Release version for Erange 4.0a

[erange.git] / geneMrnaCountsWeighted.py

diff --git a/geneMrnaCountsWeighted.py b/geneMrnaCountsWeighted.py
index 38e853aec6172be26b448066692193f1537b6926..5299d27d26c23f8729063eb31f0da390730b5ce5 100755 (executable)
--- a/geneMrnaCountsWeighted.py
+++ b/geneMrnaCountsWeighted.py
@@ -2,7 +2,7 @@ try:
     import psyco
     psyco.full()
 except:
-    print 'psyco not running'
+    print "psyco not running"
 
 import sys
 import optparse
@@ -68,12 +68,6 @@ def makeParser(usage=""):
     return parser
 
 
-#TODO: Reported user performance issue. Long run times in conditions:
-#    small number of reads ~40-50M
-#    all features on single chromosome
-#
-#    User states has been a long time problem.
-
 def geneMrnaCountsWeighted(genome, hitfile, countfile, outfilename, ignoreSense=True,
                            withUniqs=False, withMulti=False, acceptfile=None,
                            cachePages=None, doVerbose=False, extendGenome="", replaceModels=False):
@@ -206,7 +200,6 @@ def writeCountsToFile(outFilename, countFilename, allGIDs, genome, gidReadDict,
     for line in uniquecounts:
         fields = line.strip().split()
         # add a pseudo-count here to ease calculations below
-        #TODO: figure out why this was done in prior implementation...
         uniqueCountDict[fields[0]] = float(fields[-1]) + 1
 
     uniquecounts.close()
@@ -271,4 +264,4 @@ def getTagCount(uniqueCountDict, gid, gidReadDict, read2GidDict):
 
 
 if __name__ == "__main__":
-    main(sys.argv)
\ No newline at end of file
+    main(sys.argv)