C. Titus Brown
C. Titus Brown
right now, the `fromfile` format doesn't support a simple way to produce translated sequence - presumably we'd need to add a CDS column or something, or else build workflows (elsewhere)...
Adds a `FrozenSourmashSignature` class, and provides sensible `to_mutable()` and `to_frozen()` methods on `SourmashSignature` and `FrozenSourmashSignature`. Provides an `update()` context manager that wraps changes so that a `FrozenSourmashSignature` is left at...
`python -m sourmash.sig` works `python -m sourmash.tax` doesn't work `python -m sourmash.lca` doesn't work, for different reasons do we want this to work? if so, we should fix and test....
After https://github.com/sourmash-bio/sourmash/pull/1610, it seems like an obvious next set of simplifications is to remove all of the `with x.update(): ...` code blocks and replace them with `flatten` and/or `downsample` calls....
see https://octo-repo-visualization.vercel.app/?repo=sourmash-bio%2Fsourmash https://next.github.com/projects/repo-visualization?utm_source=programmingdigest&utm_medium=email&utm_campaign=432 explains how to add this to github actions.
We have a few different issues around adding `--from-file` to new commands, e.g. https://github.com/sourmash-bio/sourmash/issues/1631. As I was implementing #1657 for a different reason, though, I realized that pathlists and `--from-file`...
below, if `pathlist.txt` contains a path that cannot be loaded, sourmash tells us that `pathlist.txt` can't be loaded instead of complaining about the specific file. ``` % sourmash sig fileinfo...
we can force `sourmash` commands to load .sig/.sig.gz files from under a directory, and (with `-f`) we can ask sourmash to try to load other files that MIGHT be JSON...
I wrote a script that calculates the distribution of hashes in collections of genomes. one goal is to generate some statistics for what the pangenome overlap is between genomes. It's...
If `FrozenSourmashSignature` https://github.com/sourmash-bio/sourmash/pull/1610 goes in, we'll have a de facto documentation of everywhere in the code base where we modify signatures and sketches. This touches on a bunch of things...