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")