C. Titus Brown
C. Titus Brown
ref: https://github.com/sourmash-bio/sourmash/issues/3246
thanks! we will fix this. See #3622
posted on the [databases page](https://sourmash.readthedocs.io/en/latest/databases.html) in https://github.com/sourmash-bio/sourmash/pull/3754.
I think https://github.com/sourmash-bio/sourmash/issues/3601 is critical for this.
Hot take: I dislike this idea, but only to the -0 level. We should just prepare tax lineage files properly :)
with reference to https://github.com/sourmash-bio/sourmash/issues/3537 - perhaps we could have this work entirely on the output of `tax annotate`, for speed reasons.
see https://github.com/ctb/2025-atb-small-genomes/blob/main/round3/parse.py - gives output like so, ``` % parse.py SAMN07157241.entire.gather.with-lineages.csv -m 1 SAMN07157241 SAMN07157241 50.0% Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;Homo sapie... 37.5% d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria (2 species) 8.3% d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Stre... 4.2% unknown ``` for multiple files,...
I believe this is the same script, updated to be nicer :) https://github.com/ctb/2025-sourmash-analyzing-genomes-and-metagenomes/blob/main/scripts/display-tax.py
relevant: https://github.com/sourmash-bio/sourmash/issues/2941
https://github.com/sourmash-bio/sourmash/issues/2898