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development release: conversion of ReadDataset to use BAM files
[erange.git]
/
geneMrnaCounts.py
diff --git
a/geneMrnaCounts.py
b/geneMrnaCounts.py
index cf5065ab88c40279c7ca5dfb30b70bc99dfd2065..7b4a2cc819c30976692d9721ddb363756ebdf70a 100755
(executable)
--- a/
geneMrnaCounts.py
+++ b/
geneMrnaCounts.py
@@
-124,7
+124,7
@@
def geneMrnaCounts(genomeName, hitfile, outfilename, trackStrand=False, doSplice
continue
if countFeats:
continue
if countFeats:
- seenFeaturesByChromDict[chrom] =
[]
+ seenFeaturesByChromDict[chrom] =
set([])
print "\nchr%s" % chrom
fullchrom = "chr%s" % chrom
print "\nchr%s" % chrom
fullchrom = "chr%s" % chrom
@@
-137,18
+137,18
@@
def geneMrnaCounts(genomeName, hitfile, outfilename, trackStrand=False, doSplice
if featureSense == "R":
checkSense = "-"
if featureSense == "R":
checkSense = "-"
- region
List.append((gid, fullchrom, start, stop, checkSense)
)
+ region
Data = (gid, fullchrom, start, stop, checkSense
)
count = hitRDS.getCounts(fullchrom, start, stop, uniqs=doUniqs, multi=doMulti, splices=doSplices, sense=checkSense)
else:
count = hitRDS.getCounts(fullchrom, start, stop, uniqs=doUniqs, multi=doMulti, splices=doSplices, sense=checkSense)
else:
- region
List.append((gid, fullchrom, start, stop)
)
+ region
Data = (gid, fullchrom, start, stop
)
count = hitRDS.getCounts(fullchrom, start, stop, uniqs=doUniqs, multi=doMulti, splices=doSplices)
count = hitRDS.getCounts(fullchrom, start, stop, uniqs=doUniqs, multi=doMulti, splices=doSplices)
- if count != 0:
- print count
gidCount[gid] += count
gidCount[gid] += count
+ if markGID:
+ regionList.append(regionData)
+
if countFeats:
if countFeats:
- if (start, stop, gid, featureSense) not in seenFeaturesByChromDict[chrom]:
- seenFeaturesByChromDict[chrom].append((start, stop, gid, featureSense))
+ seenFeaturesByChromDict[chrom].add((start, stop, gid, featureSense))
except:
print "problem with %s - skipping" % gid
except:
print "problem with %s - skipping" % gid