Add load_dataset and save_dataset functions #392
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jeromekelleher
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Nov 19, 2020
eric-czech
reviewed
Nov 19, 2020
| """ | ||
| store = str(path) | ||
| for v in ds: | ||
| ds[v].encoding.pop("chunks", None) |
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Worth mentioning pydata/xarray#4380 in a comment?
eric-czech
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This fixes #298, and also incorporates some of the implementation from https://github.com/related-sciences/ukb-gwas-pipeline-nealelab/blob/4f862e31b8093d25fdaa8da7f841b9be8583cda4/scripts/gwas.py#L53-L71
Unlike #298 it does not rechunk the dataset before saving. I worry about having implicit rechunk methods that the user can't control since we have seen them perform poorly in some cases. For the moment I think it's preferable for the user to explicitly rechunk before saving. This is what I have been doing in the MalariaGEN notebooks, and Eric has too judging by this example.
I also haven't added
fsspecsupport even though the GWAS pipeline uses it. This is because I was getting a warning that files were not being closed when running on local files. That could be addressed separately.