+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--seqradius", type="int", dest="seqsize")
+ parser.add_option("--minreads", type="int", dest="minHitThresh")
+ parser.add_option("--returnTop", type="int", dest="topRegions")
+ parser.add_option("--maxsize", type="int", dest="maxsize")
+ parser.add_option("--usepeak", action="store_true", dest="usePeaks")
+ parser.add_option("--dataset", dest="hitfile")
+ parser.add_option("--cache", action="store_true", dest="doCache")
+ parser.add_option("--compact", action="store_true", dest="doCompact")
+
+ configParser = getConfigParser()
+ section = "getfasta"
+ seqsize = getConfigIntOption(configParser, section, "seqsize", 50)
+ minHitThresh = getConfigIntOption(configParser, section, "minHitThresh", -1)
+ topRegions = getConfigIntOption(configParser, section, "topRegions", 0)
+ maxsize = getConfigIntOption(configParser, section, "maxsize", 300000000)
+ usePeaks = getConfigBoolOption(configParser, section, "usePeaks", False)
+ hitfile = getConfigOption(configParser, section, "hitFile", None)
+ doCache = getConfigBoolOption(configParser, section, "doCache", False)
+ doCompact = getConfigBoolOption(configParser, section, "doCompact", False)
+
+ parser.set_defaults(seqsize=seqsize, minHitThresh=minHitThresh, topRegions=topRegions, maxsize=maxsize,
+ usePeaks=usePeaks, hitfile=hitfile, doCache=doCache, doCompact=doCompact)
+
+ return parser
+