Issue with anvi-script-process-genbank-metadata

[Emily St. John]

Hi,

I've been having an issue where the anvi-script-process-genbank-metadata program occasionally cannot recognize protein translations from standard Genbank files. Here's an example:

ncbi-genome-download --section refseq --assembly-accessions GCF_000378065.1,GCF_000212375.1 --metadata metadata.txt bacteria
anvi-script-process-genbank-metadata -m metadata.txt --output-dir processed --exclude-gene-calls-from-fasta

Both genbank files downloaded have /translation data, but only one of the external-gene-calls files has an aa_sequence column. I'm using a conda install of Anvi'o 7.1 on Mac OS Monterey.

Thanks so much for your help and time!

Best,

Emily St. John

[Florian Trigodet]

Hi Emily,

It is was a bug in the code and was fixed in the active developer branch on github.
If you need this before the next release of anvi'o, you can install the development version of anvi’o in a new conda environment by following the instructions here: https://anvio.org/install/#5-follow-the-active-development-youre-a-wizard-arry

Best,
Florian

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[Emily St. John]

Hi Florian, 

Thanks so much - I really appreciate your help!

~Emily