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'
