Merge pull request #29 from bacpop/issue_27

Update generate_network.py
bacpop · May 21, 2024 · ab252d6 · ab252d6
2 parents a59b553 + fafcc78
commit ab252d6
Showing 1 changed file with 6 additions and 2 deletions.
diff --git a/panaroo_runner/generate_network.py b/panaroo_runner/generate_network.py
@@ -200,7 +200,11 @@ def generate_network(DBG, overlap, high_scoring_ORFs, high_scoring_ORF_edges, cl
             for neighbour in edge_set:
                 pan_neigbour_id = str(genome_id) + "_0_" + str(neighbour)
 
-                neighbour_cluster = seq_to_cluster[pan_neigbour_id]
+                # ensure neighbour is high scoring ORF, otherwise ignore
+                if pan_neigbour_id in seq_to_cluster:
+                    neighbour_cluster = seq_to_cluster[pan_neigbour_id]
+                else:
+                    continue
 
                 # add edge between current ORF and neighbour
                 if G.has_edge(node, neighbour_cluster):
@@ -216,4 +220,4 @@ def generate_network(DBG, overlap, high_scoring_ORFs, high_scoring_ORF_edges, cl
                 G.nodes[node]['hasEnd'] = True
                 break
 
-    return G, centroid_context
+    return G, centroid_context