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oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
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Option for trusted HMMs #309

Closed StefDiV closed 1 month ago

StefDiV commented 3 months ago

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 commented 2 months ago

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 commented 1 month ago

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.