Handling viral taxon

[swelbo]

Hello again!

Hope you are well.

We are getting this error when running virus IDs - tested on 11709 and 2697049.

Error: invalid or unsupported assembly accession:

The accession look a bit strange (see below):

n U01866.1
n Unknown:NC_001450.1/
n NC_001452.1/L06906.1
n NC_001511.1/M34193.1

Our bacterial targets all work well but seems to fail when we try to run viruses. Is this a work in progress or perhaps not a feature?

Cheers!

[haubold]

The intention is, that neighbors can handle viruses like bacteria (and eukaryotes for that matter). So thank you for pointing out these mal-formed viral accessions it returns. I just edited neighbors to straighten them out. All accessions returned by neighbors for your two example taxa can now be parsed by datasets. The program datasets, however, treats viruses differently from bacteria and eukaryotes. So to download the genomes with accessions listed in acc.txt, you'd execute something like

datasets download virus genome accession --inputfile acc.txt --include genome