+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--rescale", action="store_true", dest="rescale")
+ parser.add_option("--truncate", type="int", dest="maxRPKM")
+ parser.add_option("--log", dest="logfilename")
+
+ configParser = getConfigParser()
+ section = "buildMatrix"
+ rescale = getConfigBoolOption(configParser, section, "rescale", False)
+ maxRPKM = getConfigOption(configParser, section, "maxRPKM", None)
+ logfilename = getConfigOption(configParser, section, "logfilename", "buildMatrix.log")
+
+ parser.set_defaults(rescale=rescale, maxRPKM=maxRPKM, logfilename=logfilename)
+
+ return parser
+
+