search

gencorefacility / reform

Modify existing reference fasta and gff3/gtf files to include a new sequence
29 stars 5 forks source link

Error creating a new gff file #9

Closed loukesio closed 2 years ago

loukesio commented 2 years ago

Thank you for the really nice tool! When I am trying to merge my genomes I take this error 

Preparing to create new annotation file
Traceback (most recent call last):
  File "reform.py", line 426, in <module>
    main()
  File "reform.py", line 64, in main
    new_gff = create_new_gff(new_gff_name, in_arg.ref_gff, in_gff_lines, position, down_position, seq.id, len(str(record.seq)))
  File "reform.py", line 209, in create_new_gff
    gff_feat_start = int(line_elements[3])
IndexError: list index out of range

Do you have any idea why?

mohammedkhalfan commented 2 years ago

It looks like there is an error parsing your annotation, can you please share it so I can take a look?