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

[Dx-wmc]

While using Bakta, I realized that one of the known genes was not predicted. However, both Prokka and PGAP accurately predicted the gene. I tried using the -region option for this. Although Prokka's gbk file can be read well, PGAP's file is not ideal. Upon examining PGAP's gbk generation, I found that some of its gene fragments are not multiples of 3 in length (these genes are labeled as pseudogenes). After removing these non-3 genes, it ran successfully. However, manually modifying these files is too costly when applying PGAP annotations to Bakta in bulk. Therefore, I would like --region to automatically identify and exclude or skip these problematic genes, significantly improving efficiency.

[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.