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Rewrite of findall.py to clean code. Configuration tested using
[erange.git]
/
getNovelSNPs.py
diff --git
a/getNovelSNPs.py
b/getNovelSNPs.py
index e95d72693c76df13871da4cf809c99e43c41d36a..4091281c8fe0f5410090b23db7276496fe49d6ed 100755
(executable)
--- a/
getNovelSNPs.py
+++ b/
getNovelSNPs.py
@@
-68,6
+68,7
@@
def doNotProcessLine(line):
def getNovelSNPInfo(genome, snpEntry, hg):
fields = snpEntry.split()
def getNovelSNPInfo(genome, snpEntry, hg):
fields = snpEntry.split()
+ #TODO: refactor naming. is fields[8] rpkm?
if fields[8].find("N\A") == -1:
return snpEntry
else:
if fields[8].find("N\A") == -1:
return snpEntry
else:
@@
-92,4
+93,4
@@
def getNovelSNPInfo(genome, snpEntry, hg):
if __name__ == "__main__":
if __name__ == "__main__":
- main(sys.argv)
+ main(sys.argv)
\ No newline at end of file