+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--prefix", dest="contigPrefix")
+ parser.add_option("--filter", dest="filterFileName")
+ parser.add_option("--min", type="int", dest="minSize")
+ parser.add_option("--keepcov", action="store_true", dest="keepCoverage")
+
+ configParser = getConfigParser()
+ section = "processvelvet"
+ contigPrefix = getConfigOption(configParser, section, "contigPrefix", "chr")
+ filterFileName = getConfigOption(configParser, section, "filterFileName", "")
+ minSize = getConfigIntOption(configParser, section, "minSize", 0)
+ keepCoverage = getConfigBoolOption(configParser, section, "keepCoverage", False)
+
+ parser.set_defaults(contigPrefix=contigPrefix, filterFileName=filterFileName, minSize=minSize, keepCoverage=keepCoverage)
+
+ return parser
+
+