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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Issue with pycisTopic on human cerebellum single-cell multiome data on HPC Fedora #475

Open Stack7 opened 1 month ago

Stack7 commented 1 month ago

Good Morning everyone,

While I was using SCENIC+ over the tutorial on human cerebellum single-cell multiome data with Pycistopic, I have met this error:

"/orfeo/cephfs/home/cdslab/astacchetti/scenicplus/tutorial/human_cerebellum_tutorial.py", line 179, in <module> cistopic_obj = create_cistopic_object_from_fragments( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/u/cdslab/astacchetti/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/cistopic_class.py", line 857, in create_cistopic_object_from_fragments fragments = fragments[fragments.Name.isin(set(valid_bc))] ^^^^^^^^^^^^^^ File "/u/cdslab/astacchetti/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pyranges/pyranges.py", line 269, in __getattr__ return _getattr(self, name) ^^^^^^^^^^^^^^^^^^^^ File "/u/cdslab/astacchetti/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pyranges/methods/attr.py", line 67, in _getattr raise AttributeError("PyRanges object has no attribute", name) AttributeError: ('PyRanges object has no attribute', 'Name') To reproduce this bug, you can follow step by step this tutorial: https://pycistopic.readthedocs.io/en/latest/notebooks/human_cerebellum.html using a conda environment with python 3.11 on a Fedora 40 OS. Scenic+ version. Scenicplus verions: 1.0a1 Thanks you very much for making SCENIC+ is a very interesting tool and thank you all for helping me in advance. Have a nice day.

yojetsharma commented 1 month ago

Can you paste your complete code as well? It may likely naming issue with the fragments.

Stack7 commented 2 weeks ago

Hi! sorry for the late answer, anyway you are right! the issue is that one! since I merged two different tutorial to overcome several errors the the fragments have different names. I attached you my very first trial on making sens of the tutorial of SCENIC+ 10x_multiome_pbmc.txt It is a txt file but actually it is python script (version of python3.11)