sourmash-bio / sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.
http://sourmash.readthedocs.io/en/latest/
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returning more & richer information from rust `SeqToHash` struct/iterator #3339

Open ctb opened 1 month ago

ctb commented 1 month ago

Over in oxli-bio/oxli, @adamtaranto and I have been implementing k-mer functionality (no sketching!) on top of SeqToHashes in Rust, and then exposing it to Python via pyo3.

Most recently, we just added a kmers_and_hashes method that returns canonical k-mers and their hashes see https://github.com/oxli-bio/oxli/pull/40. We're talking there and in https://github.com/oxli-bio/oxli/issues/66 about how to pull relevant functionality back into sourmash, too.

We are not yet using protein k-mers, but we hope to get there soon: https://github.com/oxli-bio/oxli/issues/38

Some fun related issues popped up in this repo -