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development release: conversion of ReadDataset to use BAM files
[erange.git]
/
geneMrnaCountsWeighted.py
diff --git
a/geneMrnaCountsWeighted.py
b/geneMrnaCountsWeighted.py
index 74e7a0cd817e699af6b398960578f576a030f7e4..31213c3f7a4703f9d9c8c1e87f17f4c0854e4574 100755
(executable)
--- a/
geneMrnaCountsWeighted.py
+++ b/
geneMrnaCountsWeighted.py
@@
-165,7
+165,7
@@
def getReadGIDs(hitDict, fullchrom, featList, readlen, index):
for read in hitDict[fullchrom]:
tagStart = read["start"]
tagReadID = read["readID"]
for read in hitDict[fullchrom]:
tagStart = read["start"]
tagReadID = read["readID"]
- if
read.has_key("sense")
:
+ if
"sense" in read
:
tagSense = read["sense"]
ignoreSense = False
tagSense = read["sense"]
ignoreSense = False
@@
-253,7
+253,7
@@
def getTagCount(uniqueCountDict, gid, gidReadDict, read2GidDict):
try:
tagValue = uniqueCountDict[gid]
except KeyError:
try:
tagValue = uniqueCountDict[gid]
except KeyError:
- tagValue = 1
+ pass
tagDenom = 0.
for relatedGID in read2GidDict[readID]:
tagDenom = 0.
for relatedGID in read2GidDict[readID]: