+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--raw", action="store_false", dest="normalize",
+ help="maximum region in bp")
+ parser.add_option("--max", type="int", dest="standardMinDist")
+ parser.add_option("--cache", action="store_true", dest="doCache")
+
+ configParser = getConfigParser()
+ section = "geneUpstreamBins"
+ standardMinDist = getConfigIntOption(configParser, section, "regionSize", 3000)
+ normalize = getConfigBoolOption(configParser, section, "normalize", True)
+ doCache = getConfigBoolOption(configParser, section, "doCache", False)
+
+ parser.set_defaults(standardMinDist=standardMinDist, normalize=normalize, doCache=doCache)
+
+ return parser
+
+