Allow missing columns in IrObjects

scirpy/io/_convert_anndata.py

@@ -181,8 +181,12 @@ def to_ir_objs(adata: AnnData) -> List[IrCell]:
         for cell_id, row in adata.obs.iterrows():
             tmp_ir_cell = IrCell(cell_id, multi_chain=row["multi_chain"])
             for chain_type, chain_id in itertools.product(["VJ", "VDJ"], ["1", "2"]):
+                # expr_raw is optional
+                keys = IR_OBS_KEYS[:]
+                if f"IR_{chain_type}_{chain_id}_expr_raw" not in row:
+                    keys.remove("expr_raw")
                 chain_dict = {
-                    key: row[f"IR_{chain_type}_{chain_id}_{key}"] for key in IR_OBS_KEYS
+                    key: row[f"IR_{chain_type}_{chain_id}_{key}"] for key in keys
                 }
                 # per definition, we currently only have productive chains in adata.
                 chain_dict["is_productive"] = True

scirpy/tests/test_io.py

@@ -22,7 +22,8 @@
         TESTDATA / "10x/filtered_contig_annotations.csv",
     ],
 )
-def test_read_and_convert_10x_example(path):
+@pytest.mark.parametrize("omit_cols", [True, False])
+def test_read_and_convert_10x_example(path, omit_cols):
     """Test that a full 10x CSV table can be imported without errors.
 
     Additionally test that the round-trip conversion using `to_ir_objs` and
@@ -34,6 +35,8 @@ def test_read_and_convert_10x_example(path):
     under CC-BY-4.0
     """
     anndata = read_10x_vdj(path)
+    if omit_cols:
+        del adata.obs["IR_VJ_1_expr_raw"]
     assert anndata.shape[0] > 0
 
     # Test that round-trip conversion succeeds