import os, sys, glob import utilities inFilePath = sys.argv[1] findValue = sys.argv[2].decode('string-escape') replaceValue = sys.argv[3].decode('string-escape') outFilePath = sys.argv[4] text = utilities.readTextFromFile(inFilePath) text = text.replace(findValue, replaceValue) utilities.writeScalarToFile(text, outFilePath)
return matches def getData(sectionText, dataStartText): data = [] haveHitDataStart = False for line in sectionText.splitlines(): if line.startswith(dataStartText): haveHitDataStart = True if haveHitDataStart and not line.startswith("!"): data.append(line.rstrip().split("\t")) return data softText = utilities.readTextFromFile(softFilePath) softSections = softText.split("^") softSections.pop(0) platformText = getSoftSections("PLATFORM")[0] platformData = getData(platformText, "ID") platformHeaderItems = platformData.pop(0) probeGeneDict = {} geneIndex = platformHeaderItems.index("Entrez_Gene_ID") for row in platformData: platformID = row[platformHeaderItems.index("ID")] geneID = row[geneIndex] probeGeneDict[platformID] = geneID sampleSections = getSoftSections("SAMPLE")
import os, sys, glob import utilities inFilePath = sys.argv[1] header = sys.argv[2].decode("string-escape") text = header + "\n" + utilities.readTextFromFile(inFilePath) utilities.writeScalarToFile(text, inFilePath)
def getData(sectionText, dataStartText): data = [] haveHitDataStart = False for line in sectionText.splitlines(): if line.startswith(dataStartText): haveHitDataStart = True if haveHitDataStart and not line.startswith("!"): data.append(line.rstrip().split("\t")) return data softText = utilities.readTextFromFile(softFilePath) softSections = softText.split("^") softSections.pop(0) platformText = getSoftSections("PLATFORM")[0] platformData = getData(platformText, "ID") platformHeaderItems = platformData.pop(0) probeGeneDict = {} geneIndex = platformHeaderItems.index("Entrez_Gene_ID") for row in platformData: platformID = row[platformHeaderItems.index("ID")] geneID = row[geneIndex] probeGeneDict[platformID] = geneID sampleSections = getSoftSections("SAMPLE")