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fatemeh-rafiei / DeepTraSynergy

Drug Combinations using Multi-modal Deep Learning with Transformers
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Bugs I met for running DeepTraSynergy #3

Open HelloWorldLTY opened 10 months ago

HelloWorldLTY commented 10 months ago

Hi, I met a bug when running this model:

Cell In[28], line 88
     84 smiles_unique = np.load(path_dataset + dataset + '/smiles_200.npy')
     87 # Read drug combinations data
---> 88 drugs_combinations, indx_of_drugs1_combinations, indx_of_drugs2_combinations, indx_of_cells_combinations = read_drug_combinations_data(path_dataset, dataset, list_of_prots, list_of_cells)
     90 # Apply node2vec on PPI
     91 protein_embeddings = node2vec_on_PPI(protein_protein_graph)

File /gpfs/gibbs/pi/zhao/tl688/DeepTraSynergy/auxiliary_functions.py:221, in read_drug_combinations_data(path_dataset, dataset, list_of_prots, list_of_cells)
    219 threshold2 = sort_lbl[52077]
    220 for i in range(0, data.shape[0]):
--> 221     tmp = np.argwhere(list_of_drugs == data.iloc[i, 3])[0]
    222     indx_of_drugs1_combinations.append(tmp[0])
    223     tmp = np.argwhere(list_of_drugs == data.iloc[i, 4])[0]

NameError: name 'list_of_drugs' is not defined

Could you please help me address it? Thanks.