insertSize = 100000
geneDict = {}
- mapDict = {}
- seenSpliceList = []
if dataType == 'RNA':
genedatafile = open(geneDataFileName)
for line in genedatafile:
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])
- chromstops[index] = int(chromstops[index])
- exonLengths.append(chromstops[index] - chromstarts[index])
- totalLength += exonLengths[index]
- geneDict[uname] = (sense, blockCount, totalLength, chrom, chromstarts, exonLengths)
- mapDict[uname] = []
+ geneDict[uname] = (sense, blockCount, chrom, chromstarts)
+
genedatafile.close()
rds = ReadDataset.ReadDataset(outdbname, init, dataType, verbose=True)
print '%d unique reads' % index
infile.close()
+ seenSpliceList = []
if dataType == 'RNA':
print 'mapping splices...'
index = 0
print fields
continue
- (sense, blockCount, transLength, chrom, chromstarts, blockSizes) = geneDict[model]
+ (sense, blockCount, chrom, chromstarts) = geneDict[model]
if extended:
if 'F' in thepos:
rsense = '+'