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yolksac_human.py

@@ -74,11 +74,10 @@ class RNAExp(datasets.ArrowBasedBuilder):
             citation=CITATION,
             url="https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-11673")
 
-        # features = {"raw_counts": datasets.features.Sequence(feature=datasets.Value("int32"))}
+        features = {"raw_counts": datasets.features.Sequence(feature=datasets.Value("int32"))}
 
         # features = {"raw_counts": datasets.features.Sequence(feature={"gene":datasets.Value("string"),"count":datasets.Value("int32")})}
         # features = {"raw_counts": datasets.Value("int32") for gene in adata.var.index.str.lower().tolist()}
-        features = {}
         for feature in self.config.features:
             if features.get(feature,None) is None:
                 features[feature] = datasets.Value("string")
@@ -87,7 +86,7 @@ class RNAExp(datasets.ArrowBasedBuilder):
 
         return datasets.DatasetInfo(
             description= self.config.description,
-            features=None,#,datasets.Features(features),
+            features=None, #datasets.Features(features),
             homepage=self.config.url,
             citation=self.config.citation,
         )
@@ -132,12 +131,13 @@ class RNAExp(datasets.ArrowBasedBuilder):
         adata = ad.read_h5ad(expression_file)
         genes = adata.var_names.str.lower().to_list()
 
-        # features = {"raw_counts": datasets.features.Sequence(datasets.features.ClassLabel(names = genes))}
-        # for feature in self.config.features:
-        #     if features.get(feature,None) is None:
-        #         features[feature] = datasets.Value("string")
+        features = {"raw_counts": datasets.features.Sequence(datasets.features.Value("int32"),id = ",".join(adata.var.index.str.lower().tolist()))}
+        for feature in self.config.features:
+            if features.get(feature,None) is None:
+                features[feature] = datasets.Value("string")
+
+        self.info.features = datasets.Features(features)
         
-        # self.info.features = datasets.features.Features(features)
 
         # self.info.features['gene_names'] = datasets.features.ClassLabel(names = genes)
         
@@ -145,11 +145,8 @@ class RNAExp(datasets.ArrowBasedBuilder):
         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.apply(lambda x: [(x,y) for x,y in zip(genes, x)],axis=1)
-
-            # [x for x in df.to_numpy()]
-            # df = df[["raw_counts"]]
+            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