+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--transcriptome", type="float", dest="tSize",
+ help="transcriptome size in Gbp [default 200000.0]")
+ parser.add_option("--cells", type="float", dest="cellCount",
+ help="arbitrary units [default 1e6]")
+ parser.add_option("--efficiency", type="float", dest="efficiency",
+ help="fraction [default 0.3]")
+
+ configParser = getConfigParser()
+ section = "transcripts"
+ tSize = getConfigFloatOption(configParser, section, "tSize", 200000.0)
+ cellCount = getConfigFloatOption(configParser, section, "cellCount", 1e6)
+ efficiency = getConfigFloatOption(configParser, section, "efficiency", 0.3)
+
+ parser.set_defaults(tSize=tSize, cellCount=cellCount, efficiency=efficiency)
+
+ return parser
+
+