Unpickling Error in gene_set_path

[bioinfonewguy]

Hello,

Thanks for your help on my previous query.

I'm currently working with the replogle_rpe1_essential dataset, and I have added a few unseen genes just to assess how well the model performs with them. My CSV contains all of the genes in the replogle dataset and the new genes I am interested in.

However, I am getting the following error:

`from gears import PertData, GEARS

Initialize PertData with your custom gene list

pert_data = PertData('./data', gene_set_path='/path/to/gene_list.csv')

Load the dataset

pert_data.load(data_name='replogle_rpe1_essential')

Prepare the data split

pert_data.prepare_split(split='simulation', seed=1)

Create dataloaders

pert_data.get_dataloader(batch_size=32, test_batch_size=128)

Initialize the GEARS model

gears_model = GEARS(pert_data, device='cpu') # Use 'cpu' for Mac, or 'cuda' if you have a compatible GPU

Initialize the model architecture

gears_model.model_initialize(hidden_size=64, uncertainty=True)
Found local copy...
Found local copy...
Traceback (most recent call last):

Cell In[2], line 7
pert_data.load(data_name='replogle_rpe1_essential')

File /opt/anaconda3/envs/pyg_env/lib/python3.9/site-packages/gears/pertdata.py:183 in load
self.set_pert_genes()

File /opt/anaconda3/envs/pyg_env/lib/python3.9/site-packages/gears/pertdata.py:109 in set_pert_genes
essential_genes = pickle.load(f)

UnpicklingError: invalid load key, 'A'.`

[jackbrougher]

Not 100% positive because of the formatting above, but I believe I'm hitting the same issue.

I tried changing the set_pert_genes to read in a dataframe, but no luck. I'm thinking the error is here, but unable to pin down how to change it

def set_pert_genes(self):
       """
       Set the list of genes that can be perturbed and are to be included in 
       perturbation graph
       """
       
       if self.gene_set_path is not None:
           # If gene set specified for perturbation graph, use that
           path_ = self.gene_set_path
           self.default_pert_graph = False
           with open(path_, 'rb') as f:
               essential_genes = pickle.load(f)
           

[toby-clark4]

If you're still having this issue I think could because you are importing a .csv rather than a .pkl.

The format of the default GO is a dictionary of sets with genes and their GO terms:

So, if you add your genes of interest with their terms and save with pickle.dump it should work. This code runs without errors:

[bioinfonewguy]

Thanks, @toby-clark4 - this seems like it should work. Just to ensure, the new list for the pkl file should be all of the genes from the pert dataset (repogle) + any genes of interest, correct?