convertToAdata error on write
bei import gibt es beim saving einen fehler, e.g. object
/mnt/agnerds/PROJECTS/public/GSE220514_Brandes_23/as_provided_by_john_Brandes23.Rds
index fehler beim saving adata.write_h5ad(...)
Error:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/workspace/.conda/convertToAdata_fix/lib/python3.10/site-packages/anndata/_core/anndata.py", line 2017, in write_h5ad
write_h5ad(
File "/workspace/.conda/convertToAdata_fix/lib/python3.10/site-packages/anndata/_io/h5ad.py", line 104, in write_h5ad
write_elem(f, "obs", adata.obs, dataset_kwargs=dataset_kwargs)
File "/workspace/.conda/convertToAdata_fix/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 359, in write_elem
Writer(_REGISTRY).write_elem(store, k, elem, dataset_kwargs=dataset_kwargs)
File "/workspace/.conda/convertToAdata_fix/lib/python3.10/site-packages/anndata/_io/utils.py", line 243, in func_wrapper
return func(*args, **kwargs)
File "/workspace/.conda/convertToAdata_fix/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 309, in write_elem
return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)
File "/workspace/.conda/convertToAdata_fix/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 57, in wrapper
result = func(g, k, *args, **kwargs)
File "/workspace/.conda/convertToAdata_fix/lib/python3.10/site-packages/anndata/_io/specs/methods.py", line 678, in write_dataframe
_writer.write_elem(
File "/workspace/.conda/convertToAdata_fix/lib/python3.10/site-packages/anndata/_io/utils.py", line 243, in func_wrapper
return func(*args, **kwargs)
File "/workspace/.conda/convertToAdata_fix/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 304, in write_elem
self.find_writer(dest_type, elem, modifiers),
File "/workspace/.conda/convertToAdata_fix/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 269, in find_writer
return self.registry.get_writer(dest_type, type(elem), modifiers)
File "/workspace/.conda/convertToAdata_fix/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 117, in get_writer
raise IORegistryError._from_write_parts(dest_type, src_type, modifiers)
anndata._io.specs.registry.IORegistryError: No method registered for writing <class 'pandas.core.arrays.string_.StringArray'> into <class 'h5py._hl.group.Group'>
Error raised while writing key '_index' of <class 'h5py._hl.group.Group'> to /obs
workaround
adata.obs.index = adata.obs.index.astype('object')
adata.var.index = adata.var.index.astype('object')
Edited by Hendrik Schultheis