+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--append", action="store_false", dest="init")
+ parser.add_option("--index", action="store_true", dest="doIndex")
+ parser.add_option("--rawreadID", action="store_false", dest="trimReadID")
+ parser.add_option("--forceRNA", action="store_true", dest="forceRNA")
+ parser.add_option("--flag", action="store_true", dest="flagReads")
+ parser.add_option("--strict", type="int", dest="minSpliceLength",
+ help="min required bp on each side of a splice")
+ parser.add_option("--spliceonly", action="store_true", dest="spliceOnly")
+ parser.add_option("--verbose", action="store_true", dest="verbose")
+ parser.add_option("--cache", type="int", dest="cachePages")
+ parser.add_option("--RNA", dest="geneDataFileName")
+
+ configParser = getConfigParser()
+ section = "makerdsfromblat"
+ init = getConfigBoolOption(configParser, section, "init", True)
+ doIndex = getConfigBoolOption(configParser, section, "doIndex", False)
+ trimReadID = getConfigBoolOption(configParser, section, "trimReadID", True)
+ minSpliceLength = getConfigIntOption(configParser, section, "minSpliceLength", 0)
+ forceRNA = getConfigBoolOption(configParser, section, "forceRNA", False)
+ flagReads = getConfigBoolOption(configParser, section, "flagReads", False)
+ spliceOnly = getConfigBoolOption(configParser, section, "spliceOnly", False)
+ verbose = getConfigBoolOption(configParser, section, "verbose", False)
+ cachePages = getConfigIntOption(configParser, section, "cachePages", 100000)
+ geneDataFileName = getConfigOption(configParser, section, "geneDataFileName", "")
+
+ parser.set_defaults(init=init, doIndex=doIndex, trimReadID=trimReadID, minSpliceLength=minSpliceLength, forceRNA=forceRNA,
+ flagReads=flagReads, spliceOnly=spliceOnly, verbose=verbose, cachePages=cachePages,
+ geneDataFileName=geneDataFileName)
+
+ return parser
+
+