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)
-        if geneDict.has_key(geneDescriptor):
+        if geneDescriptor in geneDict:
             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"
-            if rpkmDict.has_key(geneID):
+            if geneID in rpkmDict:
                 rpkm = str(rpkmDict[geneID])
 
             snpGeneInfoDict["rpkm"] = rpkm