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saezlab / dorothea-py

Dorothea package in Python
MIT License
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pkl files from dorothea not distributed with package. #1

Closed ilibarra closed 3 years ago

ilibarra commented 3 years ago

Hello Pau,

Thanks for implementing this. Installation works, but execution of main tutorial script fails. I think the pkl files were not distributed or downloaded in the main tutorial. Could you please take a look? They should be the rds files converted to pkl ones I suppose. E.g.

%%time
# Read Dorothea Regulons for Human
dorothea_hs = dorothea.load_regulons(['A','B','C'])

# Compute SCIRA scores, returns an AnnData object with TF activities intead of gene expresion
tf_adata = dorothea.run_scira(adata, dorothea_hs, norm='c')
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<timed exec> in <module>

~/miniconda3/envs/mypython3/lib/python3.7/site-packages/dorothea/dorothea.py in load_regulons(levels, organism)
     17 
     18     # Open pickle object
---> 19     df = pickle.load(open(path, "rb" ))
     20 
     21     #Filter by levels of confidence

FileNotFoundError: [Errno 2] No such file or directory: '~/miniconda3/envs/mypython3/lib/python3.7/site-packages/dorothea/data/dorothea_hs.pkl'

Thanks!

PauBadiaM commented 3 years ago

Hi @ilibarra,

Thank you for trying it out. Sorry that I did not answer before, somehow I forgot to activate notifications for this repo. Yes, due to a mistake in the .gitignore is was not uploading the pkl files. I changed that and now they are available. Now to install it again you should do:

pip uninstall dorothea
pip install git+https://github.com/saezlab/dorothea-py.git

Please, let me know if this works.

ilibarra commented 3 years ago

It is working now. Thanks!