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development release: conversion of ReadDataset to use BAM files
[erange.git]
/
getSNPGeneInfo.py
diff --git
a/getSNPGeneInfo.py
b/getSNPGeneInfo.py
index edcb2ceae0103af5b810c4e98d5c0521544efd34..0fbc6795121db515e27151902531f0962aa05715 100755
(executable)
--- a/
getSNPGeneInfo.py
+++ b/
getSNPGeneInfo.py
@@
-116,7
+116,7
@@
def getSNPGeneInfo(genome, infilename, rpkmfilename, doCache=False, withSense=Tr
symbol = "LOC%s" % geneID
geneDescriptor = (symbol, geneID)
symbol = "LOC%s" % geneID
geneDescriptor = (symbol, geneID)
- if geneD
ict.has_key(geneDescriptor)
:
+ if geneD
escriptor in geneDict
:
geneDict[geneDescriptor]["position"].append(pos)
else:
geneDict[geneDescriptor] = {"position": [pos],
geneDict[geneDescriptor]["position"].append(pos)
else:
geneDict[geneDescriptor] = {"position": [pos],
@@
-167,7
+167,7
@@
def getSNPGeneInfoList(geneDict, snpDict, rpkmDict, withSense):
"geneID": geneID}
rpkm = "N\A"
"geneID": geneID}
rpkm = "N\A"
- if
rpkmDict.has_key(geneID)
:
+ if
geneID in rpkmDict
:
rpkm = str(rpkmDict[geneID])
snpGeneInfoDict["rpkm"] = rpkm
rpkm = str(rpkmDict[geneID])
snpGeneInfoDict["rpkm"] = rpkm