+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--upstream", dest="upfilename")
+ parser.add_option("--downstream", dest="downfilename")
+ parser.add_option("--uplength", type="float", dest="uplength")
+ parser.add_option("--downlength", type="int", dest="")
+ parser.add_option("--gene", dest="gene")
+ parser.add_option("--genes", dest="genefile")
+ parser.add_option("--append", action="store_true", dest="doAppend")
+
+ configParser = getConfigParser()
+ section = "profilebins"
+ upfilename = getConfigOption(configParser, section, "upfilename", None)
+ downfilename = getConfigOption(configParser, section, "downfilename", None)
+ uplength = getConfigFloatOption(configParser, section, "uplength", 0.0)
+ downlength = getConfigFloatOption(configParser, section, "downlength", 0.0)
+ gene = getConfigOption(configParser, section, "gene", None)
+ genefile = getConfigOption(configParser, section, "genefile", None)
+ doAppend = getConfigBoolOption(configParser, section, "doAppend", False)
+
+ parser.set_defaults(upfilename=upfilename, downfilename=downfilename, uplength=uplength, downlength=downlength,
+ gene=gene, genefile=genefile, doAppend=doAppend)
+
+ return parser
+
+