gimme_taxa.py / ngd mismatched format

[zreitz]

ngd --taxids seems to require gimme_taxa.py have the -j. Not sure if you want to update the documentation or one of the scripts?

$ gimme_taxa.py -o taxids.txt Hyphomicrobiales
$ ngd --dry-run --taxids taxids.txt --assembly-levels complete --refseq-categories representative bacteria
ERROR: No downloads matched your filter. Please check your options.
$ gimme_taxa.py -o taxids.txt Hyphomicrobiales -j
$ ngd --dry-run --taxids taxids.txt --assembly-levels complete --refseq-categories representative bacteria
Considering the following 158 assemblies for download:
<snip>
$ ngd --version
0.3.3

[kblin]

Interesting, I guess that changed with Nick's rework of gimme_taxa some years ago. It's certainly not a change in ncbi-genome-download. I think it makes most sense to adjust the README.

[kblin]

Will be shipped with the next release, but is already correct on the GitHub project view.