fix script

openproblems-bio · Sep 25, 2024 · 6c85040 · 6c85040
1 parent 321faa9
commit 6c85040
Showing 1 changed file with 2 additions and 9 deletions.
diff --git a/src/datasets/loaders/allen_brain_cell_atlas/script.py b/src/datasets/loaders/allen_brain_cell_atlas/script.py
@@ -38,16 +38,9 @@
     f"releases/{VERSION}/manifest.json"
 )
 
-print("Downloading metadata", flush=True)
-metadata_files = [
-    "cell_metadata_with_cluster_annotation",
-]
-for file_name in metadata_files:
-    abc_cache.get_metadata_path(directory="WMB-10X", file_name=file_name)
-
 print("Reading obs", flush=True)
 obs = pd.read_csv(
-    TMP_DIR / f"metadata/WMB-10X/{VERSION}/views/cell_metadata_with_cluster_annotation.csv",
+    abc_cache.get_metadata_path(directory="WMB-10X", file_name="cell_metadata_with_cluster_annotation"),
     index_col=0,
     dtype=defaultdict(
         lambda: "category",
@@ -90,7 +83,7 @@
         file_name = f"WMB-10Xv2-{region}/raw"
         adata_path = abc_cache.get_data_path(directory="WMB-10Xv2", file_name=file_name)
 
-        adata = ad.read_h5ad(str(adata_path), backed=True)
+        adata = ad.read_h5ad(str(adata_path))
 
         adata_ = adata[adata.obs_names.isin(obs.index)]
         adata.obs["region"] = region