There are so many ranks

[shenwei356]

OMG, so many ranks:

class
family
forma
genus
infraclass
infraorder
kingdom
no rank
order
parvorder
phylum
species
species group
species subgroup
subclass
subfamily
subgenus
subkingdom
suborder
subphylum
subspecies
subtribe
superclass
superfamily
superkingdom
superorder
superphylum
tribe
varietas

[childers]

Are you planning to support filtering to output a subset of ranks?

[shenwei356]

"taxonkit list" can do this when you provide the taxid of the ranks

[lskatz]

I used grep and was happy that this toolkit works very well with piping. For example showing all subspecies of Vibrio in my custom Kraken database:

taxonkit --data-dir Kalamari_v3.4/taxonomy list --ids 662 --show-name --show-rank | grep -v 'no rank' | grep -v 'Vibrio sp'

I'd imagine that you could have an "or" in grep, something like

taxonkit --data-dir Kalamari_v3.4/taxonomy list --ids 662 --show-name --show-rank | grep -v 'tribe\|varietas'

[shenwei356]

@lskatz, grep -v -E 'tribe|varietas'?

[lskatz]

Yes that works, @shenwei356 !