+ rnaEditing(dbfile, hitfile, genome, rpkmfilename, options)
+
+
+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--goprefix", dest="prefix")
+ parser.add_option("--novelsnp", dest="novelsnpoutfilename")
+ parser.add_option("--bedfile", dest="bedoutfilename")
+ parser.add_option("--cache", type="int", dest="cachePages")
+ parser.add_option("--snpDB", action="append", dest="snpDBList",
+ help="additional snp db files to check will be searched in order given")
+
+ configParser = getConfigParser()
+ section = "rnaEditing"
+ prefix = getConfigOption(configParser, section, "prefix", None)
+ novelsnpoutfilename = getConfigOption(configParser, section, "novelsnpoutfilename", None)
+ bedoutfilename = getConfigOption(configParser, section, "bedoutfilename", None)
+ cachePages = getConfigOption(configParser, section, "cachePages", None)
+
+ parser.set_defaults(prefix=prefix, novelsnpoutfilename=novelsnpoutfilename, bedoutfilename=bedoutfilename,
+ cachePages=cachePages, snpDBList=[])
+
+ return parser
+
+
+def rnaEditing(dbfile, hitfile, genome, rpkmfilename, options):