Add OrthoSearch of reference files about bakta

[oschwengers]

Hi @Tonny-zhou , thanks a lot for your kind feedback!
Indeed, I've already thought about this sort of feature and I'll address this in the next minor release (1.2). However, that might take a while.

[oschwengers]

Hi @Tonny-zhou , I've implemented a --proteins option to allow users to provide a trusted set of protein sequences as a single Fasta file.

Sequences therein can be annotated with additional information using 2 formats: short and long as described here: https://github.com/oschwengers/bakta#input-and-output

Could you please try if this is working for you as expected? The homology search is implemented as an alignment using Diamond.

I might also implement an accompanying GenBank/EMBL converter somewhen in the future.

I hope that works for you.
Best regards!

[Tonny-zhou]

Thank you so much!!!