+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--RNA", dest="genedatafilename")
+ parser.add_option("--append", action="store_false", dest="init")
+ parser.add_option("--index", action="store_true", dest="doIndex")
+ parser.add_option("--spacer", type="int", dest="spacer")
+ parser.add_option("--rawreadID", action="store_false", dest="trimReadID")
+ parser.add_option("--forcepair", type="int", dest="forceID")
+ parser.add_option("--flip", action="store_true", dest="flip")
+ parser.add_option("--verbose", action="store_true", dest="verbose")
+ parser.add_option("--strip", action="store_true", dest="stripSpace")
+ parser.add_option("--cache", type="int", dest="cachePages")
+
+ configParser = getConfigParser()
+ section = "makerdsfrom bowtie"
+ genedatafilename = getConfigOption(configParser, section, "genedatafilename", None)
+ init = getConfigBoolOption(configParser, section, "init", True)
+ doIndex = getConfigBoolOption(configParser, section, "doIndex", False)
+ spacer = getConfigIntOption(configParser, section, "spacer", 2)
+ trimReadID = getConfigBoolOption(configParser, section, "trimReadID", True)
+ forceID = getConfigOption(configParser, section, "forceID", None)
+ flip = getConfigBoolOption(configParser, section, "flip", False)
+ verbose = getConfigBoolOption(configParser, section, "verbose", False)
+ stripSpace = getConfigBoolOption(configParser, section, "stripSpace", False)
+ cachePages = getConfigIntOption(configParser, section, "cachePages", 100000)
+
+ parser.set_defaults(genedatafilename=genedatafilename, init=init, doIndex=doIndex, spacer=spacer,
+ trimReadID=trimReadID, forceID=forceID, flip=flip, verbose=verbose,
+ stripSpace=stripSpace, cachePages=cachePages)
+
+ return parser
+
+