Tom White
Tom White
This is a case where fixed-size arrays struggle, I'm afraid. The problem is that in Zarr you can have [ragged arrays](https://zarr.readthedocs.io/en/stable/tutorial.html#ragged-arrays), or [variable-length strings](https://zarr.readthedocs.io/en/stable/tutorial.html#string-arrays), but not both. There's more discussion...
> Looks like we could improve the error message here? I've opened #1064 for this. Also, @benjeffery reminded me that the `zarr_array_sizes` function does not run in parallel, so it...
@tnguyengel I noticed that VEP allows you to export annotations as a [JSON file](https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#json), so as another way to approach the problem I wondered if you could use that to...
BTW to filter the dataset, you can do something like: ```python variant_ids = ["rs6054257", "rs6040355"] ds_filtered = ds.isel(variants=(ds.variant_id.isin(variant_ids))) ```
> We'll give the zarr_array_sizes approach a shot too! The parallel version of `zarr_array_sizes` has just been merged so you might like to try that by installing from the GitHub...
Hi @ChenDepp, you can export a dataset (e.g. `res`) as a CSV file by [converting to a Pandas dataframe](https://docs.xarray.dev/en/stable/generated/xarray.Dataset.to_pandas.html) first. You might need to subset the variables before doing that,...
Recent GPU tests seem to be failing, e.g. https://github.com/pystatgen/sgkit/actions/runs/2783193506
Thanks @aktech
Try ```python from sgkit.io.plink import read_plink read_plink(...) ```
Great - I think we need to add something to the docs.