aertslab / SCENICprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis
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KeyError: 'RegulonsAUC' when running PBMC10k_SCENIC-protocol-CLI #77

Open geenaildefonso opened 1 year ago

geenaildefonso commented 1 year ago

I am running the PBMC10k_SCENIC-protocol-CLI.ipynb file from the tutorial on the website, and I am getting an error at this step:

import json import zlib import base64

# collect SCENIC AUCell output #https://programtalk.com/python-more-examples/loompy.connect/ lf = lp.connect( f_pyscenic_output, mode='r+', validate=False ) auc_mtx = pd.DataFrame( lf.ca.RegulonsAUC, index=lf.ca.CellID) lf.close()

Returns:

KeyError Traceback (most recent call last) ~/anaconda/envs/scenic_protocol/lib/python3.7/site-packages/loompy/attribute_manager.py in __getattr__(self, name) 114 try: --> 115 vals = self.__dict__["storage"][name] 116 if vals is None:

KeyError: 'RegulonsAUC'

During handling of the above exception, another exception occurred:

AttributeError Traceback (most recent call last) /var/folders/mk/5gzhv5l57n56d6x7fnfgzpw00000gn/T/ipykernel_46588/1050340150.py in <module> 6 #https://programtalk.com/python-more-examples/loompy.connect/ 7 lf = lp.connect( f_pyscenic_output, mode='r+', validate=False ) ----> 8 auc_mtx = pd.DataFrame( lf.ca.RegulonsAUC, index=lf.ca.CellID) 9 lf.close()

~/anaconda/envs/scenic_protocol/lib/python3.7/site-packages/loompy/attribute_manager.py in __getattr__(self, name) 121 return vals 122 except KeyError: --> 123 raise AttributeError(f"'{type(self)}' object has no attribute '{name}'") 124 125 def __setitem__(self, name: str, val: np.ndarray) -> None:

AttributeError: '<class 'loompy.attribute_manager.AttributeManager'>' object has no attribute 'RegulonsAUC'

I checked and I have the loom file from the previous step pyscenic_output.loom

I am not sure how to fix the error, any help is appreciated, thank you!