Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

maybe add new command, sourmash prefetch #1310

Closed
ctb opened this issue Feb 7, 2021 · 3 comments · Fixed by #1370
Closed

maybe add new command, sourmash prefetch #1310

ctb opened this issue Feb 7, 2021 · 3 comments · Fixed by #1370

Comments

@ctb
Copy link
Contributor

ctb commented Feb 7, 2021

I'm a big fan of the prefetch_gather functionality in genome-grist that pulls out overlapping signatures from a large database for the purpose of doing downstream gather and other things, and it seems like #1238 is going to be adding the related functionality from greyhound #1226 into sourmash. However, I am wondering if there's value in explicitly adding a Python-based sourmash CLI function, sourmash prefetch, that would let us explore the behavior in non-Rust code. It seems like it would be generically useful to have it be available, and it would also prevent us from copy-pasting prefetch_gather over to other projects like charcoal and maybe thumper...

@luizirber
Copy link
Member

luizirber commented Feb 7, 2021

As supporting datapoint, yesterday I worked a bit on bringing the counter gather from greyhound into Python, and there is a bit of the functionality that is shared with prefetch.

I think it's small enough to be available in sourmash, especially since it's being copy-and-pasted into multiple projects 🙃

@ctb
Copy link
Contributor Author

ctb commented Feb 25, 2021

idle early morning thought - double check that the prefetch approach works for similarity and max_containment too.

@ctb
Copy link
Contributor Author

ctb commented Mar 6, 2021

also struck by the basic similarity between the behavior of prefetch and search --containment.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
2 participants