More efficient database use

bacpop · Oct 17, 2024 · dfc2300 · dfc2300
1 parent e399db1
commit dfc2300
Showing 1 changed file with 7 additions and 3 deletions.
diff --git a/PopPUNK/visualise.py b/PopPUNK/visualise.py
@@ -429,9 +429,13 @@ def generate_visualisations(query_db,
 
             # Merge relevant sequences into a single database
             sys.stderr.write("Generating merged database\n")
-            sequences_to_analyse = list(viz_subset) if viz_subset is not None else combined_seq
-            # Filter from reference database
-            tmp_ref_h5_file, rlist = create_pruned_tmp_db(ref_db,viz_subset)
+            if viz_subset is not None:
+              sequences_to_analyse = list(viz_subset) if viz_subset is not None else combined_seq
+              # Filter from reference database
+              tmp_ref_h5_file, rlist = create_pruned_tmp_db(ref_db,viz_subset)
+            else:
+              sequences_to_analyse = combined_seq
+              tmp_ref_h5_file = ref_db
             viz_db_name = output + "/" + os.path.basename(output)
             if query_db is not None:
                 # Add from query database