Some annotations in the GFF do not have an ID assigned? about bakta

[oschwengers]

Dear @ZarulHanifah ,
thanks for the question and bringing this up. Due to the official GFF3 specification: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md:

ID
Indicates the ID of the feature. The ID attribute is required for features that have children (e.g. gene and mRNAs), or for those that span multiple lines, but are optional for other features. IDs for each feature must be unique within the scope of the GFF file. ...

As oriC/oriV/oriT features aren't genes and do not span multiple lines I think that this behavior is in concordance with the GFF3 spec, so technically it's not a bug. However, it would be absolutely fine and make sense to assign IDs if this is covered by the spec and would help with downstream analysis.

Regarding the regulatory_region feature you're absolutely right. They are of course part of a particular gene and should be linked to the parent feature via a common ID. However, it is not that simple to automatically assign them to a certain CDS as they are detected on their own. So they somehow need to be assigned to the CDS features afterwards. I'll put that on the list and see what we are able to come up with but that might take a while.

Thanks again - I'll leave this open so that others can relate to this.

[oschwengers]

@ZarulHanifah This issue should be fixed now. You can install the latest commit version from GitHub via a pip install <github-repo-path> or just wait for the next patch release.
Best regards