Not compatible with new AnnData file format/shape

[kleurless]

Hi!

I tested out the package the other way around, I found a work-around to load an AnnData object in Seurat and did some analyses. Now I want to return with my new and improved Seurat-object to Scanpy.

So I followed the following steps:

SaveH5Seurat(object, filename = "ConvertTest.h5Seurat")
Convert("ConvertTest.h5Seurat", dest = "h5ad")

And it throws the following error when reading in with scanpy==1.4.6:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-2-977de11dd812> in <module>
----> 1 adata = sc.read_h5ad("../../data/output/embryo_Hb/embryo.test2.h5ad")

~\Anaconda3\envs\UMCU\lib\site-packages\anndata\_io\h5ad.py in read_h5ad(filename, backed, as_sparse, as_sparse_fmt, chunk_size)
    427     _clean_uns(d)  # backwards compat
    428 
--> 429     return AnnData(**d)
    430 
    431 

~\Anaconda3\envs\UMCU\lib\site-packages\anndata\_core\anndata.py in __init__(self, X, obs, var, uns, obsm, varm, layers, raw, dtype, shape, filename, filemode, asview, obsp, varp, oidx, vidx)
    296                 varp=varp,
    297                 filename=filename,
--> 298                 filemode=filemode,
    299             )
    300 

~\Anaconda3\envs\UMCU\lib\site-packages\anndata\_core\anndata.py in _init_as_actual(self, X, obs, var, uns, obsm, varm, varp, obsp, raw, layers, dtype, shape, filename, filemode)
    495             self._raw = None
    496         elif isinstance(raw, cabc.Mapping):
--> 497             self._raw = Raw(self, **raw)
    498         else:  # is a Raw from another AnnData
    499             self._raw = Raw(self, raw._X, raw.var, raw.varm)

~\Anaconda3\envs\UMCU\lib\site-packages\anndata\_core\raw.py in __init__(self, adata, X, var, varm)
     29         if adata.isbacked == (X is None):
     30             self._X = X
---> 31             self._var = _gen_dataframe(var, self.X.shape[1], ["var_names"])
     32             self._varm = AxisArrays(self, 1, varm)
     33         elif X is None:  # construct from adata

AttributeError: 'dict' object has no attribute 'shape'

And I think it has to do with the fact that they changed the file format in AnnData =>0.7

[mojaveazure]

There was a bug in early versions of SeuratDisk where an H5AD file generated by SeuratDisk could only be loaded with anndata.read(backed=True); however, more recent versions of SeuratDisk should have fixed this. Could you try again, using the latest version?

[no-response]

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