How to save results?

[UronicAcid]

I am trying to use methods in Scanpy to save results. However, it seems that it has not been implemented in evolocity yet.
My code is

adata.isbacked
adata.filename = 'cytochrome_final.h5ad'
adata.write_csvs('cytochrome_final_csvs', )

It returns:

Traceback (most recent call last):
  File "/gpfs/share/home/2101111835/anaconda3/envs/evolocity/lib/python3.7/site-packages/anndata/_io/utils.py", line 209, in func_wrapper
    return func(elem, key, val, *args, **kwargs)
  File "/gpfs/share/home/2101111835/anaconda3/envs/evolocity/lib/python3.7/site-packages/anndata/_io/h5ad.py", line 149, in write_not_implemented
    f"Failed to write value for {key}, "
NotImplementedError: Failed to write value for uns/model, since a writer for type <class 'evolocity.tools.fb_model.FBModel'> has not been implemented yet.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "test.py", line 28, in <module>
    adata.filename = 'cytochrome_final.h5ad'
  File "/gpfs/share/home/2101111835/anaconda3/envs/evolocity/lib/python3.7/site-packages/anndata/_core/anndata.py", line 1085, in filename
    self.write(filename, force_dense=True)
  File "/gpfs/share/home/2101111835/anaconda3/envs/evolocity/lib/python3.7/site-packages/anndata/_core/anndata.py", line 1918, in write_h5ad
    as_dense=as_dense,
  File "/gpfs/share/home/2101111835/anaconda3/envs/evolocity/lib/python3.7/site-packages/anndata/_io/h5ad.py", line 118, in write_h5ad
    write_attribute(f, "uns", adata.uns, dataset_kwargs=dataset_kwargs)
  File "/gpfs/share/home/2101111835/anaconda3/envs/evolocity/lib/python3.7/functools.py", line 840, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
  File "/gpfs/share/home/2101111835/anaconda3/envs/evolocity/lib/python3.7/site-packages/anndata/_io/h5ad.py", line 130, in write_attribute_h5ad
    _write_method(type(value))(f, key, value, *args, **kwargs)
  File "/gpfs/share/home/2101111835/anaconda3/envs/evolocity/lib/python3.7/site-packages/anndata/_io/h5ad.py", line 294, in write_mapping
    write_attribute(f, f"{key}/{sub_key}", sub_value, dataset_kwargs=dataset_kwargs)
  File "/gpfs/share/home/2101111835/anaconda3/envs/evolocity/lib/python3.7/functools.py", line 840, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
  File "/gpfs/share/home/2101111835/anaconda3/envs/evolocity/lib/python3.7/site-packages/anndata/_io/h5ad.py", line 130, in write_attribute_h5ad
    _write_method(type(value))(f, key, value, *args, **kwargs)
  File "/gpfs/share/home/2101111835/anaconda3/envs/evolocity/lib/python3.7/site-packages/anndata/_io/utils.py", line 216, in func_wrapper
    ) from e
NotImplementedError: Failed to write value for uns/model, since a writer for type <class 'evolocity.tools.fb_model.FBModel'> has not been implemented yet.

Above error raised while writing key 'uns/model' of <class 'h5py._hl.files.File'> from /.

[brianhie]

For now there's no anndata writer for the language model itself. You can try doing adata.uns['model'] = None before saving (i.e., don't save the model) and that should probably work.

[UronicAcid]

Adding adata.uns['model'] = None did not raise error. However, since it can not save the model, can I run on the HPC but draw on my personal computer? Only the former has enough memory, but is inconvenient to visualize and adjust.

[brianhie]

The model is only needed for velocity score computation, not any of the downstream analysis. I would compute the velocities on the HPC, save it without the model, then just do all other downstream analyses locally.

[UronicAcid]

Thank you!