Beispiel #1
0
 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        
Beispiel #2
0
 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")