TFvelo KeyError: 'n_cells' for experimental datasets

[AAA-3]

Hello,

python TFvelo_analysis_demo_mod.py --dataset_name H9_WT produces the pp.h5ad and rc.h5ad files.

python TFvelo_analysis_demo.py --dataset_name H9_WT produces an 'n_cell' error midway:

Error of `n_cell`:

Traceback (most recent call last):
  File "/home/ali/anaconda3/envs/TFvelo/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3080, in get_loc
    return self._engine.get_loc(casted_key)
  File "pandas/_libs/index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 101, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 4554, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 4562, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'n_cells'

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

Traceback (most recent call last):
  File "TFvelo_analysis_demo.py", line 202, in <module>
    main(args)
  File "TFvelo_analysis_demo.py", line 165, in main
    adata_copy = adata_copy[:, adata_copy.var['n_cells'] > thres_n_cells]
  File "/home/ali/anaconda3/envs/TFvelo/lib/python3.8/site-packages/pandas/core/frame.py", line 3024, in __getitem__
    indexer = self.columns.get_loc(key)
  File "/home/ali/anaconda3/envs/TFvelo/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3082, in get_loc
    raise KeyError(key) from err
KeyError: 'n_cells'

On comparing with the pancreas trial dataset, I can see that the pancreas rc.h5ad has .var["n_cells"] which was not generated for my dataset.

How can I fix this issue?

