implement a sourmash classify command?

[ctb]

I've been pretty impressed with the performance of gather as revealed by @luizirber and @bluegenes, vs the challenges of getting LCA-based approaches to work nicely.

Maybe it's time to implement a 'classify' command that takes a gather database and a lineages spreadsheet and classifies to the desired rank?

I'm currently only +0 on this. The + and - are described pretty well here --

ref #969

a few random thoughts --

• with sbts in zip files, this can be really lightweight
• charcoal already does something similar, and it's only a few lines. could add it there as 'charcoal classify' instead.
• not sure how to explain and/or configure the user experience around "do I use a protein database, or a DNA database?"

still +0, maybe verging on 0... it'd be nice to have as a built in command in some circumstances tho! like lca classify but better.

[bluegenes]

+1 from me, as I've been using some of your charcoal / other implementations to do this.

I was thinking it would be nice to optionally enable classification as output of multigather if a lineage file is provided.

[luizirber]

(even better if it generates a CAMI profile =])

[ctb]

also ref #984

[ctb]

I think with #1543 we ended up going in a different, slightly more complicated, but also more flexible direction. Closing this for now.