development release: conversion of ReadDataset to use BAM files

[erange.git] / combineRPKMs.py

diff --git a/combineRPKMs.py b/combineRPKMs.py
index 77f30d6fc2acb2a9424634a138a03ee30e314f91..88b57ab547edeea3f9be5387780796aadbe72bc2 100755 (executable)
--- a/combineRPKMs.py
+++ b/combineRPKMs.py
@@ -63,6 +63,8 @@ def combineRPKMs(firstfileName, expandedfileName, finalfileName, outfileName, do
     outfile.write(header)
 
     finalfile = open(finalfileName)
+    #TODO: QForAli - the output lines are driven by finalfile.  If there are genes in the first 2 that
+    #      are not in the finalfile then they will be lost.
     for line in finalfile:
         fields = line.strip().split()
         gene = fields[0]
@@ -101,4 +103,4 @@ def getRPKMDict(rpkmFileName, getGIDDict=False):
 
 
 if __name__ == "__main__":
-    main(sys.argv)
+    main(sys.argv)
\ No newline at end of file