+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--regions", dest="acceptFile")
+ parser.add_option("--downstream", type="int", dest="downMax")
+ parser.add_option("--upstream", type="int", dest="upMax")
+ parser.add_option("--mindist", type="int", dest="minDist")
+ parser.add_option("--minlocus", type="int", dest="minLocus")
+ parser.add_option("--maxlocus", type="int", dest="maxLocus")
+ parser.add_option("--samesense", action="store_true", dest="checkSense")
+
+ configParser = getConfigParser()
+ section = "geneNeighbors"
+ acceptfile = getConfigOption(configParser, section, "acceptfile", "")
+ checkSense = getConfigBoolOption(configParser, section, "checkSense", False)
+ downMax = getConfigIntOption(configParser, section, "downMax", 10000000)
+ upMax = getConfigIntOption(configParser, section, "upMax", 10000000)
+ minDist = getConfigIntOption(configParser, section, "minDist", 0)
+ minLocus = getConfigIntOption(configParser, section, "minLocus", -1)
+ maxLocus = getConfigIntOption(configParser, section, "maxLocus", 10000000)
+
+ parser.set_defaults(acceptfile=acceptfile, checkSense=checkSense, downMax=downMax,
+ upMax=upMax, minDist=minDist, minLocus=minLocus, maxLocus=maxLocus)
+
+ return parser
+
+