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Output data products as zarr zip stores? #31

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SFD5311 opened this issue May 15, 2024 · 0 comments
Open

Output data products as zarr zip stores? #31

SFD5311 opened this issue May 15, 2024 · 0 comments

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@SFD5311
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SFD5311 commented May 15, 2024

5191467742 May 14 19:45 HT_processed.h5ad
901948748 May 15 10:23 HT_processed.zip

5910040098 May 14 18:04 LK_raw.h5ad
2229303788 May 15 10:21 LK_raw.zip

Outputting data products as zip stores as opposed to hdf5 serialization results in substantial reductions in file size, which may be meaningful when transferring files over networks or making copies. Files can be pretty easily read and written anndata and zarr like:

import zarr
import anndata
store = zarr.storage.ZipStore(file_path)
adata = anndata.read_zarr(store)

or

import zarr
import anndata
store = zarr.storage.ZipStore(file_path)
adata = anndata.AnnData()
adata = anndata.write_zarr(store)

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