pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
~/.local/lib/python3.8/site-packages/anndata/_core/anndata.py in _set_dim_df(self, value, attr)
786 if not isinstance(value, pd.DataFrame):
787 raise ValueError(f"Can only assign pd.DataFrame to {attr}.")
--> 788 value_idx = self._prep_dim_index(value.index, attr)
789 if self.is_view:
790 self._init_as_actual(self.copy())
~/.local/lib/python3.8/site-packages/anndata/_core/anndata.py in _prep_dim_index(self, value, attr)
800 """
801 if self.shape[attr == "var"] != len(value):
--> 802 raise ValueError(
803 f"Length of passed value for {attr}_names is {len(value)}, but this AnnData has shape: {self.shape}"
804 )
ValueError: Length of passed value for var_names is 19629, but this AnnData has shape: (38905, 19617)
Expected behavior
A clear and concise description of what you expected to happen.
add_scenic_metadata error. This may be due to input error but not sure what may be wrong as I followed the steps in the tutorial.
Steps to reproduce the behavior
~/.local/lib/python3.8/site-packages/pyscenic/export.py in add_scenic_metadata(adata, auc_mtx, regulons, bin_rep, copy) 293 ), 294 ) --> 295 result.var = pd.merge( 296 result.var, 297 regulon_assignment,
~/.local/lib/python3.8/site-packages/anndata/_core/anndata.py in var(self, value) 872 @var.setter 873 def var(self, value: pd.DataFrame): --> 874 self._set_dim_df(value, "var") 875 876 @var.deleter
~/.local/lib/python3.8/site-packages/anndata/_core/anndata.py in _set_dim_df(self, value, attr) 786 if not isinstance(value, pd.DataFrame): 787 raise ValueError(f"Can only assign pd.DataFrame to {attr}.") --> 788 value_idx = self._prep_dim_index(value.index, attr) 789 if self.is_view: 790 self._init_as_actual(self.copy())
~/.local/lib/python3.8/site-packages/anndata/_core/anndata.py in _prep_dim_index(self, value, attr) 800 """ 801 if self.shape[attr == "var"] != len(value): --> 802 raise ValueError( 803 f"Length of passed value for {attr}_names is {len(value)}, but this AnnData has shape: {self.shape}" 804 )
ValueError: Length of passed value for var_names is 19629, but this AnnData has shape: (38905, 19617) Expected behavior A clear and concise description of what you expected to happen.
Running latest version in a jupyter notebook
These are snapshots of my files: