CSV=" + self.libsCsv)
if FastqUtils.determineQuality(self.forward) == 64:
self.addArg("PHRED_64=True")
self.addArg("PLOIDY=2")
self.addArg("OVERWRITE=1")