Example #1
0
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)
Example #2
0
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)
Example #3
0
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)