Open mcroxen opened 2 years ago
Hi, Thank you for the feedback. For the bakta gff3 implementation I would need at least an example file. Even with that, I can't promise anything, but I will consider it. You're also welcome to contribute if you will.
I've added a license.
BR, Antti
Sorry for the delay, please see an attached example ABU83972.gff3.gz .
Sorry that I haven't had time for this. But I might have a better solution for this.
If you're using bakta for metagenome annotation and would like to import those annotations to anvi'o, I would suggest to use the genbank file from bakta and anvi-script-process-genbank
.
Something like this:
bakta $ASSEMBLY.fasta -o $ASSEMBLY_bakta -p $ASSEMBLY
anvi-script-process-genbank -i $ASSEMBLY_bakta/I$ASSEMBLY.gbff -O $ASSEMBLY \
--annotation-source $GENE_CALLER \
--annotation-version $VERSION
anvi-gen-contigs-database -f $ASSEMBLY-contigs.fa --external-gene-calls $ASSEMBLY-external-gene-calls.txt \
-o $ASSEMBLY.db -n $ASSEMBLY -T $THREADS \
--ignore-internal-stop-codons
anvi-import-functions -c $ASSEMBLY.db -i $ASSEMBLY-external-functions.txt
This looks to be a handy tool. I was wondering if you could add support for bakta gff3, which is similar to prokka, but doesn't seem to read the file properly:
https://github.com/oschwengers/bakta
https://doi.org/10.1099/mgen.0.000685
Also could you please also add a license.
Thank you