Unable to read gff "no parent..."

[arsilan324]

Hi,

I really like the tool but its not working at all for me! For some reason, it keeps saying no parent while reading gff file. I tried to fix my file as well but sadly nothing is working. I would be glad if someone can help!

Thanks

ubt80:examples arslan$ python gag.py --fasta je.fasta.dammit.fasta --gff newfile.gff3 --out gag_output
Reading fasta...
Done.
Reading gff...
no parent
no parent
no parent
no parent
no parent
no parent
no parent
Traceback (most recent call last):
File "gag.py", line 50, in
main()
File "gag.py", line 46, in main
controller.execute(args)
File "/Users/arslan/Documents/src/controller.py", line 74, in execute
self.read_gff(gffpath, out_dir)
File "/Users/arslan/Documents/src/controller.py", line 286, in read_gff
genes, comments, invalids, ignored = gffreader.read_file(reader)
File "/Users/arslan/Documents/src/gff_reader.py", line 344, in read_file
line_added = self.process_line(splitline)
File "/Users/arslan/Documents/src/gff_reader.py", line 241, in process_line
self.process_cds_line(line)
File "/Users/arslan/Documents/src/gff_reader.py", line 277, in process_cds_line
kwargs = self.extract_cds_args(line)
File "/Users/arslan/Documents/src/gff_reader.py", line 139, in extract_cds_args
'strand': line[6], 'phase': int(line[7])}
ValueError: invalid literal for int() with base 10: '.'