Make the --region parameter better match the output of PGAP about bakta

[Dx-wmc]

Also, another point of confusion for me is, is it not possible to use a gbk file with -- region parameter for different genomes, I have now manually annotated a gbk file. But when I want to apply it to another genome the --region parameter reports an error.

[oschwengers]

Hi, and sorry for responding late.

First: To take a deeper look into the first issue: Could you provide me with an example of this? genome in Fasta and both the raw/fixed gbk files?

Second: I'm not sure if I understand correctly what you're trying to achieve. You would like to re-use a Genbank file via --region for another genome?

[Dx-wmc]

Hi, I have prepared the example data as requested:

1. s5.fasta: The genome sequence annotated by PGAP pipeline.
2. s5.gbk: The raw GenBank file generated by PGAP for s5.fasta contains genes not multiple of 3 in length.
3. s5_edited.gbk: The manually modified GenBank file where I removed the problematic genes so that Bakta's --region parameter works correctly. Directly using --region s5.gbk results in errors.
4. 1011.fasta: Another genome sequence for which I would like to reuse the annotations from s5_edited.gbk. However, this fails unless I manually change the first line of s5_edited.gbk from s5 to 1011, which is cumbersome.

Based on these observations, I would like to propose the following enhancements to Bakta:

1. Automatically exclude or skip genes that are not multiples of 3 in length when using the --region parameter.
2. Reuse an annotated GenBank file for different genomes without manual modification of the file.

I have attached the example data for your review.
test.tar.gz