import os, sys, glob import utilities gmtFilePath = sys.argv[1] ignorePattern = sys.argv[2] outFilePattern = sys.argv[3] for line in file(gmtFilePath): lineItems = line.rstrip().split("\t") name = lineItems[0] genes = lineItems[2:] if ignorePattern in name: print "Ignoring %s" % name continue outFilePath = outFilePattern.replace("{PATHWAY_NAME}", name) print "Saving to %s" % outFilePath utilities.writeVectorToFile(genes, outFilePath)
import os, sys, glob import utilities inDirPath = sys.argv[1] metric = sys.argv[2] outFilePath = sys.argv[3] values = [] for inFilePath in utilities.globRecursive(inDirPath, "*Results.txt"): for line in file(inFilePath): lineItems = line.rstrip().split("\t") if lineItems[0] == metric: values.append(float(lineItems[1])) utilities.writeVectorToFile(values, outFilePath)
import os, sys, glob import utilities gmtFilePath = sys.argv[1] outFilePattern = sys.argv[2] for line in file(gmtFilePath): lineItems = line.rstrip().split("\t") name = lineItems[0] genes = lineItems[2:] outFilePath = outFilePattern.replace("{PATHWAY_NAME}", name) utilities.writeVectorToFile(genes, outFilePath)