def createHeatMap(runFile, i):
run = Run(runFile)
run.loadRun(runFile)
fileOP = re.split("/", runFile)
file = fileOP[len(fileOP)-1]
fileName = file.split(".")
print runFile
print fileName[0]
run.createHeatMapRaw("HeatMap_"+fileName[0])
batch = 1
for line in inF.readlines():
lineSplit = line.split(",")
runFile = lineSplit[0].rstrip()
normalFile = lineSplit[1].rstrip()
weightFile = lineSplit[2].rstrip()
fileOP = re.split("/", runFile)
file = fileOP[len(fileOP) - 1]
runF = file.split(".")[0]
sampleFilter = ""
if (len(lineSplit) > 3):
sampleFilter = lineSplit[3].rstrip()
# Do this repeatedly
run = Run(runFile)
run.loadRun(runFile)
run.setSampleFiler(sampleFilter)
print "##################################################"
print "Processing " + line.rstrip()
run.processNormal(normalFile)
run.exportNormalized(outputDir + "/Normalized_" + runF + ".csv")
print "Normalized!"
run.processWeights(weightFile)
run.exportLipidWeightNormalization(outputDir + "/WeightNormalized_" +
runF + ".csv")
print "Weight Normalization Done!"
run.calcLipidAbundance()
run.exportLipidAbundance(outputDir + "/Abundance_" + runF + ".csv")
print "Lipid Relative Abundance Done!"
run.performQualityCheck()
