def parsePSL(filename):
for pslObj in pslparser.read(open(filename)):
strand = pslObj.strand
chrom = pslObj.tName
name = pslObj.qName
chromStart = pslObj.tStart
chromEnd = pslObj.tEnd
blockCount = pslObj.blockCount
blockSizes = ','.join([str(i) for i in pslObj.blockSizes])
blockStarts = ','.join([str(i - chromStart) \
for i in pslObj.tStarts])
thickStart = chromStart
thickEnd = chromEnd
writer = csv.writer(sys.stdout, dialect='excel-tab')
writer.writerow((chrom,
chromStart,
chromEnd,
name,
255,
strand,
thickStart,
thickEnd,
'0,0,0',
blockCount,
blockSizes,
blockStarts))
def parse_psl(filename):
'''Reads alignments from PSL format and create
exon objects from each transcript.
'''
for pslobj in pslparser.read(open(filename)):
exons = []
for i in range(len(pslobj.tStarts)):
start = pslobj.tStarts[i]
end = start + pslobj.blockSizes[i]
strand = pslobj.strand
exon = Exon(pslobj.tName, start, end, strand)
exons.append(exon)
yield exons
def parse_psl(filename):
'''Reads alignments from PSL format and create
exon objects from each transcript.
'''
for pslobj in pslparser.read(open(filename)):
exons = []
for i in range(len(pslobj.tStarts)):
start = pslobj.tStarts[i]
end = start + pslobj.blockSizes[i]
strand = pslobj.strand
exon = Exon(pslobj.tName, start, end, strand)
exons.append(exon)
yield exons
