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sgkit-dev / sgkit

Scalable genetics toolkit
https://sgkit-dev.github.io/sgkit
Apache License 2.0
231 stars 32 forks source link

read_plink failing with 0.7.0 release #1149

Closed hammer closed 10 months ago

hammer commented 10 months ago

I've tried read_plink on 2 different PLINK file families and gotten the same error both times (pasting from VS Code with nice formatting):

Screenshot 2023-11-28 at 11 02 38 PM

This looks to be https://github.com/pystatgen/sgkit/issues/1085. I will try installing from source and see if the error clears up.

hammer commented 10 months ago

I have confirmed that building from source restores read_plink functionality. Should we cut a 0.7.1 release so that a release version can read PLINK files?

jeromekelleher commented 10 months ago

Yes, we probably should. Should we make a milestone and triage stuff we want to get into 0.7.1?

PxxxxN commented 10 months ago

I have confirmed that building from source restores read_plink functionality. Should we cut a 0.7.1 release so that a release version can read PLINK files? Hello, could you please tell me more about your solution process? I also encountered the same problem:)

hammer commented 10 months ago

@PxxxxN one solution would be to install sgkit with pip from GitHub. Here's a useful guide: https://adamj.eu/tech/2019/03/11/pip-install-from-a-git-repository.

The precise syntax will depend on your python installation (for example your python executable might be named python3), but it will probably look something like:

python -m pip install 'sgkit @ git+https://github.com/pystatgen/sgkit.git#sgkit[plink]'
jeromekelleher commented 10 months ago

Closing this as the code has already been fixed.