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Error in conversion from AnnData to Zarr #112

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stefraptis opened this issue Dec 4, 2023 · 0 comments
Open

Error in conversion from AnnData to Zarr #112

stefraptis opened this issue Dec 4, 2023 · 0 comments

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@stefraptis
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stefraptis commented Dec 4, 2023

I have an anndata object (
AnnData object with n_obs × n_vars = 638 × 20564
obs: 'Condition', 'SizeFactor', 'Cell'
var: 'Counts', 'gene_short_name', 'Gene')

which is being converted to h5ad successfully, and pass this step as well.

 # Note here we only give name of directory containing MTX file (along with barcodes and features file)
reader = scarf.H5adReader(
    'final_anndata.h5ad',
    cell_ids_key = 'Cell',               # Where Cell/barcode ids are saved under 'obs' slot
    feature_ids_key = 'Gene',            # Where gene ids are saved under 'var' slot
    feature_name_key = 'gene_short_name'  # Where gene names are saved under 'var' slot
)

In the next step,

writer = scarf.H5adToZarr(
    reader,
    zarr_loc='scarf_datasets/sg_cell.zarr'
)
writer.dump()

This returns the following error

image

The odd about this is that I was able to execute the code few days ago.

Thanks,
Stefanos

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