setattr(txt, field, value)
txts[txt_name].exons.append([int(start), int(end)])
for txt in txts.values():
txt.exons.sort(lambda x,y: int(x[0])-int(y[0]))
txt.txStart = int(txt.exons[0][0])
txt.txEnd = int(txt.exons[-1][1])
return txts.values()
def get_attrs(text):
"""Extracts attributes(gene, transcript, etc) from attribute string in GTF file"""
attrs = {}
for pair in text.rstrip(';').split(';'):
name, value = pair.rstrip().lstrip().split(' ')
value = value.strip('"')
attrs[name] = value
return attrs
if __name__ == '__main__':
usage = "Usage: %prog gtf-file outfile"
parser = OptionParser(usage=usage)
parser.add_option("-i", "--index", dest="index", help="index output file")
(options, args) = parser.parse_args()
if len(args) == 2:
output(parse(args[0]), args[1])
txts[pp].exons.append([int(start), int(end)])
for txt in txts.values():
txt.exons.sort(lambda x,y: int(x[0])-int(y[0]))
if not txt.cdsStart:
txt.cdsStart = txt.exons[0][0]
if not txt.cdsEnd:
txt.cdsEnd = txt.exons[-1][1]
return txts.values()
def get_attrs(text):
"""Extracts attributes(gene, transcript, etc) from attribute string in GFF file"""
attrs = {}
for pair in text.split(';'):
if '=' in pair:
name, value = pair.split('=')
attrs[name] = value
return attrs
if __name__ == '__main__':
usage = "Usage: %prog gff-file outfile"
parser = OptionParser(usage=usage)
parser.add_option("-i", "--index", dest="index", help="index output file")
parser.add_option("-c", "--use_cds", dest="use_cds", help="use CDS as exon", action="store_true", default=False)
(options, args) = parser.parse_args()
if len(args) == 2:
output(parse(args[0], use_cds=options.use_cds), args[1])
