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yolksac_human.py

@@ -22,6 +22,7 @@ import os
 import anndata as ad
 import pyarrow as pa
 import pandas as pd
+import numpy as np
 
 import datasets
 CITATION = """
@@ -79,7 +80,7 @@ class RNAExp(datasets.ArrowBasedBuilder):
             if features.get(feature,None) is None:
                 features[feature] = datasets.Value("string")
 
-
+        # features["gene_names"] = datasets.Sequence(datasets.Value("string"))
 
         return datasets.DatasetInfo(
             description= self.config.description,
@@ -105,6 +106,7 @@ class RNAExp(datasets.ArrowBasedBuilder):
 
         # genes = pd.read_csv(gene_names_file)
         adata = ad.read_h5ad(expression_file)
+        self.genes_list = adata.var.index.str.lower().tolist()
         if self.config.raw_counts =="X":
             X = adata.X
         else:
@@ -122,6 +124,8 @@ 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()
         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())
@@ -130,7 +134,8 @@ class RNAExp(datasets.ArrowBasedBuilder):
             for feature in self.config.features:
                 if feature != "raw_counts":
                     df[feature] = adata.obs[feature][batch:batch+batch_size].tolist()
-            print(df.shape)
+            
+            # df['gene_names'] = [adata.var.index.str.lower().tolist()]*batch_size
             pa_table = pa.Table.from_pandas(df)
             yield idx, pa_table
             idx += 1