sceasy::convertFormat(h5ad_file, from="anndata", to="seurat", outFile='neurons.rds')
Loading required namespace: Seurat
/home/sherine/R/x86_64-pc-linux-gnu-library/4.3/reticulate/python/rpytools/loader.py:117: FutureWarning: pandas.core.index is deprecated and will be removed in a future version. The public classes are available in the top-level namespace.
return find_and_load(name, import)
Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
AttributeError: 'dict' object has no attribute 'dtype'
Run reticulate::py_last_error() for details.
reticulate::py_last_error()
── Python Exception Message ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Traceback (most recent call last):
File "/home/sherine/anaconda3/envs/sceasy_env/lib/python3.11/site-packages/anndata/readwrite/read.py", line 447, in read_h5ad
constructor_args = _read_args_from_h5ad(filename=filename, chunk_size=chunk_size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sherine/anaconda3/envs/sceasy_env/lib/python3.11/site-packages/anndata/readwrite/read.py", line 502, in _read_args_from_h5ad
return AnnData._args_from_dict(d)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sherine/anaconda3/envs/sceasy_env/lib/python3.11/site-packages/anndata/core/anndata.py", line 2157, in _args_from_dict
if key in d_true_keys[true_key].dtype.names:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'dict' object has no attribute 'dtype'
── R Traceback ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
▆
- └─sceasy::convertFormat(...)
- └─sceasy (local) func(obj, outFile = outFile, main_layer = main_layer, ...)
-
└─anndata$read_h5ad(inFile)
Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
AttributeError: 'dict' object has no attribute 'dtype'
Run
reticulate::py_last_error()for details.── Python Exception Message ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Traceback (most recent call last):
File "/home/sherine/anaconda3/envs/sceasy_env/lib/python3.11/site-packages/anndata/readwrite/read.py", line 447, in read_h5ad
constructor_args = _read_args_from_h5ad(filename=filename, chunk_size=chunk_size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sherine/anaconda3/envs/sceasy_env/lib/python3.11/site-packages/anndata/readwrite/read.py", line 502, in _read_args_from_h5ad
return AnnData._args_from_dict(d)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sherine/anaconda3/envs/sceasy_env/lib/python3.11/site-packages/anndata/core/anndata.py", line 2157, in _args_from_dict
if key in d_true_keys[true_key].dtype.names:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'dict' object has no attribute 'dtype'
── R Traceback ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
▆