Issue in gff2gff.py script - does not generate the output file

[Maxime5G]

Hi,

I recently tried to convert bacterial GFF files with the provided gff2gff.py script, to make it compatible for bcftools csq, to no avail (i.e., no GFF file were written in the stdout as it should).

Command used: python3 bcftools-1.23.1/misc/gff2gff.py /full/path/to/genomic.gff /full/path/to/genomic.gfffutils > output_gff

Error shown:

Traceback (most recent call last):
  File "bcftools-1.23.1/misc/gff2gff.py", line 180, in <module>
    main()
  File "bcftools-1.23.1/misc/gff2gff.py", line 172, in main
    check_feature_groups(feature_groups)
  File "bcftools-1.23.1/misc/gff2gff.py", line 136, in check_feature_groups
    assert len(feature_groups[gene_id].CDSs) > 0
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError

I have attached the gff file for reproducibility (gff file of Escherichia coli, obtained from accession number GCF_000005845.2).

genomic.zip