GFF error when using a mtDNA annotation file

[hoelzer]

Hey, me again : )

I am trying to use a GFF annotation from MITOS2 for a mtDNA genome:

CM022781.1.gff.zip

But I get:

virheat 2024-11-07-vcf-results/vcf-filtered/ results-filtered -g CM022781.1.gff -r CM022781.1

Traceback (most recent call last):
  File "/Users/martin/miniconda3/envs/virheat/bin/virheat", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/martin/miniconda3/envs/virheat/lib/python3.12/site-packages/virheat/command.py", line 192, in main
    gff3_info = data_prep.parse_gff3(args.gff3_path, args.reference)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/martin/miniconda3/envs/virheat/lib/python3.12/site-packages/virheat/scripts/data_prep.py", line 310, in parse_gff3
    gff3_dict[gff_values[2]][attribute_id][identifier] = val.replace("\n", "")
    ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
KeyError: 'transcript_trnF(gaa)'

So I guess this is a GFF file format you were not expecting ;)

Any easy way to get that visualized w/ virHEAT?

(and sorry for repurposing your tool for mtDNA... but it would be very neat also for such an application!)

[jonas-fuchs]

@hoelzer Thanks! This is enhancing the tool a bit :).

So basically what I do for the nested dictionary is to set the final keys with the ID= identifier. The gff format was not the problem, but in your case that exons only have parents . I have checked quite a few gffs and never seen that there is no unique identifier. I introduced now a simple check if ID= is present in each line.

I also checked NCBI a bit and it seems that exons can have IDs e.g.:

WJXW01000006.1 Genbank exon 32023 33421 . + . ID=exon-gnl

So I think this simple check is ok for now. Probably depends on who annotates these genomes.

Can you again have a look? It should work fine now. Same branch as the last issue :)

[hoelzer]

Yes thanks, works as reported in the PR!

virheat 2024-11-07-vcf-results/vcf-filtered/ results-filtered -g CM022781.1.gff -r CM022781.1

virHEAT_plot.pdf

Yeah, the tool I used is MITOS2 which is a special annotation tool for mtDNAs. And as it seems provides a bit weird GFF output.