Does anyone have a simple solution to downloading all the refseq genomes for a particular taxon?

Using `ncbi-genome-download` its possible to specify the species or genus TaxIDs and download them, but apparently you can't go higher up the taxonomic ranks (even though enterobacteria has a TaxID of 543 for instance).

If anyone knows of a way to download all the Enterobacteria I'm all ears.

Alternatively, if there is a method of extracting the species TaxIDs from the Enterobacterial taxid in NCBI such that I can pass them all directly to `ncbi-genome-download` that would work too.
From speaking with a few other pros, this was the solution in the end (though only very rough at the mo):

Use the `ete3` toolkit to get a list of IDs:

    from ete3 import NCBITaxa
    import sys
    
    taxon_name = sys.argv[1]
    
    ncbi = NCBITaxa()
    ncbi.update_taxonomy_database()
    ebact = ncbi.get_descendant_taxa(taxon_name)
    
    with open('./taxids', 'w') as ofh:
        for i in ebact:
            ofh.write("%s\n" % i)

    # At this point, one could import ncbi-genome-download as a python method and continue


Which gave me a list of IDs (though this includes ALL descendent taxa, even ones without complete genomes etc).

I passed these to the latest version of `ncbi-genome-download` which accepts a `--taxid 12345,65890` format for specifiying the IDs.

So I just ran:

    for file in * ; 
    do python ~/bin/ncbi-genome-download/ncbi-genome-download-runner.py -l complete -v -p 10  --taxid $(paste -s -d ',' "$file") bacteria ; 
    done

I had to run this iteratively on many files after I split my `taxids` file up as there is a limit to how many args can be passed to `--taxid` at once.


EDIT Sept 2018:

I contributed a script to the `ncbi-genome-download` repo to make getting the TaxIDs nice and easy. It uses the approach above, but there’s no need to rewrite it for oneself now.