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first pass cleanup of cistematic/genomes; change bamPreprocessing
[erange.git]
/
combineRPKMs.py
diff --git
a/combineRPKMs.py
b/combineRPKMs.py
index 77f30d6fc2acb2a9424634a138a03ee30e314f91..1e2d2aaedbf3476fc43058500c30c76c2b7c3e03 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)
outfile.write(header)
finalfile = open(finalfileName)
+ #TODO: 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]
for line in finalfile:
fields = line.strip().split()
gene = fields[0]
@@
-101,4
+103,4
@@
def getRPKMDict(rpkmFileName, getGIDDict=False):
if __name__ == "__main__":
if __name__ == "__main__":
- main(sys.argv)
+ main(sys.argv)
\ No newline at end of file