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

The odd about this is that I was able to execute the code few days ago.
Thanks,
Stefanos
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.
In the next step,
This returns the following error
The odd about this is that I was able to execute the code few days ago.
Thanks,
Stefanos