KeyError: 'RegulonsAUC' when running PBMC10k_SCENIC-protocol-CLI #406
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geenaildefonso
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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!
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