search

oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
448 stars 55 forks source link

Is it possible to import my own cds fasta file for annotation? #245

Closed PengfanZhang closed 11 months ago

PengfanZhang commented 1 year ago

Hi, I have my own cds file predicted from prodigal with customized translation table. I'm wondering if bakta offers the option to annotate user-specified cds files rather than starting from scratch?

oschwengers commented 1 year ago

Hi @PengfanZhang , thanks for asking. Unfortunately, this is currently not possible. As this is asked for more and more often, we might consider implementing this - however, we cannot provide any reasonable ETA.

oschwengers commented 1 year ago

Ok, since more and more users ask for a feature like this, I've started a new issue #250 collecting ideas and requirements. Feedback and input is highly welcome!

oschwengers commented 11 months ago

OK, with #250 I'd consider this as addressed. You can now provide CDS coordindates as GFF/Genbank via --regions and if required or desired, in addition, provide accompanying functional information via --proteins.

Just in case there are any questions or unaddressed use cases, please, do not hesitate to re-open this or another issue.