Tessa Pierce Ward

I find myself using `fromfile` for everything these days, because it makes naming sketches properly so easy!! So I _would_ like us to support `translate` if we can -- perhaps...

yep - that's the quick fix! The slightly larger fix is `containment_ani` --> `contained_by_as_ani` (which I quite like). This would fix `compare` direction as well, #2194

> yep - contained_by resulted from one of the earliest confusions for me! https://github.com/sourmash-bio/sourmash/pull/199 Also, I can('t) believe I repeated your journey to `contained_by`. I found `contained_by` pretty frustrating and...

> OR... maybe we could just provide duplicate tax entries in the taxonomy spreadsheet, i.e. include the same lineage for `GCF_XYZ` and `GCA_XYZ`? There's not much of a penalty beyond...

This is mostly just confirmation -- I ran into this issue recently, because I ran `gather` against gtdb and genbank together (in hindsight unnecessary, but I wanted gtdb assignments for...

This continues to be a problem when running 6-frame translated read searches against protein databases for classification. We know the `% classified` will be incorrect, but I'm not sure we...

...especially a problem for downstream use of gather --> tax, e.g. krona output, where the 'fraction' reported is of the 6-frame translated sketch... ``` fraction superkingdom phylum class order family...

side note, we could also let folks input a lineages gather file into this utility (the requisite columns exist!) to produce a nice human-readable summary. Not quite as nice as...

Adding action="extend" should handle this nicely. Will PR later today.

Note that we need `--force` to continue past empty gather csvs, so fixing this is important (nudges self)