Environment:

``` # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge anndata 0.8.0 pypi_0 pypi anyio 4.4.0 pyhd8ed1ab_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py38h01eb140_4 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pyhd8ed1ab_0 conda-forge attrs 24.2.0 pyh71513ae_0 conda-forge babel 2.14.0 pyhd8ed1ab_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge beautifulsoup4 4.12.3 pyha770c72_0 conda-forge bleach 6.1.0 pyhd8ed1ab_0 conda-forge blosc2 2.0.0 pypi_0 pypi brotli-python 1.1.0 py38h17151c0_1 conda-forge ca-certificates 2024.8.30 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge certifi 2024.8.30 pyhd8ed1ab_0 conda-forge cffi 1.17.0 py38heb5c249_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 pypi_0 pypi comm 0.2.2 pyhd8ed1ab_0 conda-forge cycler 0.12.1 pypi_0 pypi cython 3.0.11 pypi_0 pypi debugpy 1.8.5 py38h6d02427_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge executing 2.1.0 pyhd8ed1ab_0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge h11 0.14.0 pyhd8ed1ab_0 conda-forge h2 4.1.0 py38h578d9bd_0 conda-forge h5py 3.11.0 pypi_0 pypi hpack 4.0.0 pyh9f0ad1d_0 conda-forge httpcore 1.0.5 pyhd8ed1ab_0 conda-forge httpx 0.27.2 pyhd8ed1ab_0 conda-forge hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge idna 3.8 pyhd8ed1ab_0 conda-forge importlib-metadata 8.4.0 pyha770c72_0 conda-forge importlib_metadata 8.4.0 hd8ed1ab_0 conda-forge importlib_resources 6.4.4 pyhd8ed1ab_0 conda-forge ipykernel 6.29.5 pyh3099207_0 conda-forge ipython 8.12.0 pyh41d4057_0 conda-forge isoduration 20.11.0 pyhd8ed1ab_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jinja2 3.1.4 pyhd8ed1ab_0 conda-forge joblib 1.4.2 pypi_0 pypi json5 0.9.25 pyhd8ed1ab_0 conda-forge jsonpointer 3.0.0 py38h578d9bd_0 conda-forge jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_0 conda-forge jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 py38h578d9bd_0 conda-forge jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge jupyter_server 2.14.2 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge jupyterlab 4.2.5 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge jupyterlab_server 2.27.3 pyhd8ed1ab_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 pypi_0 pypi krb5 1.21.3 h659f571_0 conda-forge ld_impl_linux-64 2.40 hf3520f5_7 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc 14.1.0 h77fa898_1 conda-forge libgcc-ng 14.1.0 h69a702a_1 conda-forge libgomp 14.1.0 h77fa898_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.46.0 hde9e2c9_0 conda-forge libstdcxx 14.1.0 hc0a3c3a_1 conda-forge libstdcxx-ng 14.1.0 h4852527_1 conda-forge libzlib 1.3.1 h4ab18f5_1 conda-forge llvmlite 0.40.1 pypi_0 pypi loompy 3.0.7 pypi_0 pypi markupsafe 2.1.5 py38h01eb140_0 conda-forge matplotlib 3.3.4 pypi_0 pypi matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge mistune 3.0.2 pyhd8ed1ab_0 conda-forge msgpack 1.0.8 pypi_0 pypi natsort 8.4.0 pypi_0 pypi nbclient 0.10.0 pyhd8ed1ab_0 conda-forge nbconvert-core 7.16.4 pyhd8ed1ab_1 conda-forge nbformat 5.10.4 pyhd8ed1ab_0 conda-forge ncurses 6.5 he02047a_1 conda-forge nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge networkx 3.1 pypi_0 pypi notebook 7.2.2 pyhd8ed1ab_0 conda-forge notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge numba 0.57.0 pypi_0 pypi numexpr 2.8.6 pypi_0 pypi numpy 1.21.6 pypi_0 pypi numpy-groupies 0.9.22 pypi_0 pypi openssl 3.3.1 hb9d3cd8_3 conda-forge overrides 7.7.0 pyhd8ed1ab_0 conda-forge packaging 24.1 pyhd8ed1ab_0 conda-forge pandas 1.2.3 pypi_0 pypi pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge parso 0.8.4 pyhd8ed1ab_0 conda-forge patsy 0.5.6 pypi_0 pypi pexpect 4.9.0 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 10.4.0 pypi_0 pypi pip 24.2 pyh8b19718_1 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.47 pyha770c72_0 conda-forge prompt_toolkit 3.0.47 hd8ed1ab_0 conda-forge psutil 6.0.0 py38hfb59056_0 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge py-cpuinfo 9.0.0 pypi_0 pypi pycparser 2.22 pyhd8ed1ab_0 conda-forge pygments 2.18.0 pyhd8ed1ab_0 conda-forge pynndescent 0.5.13 pypi_0 pypi pyparsing 3.1.4 pypi_0 pypi pysocks 1.7.1 pyha2e5f31_6 conda-forge python 3.8.12 h0744224_3_cpython conda-forge python-dateutil 2.9.0.post0 pypi_0 pypi python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge python_abi 3.8 5_cp38 conda-forge pytz 2024.1 pyhd8ed1ab_0 conda-forge pyyaml 6.0.2 py38h2019614_0 conda-forge pyzmq 26.2.0 py38h6c80b9a_0 conda-forge readline 8.2 h8228510_1 conda-forge referencing 0.35.1 pyhd8ed1ab_0 conda-forge requests 2.32.3 pyhd8ed1ab_0 conda-forge rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge rpds-py 0.20.0 py38h4005ec7_0 conda-forge scanpy 1.8.2 pypi_0 pypi scikit-learn 1.3.2 pypi_0 pypi scipy 1.10.1 pypi_0 pypi scvelo 0.2.4 pypi_0 pypi seaborn 0.13.0 pypi_0 pypi send2trash 1.8.3 pyh0d859eb_0 conda-forge setuptools 72.2.0 pyhd8ed1ab_0 conda-forge sinfo 0.3.4 pypi_0 pypi six 1.16.0 pyh6c4a22f_0 conda-forge sniffio 1.3.1 pyhd8ed1ab_0 conda-forge soupsieve 2.5 pyhd8ed1ab_1 conda-forge sqlite 3.46.0 h6d4b2fc_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge statsmodels 0.14.1 pypi_0 pypi stdlib-list 0.10.0 pypi_0 pypi tables 3.8.0 pypi_0 pypi terminado 0.18.1 pyh0d859eb_0 conda-forge threadpoolctl 3.5.0 pypi_0 pypi tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tornado 6.4.1 py38hfb59056_0 conda-forge tqdm 4.66.5 pypi_0 pypi traitlets 5.14.3 pyhd8ed1ab_0 conda-forge types-python-dateutil 2.9.0.20240821 pyhd8ed1ab_0 conda-forge typing-extensions 4.12.2 hd8ed1ab_0 conda-forge typing_extensions 4.12.2 pyha770c72_0 conda-forge typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge umap-learn 0.5.6 pypi_0 pypi uri-template 1.3.0 pyhd8ed1ab_0 conda-forge urllib3 2.2.2 pyhd8ed1ab_1 conda-forge wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge webcolors 24.8.0 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 pyhd8ed1ab_2 conda-forge websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge wheel 0.44.0 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zeromq 4.3.5 h75354e8_4 conda-forge zipp 3.20.1 pyhd8ed1ab_0 conda-forge zstandard 0.23.0 py38h62bed22_0 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge ```

[qm713152]

I have same problem。how you solve this problem

[Li-ZhiD]

Same error!