+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--append", action="store_false", dest="init",
+ help="append to existing rds file [default: create new]")
+ parser.add_option("--RNA", dest="geneDataFileName",
+ help="set data type to RNA [default: DNA]")
+ parser.add_option("--index", action="store_true", dest="doIndex",
+ help="index the output rds file")
+ parser.add_option("--cache", type="int", dest="cachePages",
+ help="number of cache pages to use [default: 100000")
+ parser.add_option("--olddelimiter", action="store_true", dest="useOldDelimiter",
+ help="use : as the delimiter")
+ parser.add_option("--paired", dest="pairID",
+ help="pairID value")
+ parser.add_option("--extended", action="store_true", dest="extended",
+ help="use eland_extended input")
+ parser.add_option("--verbose", action="store_true", dest="verbose")
+ parser.add_option("--maxlines", type="int", dest="maxLines",
+ help="[default: 1000000000")
+
+ configParser = getConfigParser()
+ section = "makerdsfromeland2"
+ init = getConfigBoolOption(configParser, section, "init", True)
+ doIndex = getConfigBoolOption(configParser, section, "doIndex", False)
+ cachePages = getConfigIntOption(configParser, section, "cachePages", 100000)
+ geneDataFileName = getConfigOption(configParser, section, "geneDataFileName", None)
+ useOldDelimiter = getConfigBoolOption(configParser, section, "useOldDelimiter", False)
+ pairID = getConfigOption(configParser, section, "pairID", None)
+ maxLines = getConfigIntOption(configParser, section, "maxLines", 1000000000)
+ extended = getConfigBoolOption(configParser, section, "extended", False)
+ verbose = getConfigBoolOption(configParser, section, "verbose", False)
+
+ parser.set_defaults(init=init, doIndex=doIndex, cachePages=cachePages,
+ geneDataFileName=geneDataFileName, useOldDelimiter=useOldDelimiter,
+ pairID=pairID, maxLines=maxLines, extended=extended, verbose=verbose)
+
+ return parser
+
+
+def makeRDSFromEland2(label, filename, outdbname, doIndex=False, delimiter="|", paired=False,
+ init=True, pairID="1", dataType="DNA", geneDataFileName=None,
+ cachePages=100000, maxLines=1000000000, extended=False, verbose=False):
+