Fix reading of non gene expression data from 10x h5 files

My bad.
dwnorton · Mar 11, 2020 · 8d26ad5 · 8d26ad5
1 parent f963a7a
commit 8d26ad5
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Showing 2 changed files with 11 additions and 2 deletions.
diff --git a/scanpy/readwrite.py b/scanpy/readwrite.py
@@ -186,9 +186,10 @@ def read_10x_h5(
                 list(map(lambda x: x == 'Gene Expression', adata.var['feature_types'])),
             ]
         if adata.is_view:
-            return adata.copy()
+            adata = adata.copy()
     else:
-        return _read_legacy_10x_h5(filename, genome=genome, start=start)
+        adata = _read_legacy_10x_h5(filename, genome=genome, start=start)
+    return adata
 
 
 def _read_legacy_10x_h5(filename, *, genome=None, start=None):

diff --git a/scanpy/tests/test_read_10x.py b/scanpy/tests/test_read_10x.py
@@ -95,3 +95,11 @@ def test_read_visium_counts():
     spec_genome_v3 = sc.read_10x_h5(h5_pth, genome='GRCh38')
     nospec_genome_v3 = sc.read_10x_h5(h5_pth)
     assert_anndata_equal(spec_genome_v3, nospec_genome_v3)
+
+
+def test_10x_h5_gex():
+    # Tests that gex option doesn't, say, make the function return None
+    h5_pth = ROOT / '3.0.0' / 'filtered_feature_bc_matrix.h5'
+    assert_anndata_equal(
+        sc.read_10x_h5(h5_pth, gex_only=True), sc.read_10x_h5(h5_pth, gex_only=False)
+    )