Closed Anju-h closed 8 months ago
Unless the categorisation is part of the assembly summary file that ngd addresses, you cannot gather that information in this way. The file doesn't include information above I believe genus level.
You can use the script in the contrib/ folder gimme_taxa.py if you find out the TaxID at NCBI which corresponds to the Platyhelminthes group
I understand your point. But is there a way to find a list of the of the supported groups? Also, Platyhelminthes/flatworms is a well described group, so it is hard to believe that there is not available information.
I can see how the term "group" here is confusing, but I am using the terminology NCBI used to describe things here. NCBI's "taxonomic groups" for FTP download purposes are "archaea, bacteria, fungi, invertebrate, metagenomes, plant, protozoa, vertebrate_mammalian, vertebrate_other, viral", corresponding to how NCBI organises the separate folders on their download servers.
As Joe mentioned, ncbi-genome-download
is limited to the information the NCBI provides in the assembly summary files, which does not include a full taxonomy. The only things available are the "taxid", and the "species taxid". For any more complex taxonomy, check out the gimme_taxa.py
script in the contrib/
folder.
Thank you. It works
I have been trying to download genomes using command for eg. "ncbi-genome-download --refseq-categories reference platyhelminthes", but I keep getting the error "Unsupported group: platyhelminthes". I have tried different combinations of options as well. I was wondering is there a list or an option to see the supported format (or a name list) for a groups I wish to download genomes from ncbi.