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Release version for Erange 4.0a
[erange.git]
/
makerdsfromeland2.py
diff --git
a/makerdsfromeland2.py
b/makerdsfromeland2.py
index 66209eef973f36072ba964aac73f8579685aed99..b11848d7a93e3968d7b76b286fa415d04ffa078d 100755
(executable)
--- a/
makerdsfromeland2.py
+++ b/
makerdsfromeland2.py
@@
-106,8
+106,6
@@
def makeRDSFromEland2(label, filename, outdbname, doIndex=False, delimiter="|",
insertSize = 100000
geneDict = {}
insertSize = 100000
geneDict = {}
- mapDict = {}
- seenSpliceList = []
if dataType == 'RNA':
genedatafile = open(geneDataFileName)
for line in genedatafile:
if dataType == 'RNA':
genedatafile = open(geneDataFileName)
for line in genedatafile:
@@
-120,17
+118,11
@@
def makeRDSFromEland2(label, filename, outdbname, doIndex=False, delimiter="|",
chrom = fields[1]
sense = fields[2]
chromstarts = fields[8][:-1].split(',')
chrom = fields[1]
sense = fields[2]
chromstarts = fields[8][:-1].split(',')
- chromstops = fields[9][:-1].split(',')
- exonLengths = []
- totalLength = 0
for index in range(blockCount):
chromstarts[index] = int(chromstarts[index])
for index in range(blockCount):
chromstarts[index] = int(chromstarts[index])
- chromstops[index] = int(chromstops[index])
- exonLengths.append(chromstops[index] - chromstarts[index])
- totalLength += exonLengths[index]
- geneDict[uname] = (sense, blockCount,
totalLength, chrom, chromstarts, exonLength
s)
- mapDict[uname] = []
+ geneDict[uname] = (sense, blockCount,
chrom, chromstart
s)
+
genedatafile.close()
rds = ReadDataset.ReadDataset(outdbname, init, dataType, verbose=True)
genedatafile.close()
rds = ReadDataset.ReadDataset(outdbname, init, dataType, verbose=True)
@@
-322,6
+314,7
@@
def makeRDSFromEland2(label, filename, outdbname, doIndex=False, delimiter="|",
print '%d unique reads' % index
infile.close()
print '%d unique reads' % index
infile.close()
+ seenSpliceList = []
if dataType == 'RNA':
print 'mapping splices...'
index = 0
if dataType == 'RNA':
print 'mapping splices...'
index = 0
@@
-441,7
+434,7
@@
def makeRDSFromEland2(label, filename, outdbname, doIndex=False, delimiter="|",
print fields
continue
print fields
continue
- (sense, blockCount,
transLength, chrom, chromstarts, blockSize
s) = geneDict[model]
+ (sense, blockCount,
chrom, chromstart
s) = geneDict[model]
if extended:
if 'F' in thepos:
rsense = '+'
if extended:
if 'F' in thepos:
rsense = '+'