Tutorial works knowing the presence of the example PBMC gmt in the docs/tutorial/folder and works when using the tutorial notebook present in that destination. However, in the documentation it is indicated:
gmt=investigate.load_signatures('data/atlas.gmt')
But following the tutorial in a "blind" mode rise an error like this:
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[436], line 1
----> 1 gmt=investigate.load_signatures('data/atlas.gmt')
File ~/miniconda3/envs/TCellsProj/lib/python3.9/site-packages/cia/investigate.py:42, in load_signatures(signatures_input, description_field_available)
8 """
9 Load gene signatures from a given source.
10
(...)
39 ['gene1', 'gene2']
40 """
41 if isinstance(signatures_input, str):
---> 42 with open(signatures_input, 'r') as f:
43 lines = f.readlines()
45 signatures = {}
FileNotFoundError: [Errno 2] No such file or directory: 'data/atlas.gmt'
Can we make the life easier directly importing the data with a function as for scanpy datasets or simply putting a download link (from github) in the tutorial documentation?
Tutorial works knowing the presence of the example PBMC gmt in the docs/tutorial/folder and works when using the tutorial notebook present in that destination. However, in the documentation it is indicated:
But following the tutorial in a "blind" mode rise an error like this:
Can we make the life easier directly importing the data with a function as for scanpy datasets or simply putting a download link (from github) in the tutorial documentation?