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yolksac_human.py

@@ -124,13 +124,14 @@ class RNAExp(datasets.ArrowBasedBuilder):
     def _generate_tables(self, expression_file,batch_size,split):
         idx = 0
         adata = ad.read_h5ad(expression_file)
-        self.info.description   = adata.var.index.str.lower().tolist() #"+".join(adata.var.index.str.lower().tolist())
-        self.column_names = adata.var.index.str.lower().tolist()
+        # self.info.description   = adata.var.index.str.lower().tolist() #"+".join(adata.var.index.str.lower().tolist())
         for batch in range(0,adata.shape[0],batch_size):
             chunk = adata.X[batch:batch+batch_size].todense().astype('int32')
             df = pd.DataFrame(chunk,columns=adata.var.index.str.lower())
             df["raw_counts"] = [x for x in df.to_numpy()]
             df = df[["raw_counts"]]
+            ## We create a dummy column with all the names of the genes as list. We don't use this as value since this would unnecessarily increase the size of the dataset
+            ## Another option would be to replace the description with the list of genes 
             df[",".join(adata.var.index.str.lower().tolist())] = True
             for feature in self.config.features:
                 if feature != "raw_counts":