Option for trusted HMMs

[StefDiV]

Is your feature request related to an existing issue or bug?
Similar to #295, using hmm instead of a protein set.

An option like: "--hmms: Trusted HMM to first annotate from (default '')" from prokka, so the user can provide a custom hmm or hmm database that bakta could use to derive annotation first and its not overlapped by following annotation steps.

Example: given a particular protein of interest which has been used to create and curate a hmm, bakta could take the hmm (with defined cutoff scores) to identify it first in the dataset and the annotation is preserved in the final outputs.

[oschwengers]

Hi @StefDiV ,
thanks for reaching out with this. This is certainly a great idea and a feature that Bakta is currently missing. I'll put this on my lis. Hopefully for the next version, but I cannot promise yet.

[oschwengers]

OK, now, this is implemented and live in the main branch. If you like, you can give it an early try. This will be part of the upcoming v1.10.0 release.

Again, thanks a lot @StefDiV for bringing this up! If you have any feedback, comments or further ideas, please do not hesitate to re-open this or file a new issue.