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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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ValueError: '_index' is a reserved name for dataframe columns. Above error raised while writing key 'var' of to / #129

Open denvercal1234GitHub opened 1 year ago

denvercal1234GitHub commented 1 year ago

Hi there,

I was trying to write my adata with write_h5ad which has my loom objects merged with my Seurat object in Python so that I can then convert it to Seurat object to use SCP, but it threw an error as below.

Would you mind helping me fix this issue?

Thank you.

My AnnData object:

Screenshot 2023-05-04 at 17 13 52 
loomGEX_adata.write_h5ad('...Velocity_scVelo_Objects/loomGEX_adata.h5ad')
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/utils.py:246](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/utils.py:246), in report_write_key_on_error..func_wrapper(*args, **kwargs)
    245 try:
--> 246     return func(*args, **kwargs)
    247 except Exception as e:

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/registry.py:311](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/registry.py:311), in Writer.write_elem(self, store, k, elem, dataset_kwargs, modifiers)
    310 else:
--> 311     return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/registry.py:52](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/registry.py:52), in write_spec..decorator..wrapper(g, k, *args, **kwargs)
     50 @wraps(func)
     51 def wrapper(g, k, *args, **kwargs):
---> 52     result = func(g, k, *args, **kwargs)
     53     g[k].attrs.setdefault("encoding-type", spec.encoding_type)

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/methods.py:560](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/methods.py:560), in write_dataframe(f, key, df, _writer, dataset_kwargs)
    559     if reserved in df.columns:
--> 560         raise ValueError(f"{reserved!r} is a reserved name for dataframe columns.")
    561 group = f.create_group(key)

ValueError: '_index' is a reserved name for dataframe columns.

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

ValueError                                Traceback (most recent call last)
Cell In[13], line 2
      1 # Save file after running scv.tl.recover_dynamics
----> 2 Tonsil_cd8_loomGEX_adata.write_h5ad('[/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/DATA/RNA_Velocity_scVelo_Objects/Tonsil_cd8_loomGEX_adata.h5ad](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/DATA/RNA_Velocity_scVelo_Objects/Tonsil_cd8_loomGEX_adata.h5ad)')
      3 #adata = scv.read('data[/pancreas.h5ad](https://file+.vscode-resource.vscode-cdn.net/pancreas.h5ad)')

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_core/anndata.py:1951](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_core/anndata.py:1951), in AnnData.write_h5ad(self, filename, compression, compression_opts, as_dense)
   1948 if filename is None:
   1949     filename = self.filename
-> 1951 _write_h5ad(
   1952     Path(filename),
   1953     self,
   1954     compression=compression,
   1955     compression_opts=compression_opts,
   1956     as_dense=as_dense,
   1957 )
   1959 if self.isbacked:
   1960     self.file.filename = filename

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/h5ad.py:91](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/h5ad.py:91), in write_h5ad(filepath, adata, as_dense, dataset_kwargs, **kwargs)
     87     write_elem(
     88         f, "raw[/varm](https://file+.vscode-resource.vscode-cdn.net/varm)", dict(adata.raw.varm), dataset_kwargs=dataset_kwargs
     89     )
     90 elif adata.raw is not None:
---> 91     write_elem(f, "raw", adata.raw, dataset_kwargs=dataset_kwargs)
     92 write_elem(f, "obs", adata.obs, dataset_kwargs=dataset_kwargs)
     93 write_elem(f, "var", adata.var, dataset_kwargs=dataset_kwargs)

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/registry.py:353](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/registry.py:353), in write_elem(store, k, elem, dataset_kwargs)
    329 def write_elem(
    330     store: GroupStorageType,
    331     k: str,
   (...)
    334     dataset_kwargs: Mapping = MappingProxyType({}),
    335 ) -> None:
    336     """
    337     Write an element to a storage group using anndata encoding.
    338 
   (...)
    351         E.g. for zarr this would be `chunks`, `compressor`.
    352     """
--> 353     Writer(_REGISTRY).write_elem(store, k, elem, dataset_kwargs=dataset_kwargs)

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/utils.py:248](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/utils.py:248), in report_write_key_on_error..func_wrapper(*args, **kwargs)
    246     return func(*args, **kwargs)
    247 except Exception as e:
--> 248     re_raise_error(e, elem, key)

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/utils.py:246](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/utils.py:246), in report_write_key_on_error..func_wrapper(*args, **kwargs)
    244         break
    245 try:
--> 246     return func(*args, **kwargs)
    247 except Exception as e:
    248     re_raise_error(e, elem, key)

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/registry.py:311](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/registry.py:311), in Writer.write_elem(self, store, k, elem, dataset_kwargs, modifiers)
    302     return self.callback(
    303         write_func,
    304         store,
   (...)
    308         iospec=self.registry.get_spec(elem),
    309     )
    310 else:
--> 311     return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/registry.py:52](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/registry.py:52), in write_spec..decorator..wrapper(g, k, *args, **kwargs)
     50 @wraps(func)
     51 def wrapper(g, k, *args, **kwargs):
---> 52     result = func(g, k, *args, **kwargs)
     53     g[k].attrs.setdefault("encoding-type", spec.encoding_type)
     54     g[k].attrs.setdefault("encoding-version", spec.encoding_version)

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/methods.py:261](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/specs/methods.py:261), in write_raw(f, k, raw, _writer, dataset_kwargs)
    259 g = f.create_group(k)
    260 _writer.write_elem(g, "X", raw.X, dataset_kwargs=dataset_kwargs)
--> 261 _writer.write_elem(g, "var", raw.var, dataset_kwargs=dataset_kwargs)
    262 _writer.write_elem(g, "varm", dict(raw.varm), dataset_kwargs=dataset_kwargs)

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/utils.py:248](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/utils.py:248), in report_write_key_on_error..func_wrapper(*args, **kwargs)
    246     return func(*args, **kwargs)
    247 except Exception as e:
--> 248     re_raise_error(e, elem, key)

File [~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/utils.py:229](https://file+.vscode-resource.vscode-cdn.net/Users/stillhere/Documents/01_DPhil/scRNAseq/T230T240T246_CXCR5Project/Final_Objects_preAzimuth_2023Feb23/RNA_Velocity_scVelo/RNA_Velocity/SCRIPTS/~/.pyenv/versions/3.10.11/envs/RNAVELO_310/lib/python3.10/site-packages/anndata/_io/utils.py:229), in report_write_key_on_error..re_raise_error(e, elem, key)
    227 else:
    228     parent = _get_parent(elem)
--> 229     raise type(e)(
    230         f"{e}\n\n"
    231         f"Above error raised while writing key {key!r} of {type(elem)} "
    232         f"to {parent}"
    233     ) from e

ValueError: '_index' is a reserved name for dataframe columns.

Above error raised while writing key 'var' of  to /

Posted at https://github.com/scverse/anndata/issues/990

zunyun-Gong commented 4 months ago

you can use this code to deal with this problem out.raw.var.columns=["Genes"],change the column name directly. it works for me.