Investigate granges rust crate

[ghuls]

Investigate granges rust crate for allowing GenomicRanges like functionality: https://github.com/vsbuffalo/granges

[tshauck]

Thanks! I'm aware of it... I recently added a page to the docs showing how to work with the genomicranges package, but it's unlikely to be as fast as granges.

If you have a sec, would you be able to briefly sketch out the API you'd imagine? Are these like methods on the result object, something else?

Also, FWIW, you can recreate a lot of granges like functionality with SQL if you're comfortable with it.

[ghuls]

Yes, I saw the genomicranges integration, but it is very slow if you have a lot of intersections (e.g. intersecting a bed file with a bigwig (yesterday more than 1 hour, with latest version of iranges 15minutes):
BiocPy/GenomicRanges#98

With my own implementation based on Polars and ncls (intersect library behind pyranges) it takes less than 17 seconds.

Also, FWIW, you can recreate a lot of granges like functionality with SQL if you're comfortable with it.

When you have a lot of intersections, this will likely be slow if you don't use specific structures that can handle intervals efficiently.

If you have a sec, would you be able to briefly sketch out the API you'd imagine? Are these like methods on the result object, something else?

I didn't look closely at it yet. So no idea at the moment.

Another similar crate: https://github.com/noamteyssier/bedrs

[tshauck]

Thanks yeah, I agree with all of that.

My initial thought is similar to how biobear works with VCF/BAM indices, as I'd ideally want it to be compatible with SQL then expose a more pythonic API on top of it.

[jkanche]

but it's unlikely to be as fast as granges.

Definitely not going to reach rust like speeds in Python :)

Our focus initially has been to bring Bioconductor-like representations to Python. Its time I find some focus time and optimize the methods that were implemented.