add check

DendrouLab · Feb 26, 2024 · 8ec715a · 8ec715a
1 parent 9ba83b7
commit 8ec715a
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/panpipes/python_scripts/run_scanpyQC_spatial.py b/panpipes/python_scripts/run_scanpyQC_spatial.py
@@ -129,7 +129,7 @@
 percent_top = [x for x in percent_top if x <= spatial.n_vars]
 sc.pp.calculate_qc_metrics(spatial, qc_vars=qc_vars, percent_top=percent_top, inplace=True)
 
-if args.spatial_filetype == "vizgen":
+if (args.spatial_filetype == "vizgen") and ("blank_genes" in spatial.obsm):    
     spatial.obsm["blank_genes"].to_numpy().sum() / spatial.var["total_counts"].sum() * 100
 
 # Calculate cc scores