Comments (3)
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.
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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!
from bakta.
Thank you so much!!!
from bakta.
Related Issues (20)
- update AMRFinderPlus database fails HOT 3
- Bakta_proteins connection to dbxrefs/json-type identifier HOT 2
- --force not working HOT 3
- adding deepsig to conda recipe HOT 3
- Add the ability to annotate only one's own database HOT 1
- User proteins fasta file formatting issue HOT 1
- `bakta_db download` downloads database every time it is run HOT 1
- amrfinder_update with local database breaks bakta HOT 6
- getting databases with singularity HOT 2
- conda installs version 1.3.1 while latest is 1.7 HOT 2
- Rare extended-ascii character in product field breaks ascii-only tools HOT 8
- When using --proteins, are the sequences only used for annotation? HOT 10
- re-allow biopython 1.78 HOT 1
- wrong db version info file format
- CWL unrecognised argument GCA_...fasta HOT 5
- bakta encounters issues annotating assemblies with presence of N's HOT 2
- More conda 101 instructions in bioconda-driven installation HOT 2
- fasta format protein file HOT 6
- Swap tRNAscan-SE model to general HOT 2
- gene missing from final output files HOT 2
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