+def getParser(usage):
+
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--dataset", dest="chipfilename")
+ parser.add_option("--min", type="float", dest="minHeight")
+ parser.add_option("--minfraction", type="float", dest="minFraction")
+ parser.add_option("--plot", dest="plotname")
+ parser.add_option("--cache", action="store_true", dest="doCache")
+ parser.add_option("--raw", action="store_false", dest="normalize")
+ parser.add_option("--verbose", action="store_true", dest="doVerbose")
+ parser.add_option("--markov1", action="store_true", dest="doMarkov1")
+ parser.add_option("--peakdist", type="int", dest="maxpeakdist")
+ parser.add_option("--fullOnly", action="store_true", dest="fullOnly")
+ parser.add_option("--motifdir", dest="motifDir")
+
+ configParser = getConfigParser()
+ section = "getallNRSE"
+ chipfilename = getConfigOption(configParser, section, "chipfilename", "")
+ minHeight = getConfigFloatOption(configParser, section, "minHeight", -2.)
+ minFraction = getConfigFloatOption(configParser, section, "minFraction", -2.)
+ plotname = getConfigOption(configParser, section, "plotname", "")
+ doCache = getConfigBoolOption(configParser, section, "doCache", False)
+ normalize = getConfigBoolOption(configParser, section, "normalize", True)
+ doVerbose = getConfigBoolOption(configParser, section, "doVerbose", False)
+ doMarkov1 = getConfigBoolOption(configParser, section, "doMarkov1", False)
+ maxpeakdist = getConfigOption(configParser, section, "maxpeakdist", None)
+ fullOnly = getConfigBoolOption(configParser, section, "fullOnly", False)
+ motifDir = getConfigOption(configParser, section, "motifDir", "./")
+
+ parser.set_defaults(chipfilename=chipfilename, minHeight=minHeight, minFraction=minFraction, plotname=plotname,
+ doCache=doCache, normalize=normalize, doVerbose=doVerbose, doMarkov1=doMarkov1,
+ maxpeakdist=maxpeakdist, fullOnly=fullOnly, motifDir=motifDir)
+
+ return parser
+
+