if not argv:
argv = sys.argv
- usage = "usage: python %prog rdsfile expandedRPKMfile multicountfile outfile [--multifraction] [--multifold] [--minrpkm minThreshold] [--cache] [--withGID]"
+ usage = "usage: python normalizeFinalExonic rdsfile expandedRPKMfile multicountfile outfile [--multifraction] [--multifold] [--minrpkm minThreshold] [--cache] [--withGID]"
parser = makeParser(usage)
(options, args) = parser.parse_args(argv[1:])
multicountfile = args[2]
outfilename = args[3]
- normalizeFinalExonic(rdsfilename, expandedRPKMfile, multicountfile, outfilename,
+ readCounts = {}
+ RDS = ReadDataset.ReadDataset(rdsfilename, verbose=True, cache=options.doCache, reportCount=False)
+ readCounts["uniq"] = RDS.getUniqsCount()
+ readCounts["splice"] = RDS.getSplicesCount()
+ readCounts["multi"] = RDS.getMultiCount()
+
+ normalizeFinalExonic(readCounts, expandedRPKMfile, multicountfile, outfilename,
options.reportFraction, options.reportFold, options.minThreshold,
options.doCache, options.writeGID)
return parser
-def normalizeFinalExonic(rdsfilename, expandedRPKMfilename, multicountfilename, outfilename,
+def normalizeFinalExonic(readCounts, expandedRPKMfilename, multicountfilename, outfilename,
reportFraction=False, reportFold=False, minThreshold=0., doCache=False,
writeGID=False):
elif reportFold:
print "reporting fold contribution of multireads"
- RDS = ReadDataset.ReadDataset(rdsfilename, verbose=True, cache=doCache, reportCount=False)
- uniqcount = RDS.getUniqsCount()
- splicecount = RDS.getSplicesCount()
- multicount = RDS.getMultiCount()
+ uniqcount = readCounts["uniq"]
+ splicecount = readCounts["splice"]
+ multicount = readCounts["multi"]
countDict = {}
multicountDict = {}
lengthDict = {}