Existing but empty raw layer must be recognized as no raw layer (#27)

* Existing but empty raw layer must be recognized as no raw layer * minor readme fix
cellannotation · Sep 19, 2024 · 6ec655c · 6ec655c
1 parent 655c85a
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diff --git a/README.md b/README.md
@@ -260,8 +260,9 @@ with read_h5ad(file_path, edit=True) as cap_adata:
     sparse_dataset = cap_adata.layers["empty_sparse_matrix"]
     sparse_dataset.append(chunk_data) # chunk_data must be 'csr' or 'csc' matrix
 
-# Remove layer
-cap_adata.remove_layer("dense_array")
+with read_h5ad(file_path, edit=True) as cap_adata:
+    # Remove layer
+    cap_adata.remove_layer("dense_array")
 ```
 
 #### 8. Join and Merge DataFrames

diff --git a/cap_anndata/cap_anndata.py b/cap_anndata/cap_anndata.py
@@ -255,6 +255,10 @@ def raw(self) -> RawLayer:
                 logger.warning("Can't read raw.var since raw layer doesn't exist!")
                 return
 
+            if len(self._file["raw"].keys()) == 0:
+                logger.warning("The raw layer is empty!")
+                return
+
             self._raw = RawLayer(self._file)
         return self._raw