+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--radius", type="int", dest="maxRadius")
+ parser.add_option("--nomatch", dest="nomatchfilename")
+ parser.add_option("--trackfar", action="store_true", dest="trackFar")
+ parser.add_option("--stranded", action="store_true", dest="trackStrand")
+ parser.add_option("--cache", action="store_true", dest="cachePages")
+ parser.add_option("--compact", action="store_true", dest="compact")
+ parser.add_option("--step", type="int", dest="step")
+ parser.add_option("--startField", type="int", dest="colID")
+ parser.add_option("--models", dest="extendGenome")
+ parser.add_option("--replacemodels", action="store_true", dest="replaceModels")
+
+ configParser = getConfigParser()
+ section = "getallgenes"
+ maxRadius = getConfigIntOption(configParser, section, "maxRadius", 20002)
+ nomatchfilename = getConfigOption(configParser, section, "nomatchfilename", "")
+ step = getConfigOption(configParser, section, "step", None)
+ trackFar = getConfigBoolOption(configParser, section, "trackFar", False)
+ trackStrand = getConfigBoolOption(configParser, section, "trackStrand", False)
+ compact = getConfigBoolOption(configParser, section, "compact", False)
+ colID = getConfigIntOption(configParser, section, "colID", 1)
+ doCache = getConfigBoolOption(configParser, section, "doCache", False)
+ extendGenome = getConfigOption(configParser, section, "extendGenome", "")
+ replaceModels = getConfigBoolOption(configParser, section, "replaceModels", False)
+
+ parser.set_defaults(maxRadius=maxRadius, nomatchfilename=nomatchfilename, step=step, trackFar=trackFar,
+ trackStrand=trackStrand, compact=compact, colID=colID, doCache=doCache,
+ extendGenome=extendGenome, replaceModels=replaceModels)
+
+ return parser
+
+