fp = open(galaxyEvalFile2, 'r') valJson = json.load(fp) fp.close() encoding2 = str(valJson['encoding']) tagLength2 = int(valJson['tagLength']) except: pass if encoding != encoding2: raise Exception("Validation files suggest that paired fastq files are formats.") if tagLength != tagLength2: raise Exception("Validation files suggest that paired fastq files have different" + \ " tag lengths.") # Set up 'ana' so she can do all the work. If anaId matches another, then it's log is extended ana = GalaxyAnalysis(settingsFile, anaId, genome, expType) ana.gender = gender if testOnly: ana.dryRun = testOnly ana.readType = pairedOrUnpaired # What step expects: # Inputs: 1 or 2 fastq files, pre-registered in the analysis keyed as: # Single: 'tagsRep'+replicate+'.fastq' # Paired: 'tagsRd1Rep'+replicate+'.fastq' and 'tagsRd2Rep'+replicate+'.fastq' # Outputs: target genome bam keyed as: 'genomeAlignedStarRep' + replicate + '.bam' # interim annotation bam keyed as: 'annotationAlignedStarRep' + replicate + '.bam' # interim statistics txt file keyed as: 'statisticsStarRep' + replicate + '.txt' # and either 4 (paired) signal files: 'signalStarRep' + replicate + 'UniqMinus.bw' # 'signalStarRep' + replicate + 'UniqPlus.bw' # 'signalStarRep' + replicate + 'AllMinus.bw' # 'signalStarRep' + replicate + 'AllPlus.bw'