+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--prefix", dest="pathPrefix")
+ parser.add_option("--overlap", type="int", dest="overlap")
+
+ configParser = getConfigParser()
+ section = "RNAPATH"
+ pathPrefix = getConfigOption(configParser, section, "pathPrefix", "RNAPATH")
+ overlap = getConfigIntOption(configParser, section, "overlap", 30)
+
+ parser.set_defaults(pathPrefix=pathPrefix, overlap=overlap)
+
+ return parser
+
+