+ analyzeGOFromFile(genome, infilename, prefix, options.translateGene, fieldID, numTests=options.numTests)
+
+
+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--geneName", action="store_true", dest="translateGene",
+ help="translate gene")
+ parser.add_option("--field", type="int", dest="fieldID",
+ help="column containing gene ID/Name")
+ parser.add_option("--trials", type="int", dest="numTests",
+ help="column containing gene ID/Name")
+
+ configParser = getConfigParser()
+ section = "analyzego"
+ translateGene = getConfigOption(configParser, section, "translateGene", False)
+ fieldID = getConfigOption(configParser, section, "fieldID", None)
+ numTests = getConfigIntOption(configParser, section, "numTests", 1)
+
+ parser.set_defaults(translateGene=translateGene, fieldID=fieldID, numTests=numTests)