C. Titus Brown

icon indicating a website link http://ivory.idyll.org/blog/ icon indicating an email [email protected]

icon company University of California, Davis icon location Davis, CA icon location Prof at UC Davis. Blogs at http://ivory.idyll.org/blog/ and uses bluesky under ctitusbrown.

Results 1175 comments of C. Titus Brown

sourmash gather and/or tax metagenome seems to round incorrectly?

Still tracking this down. Not clear where things are going wrong 😆

tutorial: Annotate the eukaryotic and bacterial taxonomy of a metagenome using sourmash

note to self: integrate with https://github.com/sourmash-bio/sourmash/issues/3534

Update pytest-cov requirement from <5.0,>=4 to >=4,<6.0

@dependabot rebase

script: options for shuffling the order in which sketches are searched in a database

note to self: write some example code using `src/sourmash/manifest.py` to do the shuffling 😅

script: options for shuffling the order in which sketches are searched in a database

code & instructions in https://github.com/ctb/2025-sourmash-shuffle-manifest

support name output from `sig grep`

> And/or can we output a picklist directly? ooh lovely idea!!!

support name output from `sig grep`

> And/or can we output a picklist directly? funny story, it turns out that: ``` sourmash sig grep -i shewanella podar-ref.zip --no-sig --csv xxx.csv ``` outputs a manifest file `xxx.csv`...

support name output from `sig grep`

in #3820 I'm adding aliases - `--no-sigs` for `--silent` `--save-picklist` for `--csv` and also `-l/--print-matched-names` for, well, print matching names!

sourmash compute/sketch doesn't recognize signature files when erroneously provided on command line

a simple "if it's not loadable by screed, is it JSON-like?" might be enough here.

sourmash compute/sketch doesn't recognize signature files when erroneously provided on command line

in line with #1078, maybe see if we can use a streaming JSON parser to evaluate the first few elements? I don't remember if we're doing any JSON parsing in...