Incompatible with pandas plink 2.2

[broadinstitute]

Incompatible with pandas plink 2.2

[francois-a]

Hi @liangyy, the latest commit actually fixes this. I'm checking a few more things but will release v1.0.5 later today. This specific error actually comes from a change in pandas, not pandas-plink.

[liangyy]

Hi @francois-a, thank you very much! We have a follow-up question on loading genotype file. We got the warning:

softwares/tensorqtl/tensorqtl/genotypeio.py:146: PerformanceWarning: Slicing is producing a large chunk. To accept the large
chunk and silence this warning, set the option
    >>> with dask.config.set(**{'array.slicing.split_large_chunks': False}):
    ...     array[indexer]

To avoid creating the large chunks, set the option
    >>> with dask.config.set(**{'array.slicing.split_large_chunks': True}):
    ...     array[indexer]
  self.bed = self.bed[:,ix]

, which may be due the fact that our phenotype and genotype do not have the same ordering of individuals.

What would you suggest to do with this warning?

Thanks!

[francois-a]

Based on my experience it's fine to ignore this. It doesn't noticeably impact performance.

[liangyy]

Got you, thanks! I will close this issue.