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")
