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althonos / pyhmmer

Cython bindings and Python interface to HMMER3.
https://pyhmmer.readthedocs.io
MIT License
129 stars 12 forks source link

[question] PyInfernal? #68

Open tomdstanton opened 7 months ago

tomdstanton commented 7 months ago

Hi Martin,

Many thanks for all your work on Python-izing useful tools! 😄 I wondered if there was a plan to build Cython bindings and Python interface to infernal?

Cheers, Tom

jpjarnoux commented 6 months ago

Hi,

I would also be interested.

It would be better to create a collaborative project/team with all the people who would be interested.

Suppose other people are interested in taking part in this. Let me know. If we are enough, we can start something.

althonos commented 6 months ago

Hi both!

This is something I would be interested in in the long run, but at the moment this is not something my research team needs so my space for freeing for development really limited (and I need to write my PhD thesis :sweat_smile:). I'd be interested in helping a community effort as you proposed @jpjarnoux.

Given that Infernal is also based on Easel and HMMER which are already wrapped here, the question would be whether the PyHMMER API is sufficient enough to be used the way it is, allowing to do a pure-python implementation (like pybarrnap) or if it needs some more Cython/C bindings to the Infernal code.

jpjarnoux commented 6 months ago

So if you agree I propose to create a GitHub team to exchange about this project and maybe others. That way the issue here can be closed when the team is created.