MS Tutorial Error

[rafehelwer]

I tried to run the MS tutorial on a computer running macOS 26.6.2 but encountered an error:

user$ python
Python 3.12.8 | packaged by Anaconda, Inc. | (main, Dec 11 2024, 10:37:40) [Clang 14.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.

import nease
import pandas as pd
table=pd.read_table('AL_NAWM.deltapsi.tsv')
events=nease.run(table, organism='Human',input_type='MAJIQ')
Processing MAJIQ format...
MAJIQ output converted successfully to NEASE format.

	Data Summary

---

24 protein domains are affected by AS.

1 linear motifs are affected by AS.
7 interacting residue are affected by AS.

17 of the affected domains/motifs have known interactions.
181 protein interactions/binding affected.

---

Running enrichment analysis...
Traceback (most recent call last):
File "", line 1, in
File "/opt/miniconda3/lib/python3.12/site-packages/nease/nease.py", line 255, in init
self.enrichment=pathway_enrichment(self.g2edges,self.path, self.mapping,organism,p_value_cutoff,self.only_DDIs).reset_index(drop=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/lib/python3.12/site-packages/nease/functions.py", line 230, in pathway_enrichment
tmp=len([x for x in g2edges[gene] if x in path_genes ])
^^^^^^^^^^
UnboundLocalError: cannot access local variable 'path_genes' where it is not associated with a value

Trying the same code in a linux computing cluster resulted in a similar error:
NameError: cannot access free variable 'path_genes' where it is not associated with a value in enclosing scope