decovolution simplification

deconvolution/dgraph/CliqueDGFactory.py

@@ -31,11 +31,9 @@ class CliqueDGFactory(AbstractDGFactory):
                 clq_per_node[node].append(idx)
 
         # clq_per_node for nei can be empty because of minimum clique size
-        # So we add singleton cliques for those nodes
         for node in subgraph.nodes:
             if node not in clq_per_node:
-                cliques.append([node])
-                clq_per_node[node] = [len(cliques) - 1]
+                clq_per_node[node] = []
 
         # Pair cliques
         clq_pairs = set()

deconvolution/main/d2_reduction.py

@@ -30,14 +30,17 @@ def main():
         exit(1)
     
     # Loading
+    print("--- d2 graph loading ---")
     G = nx.read_gexf(barcode_file)
     d2g = d2.D2Graph(G)
     d2g.load(d2_file)
 
     # Algorithms for reduction
+    print("--- 3-reduction processing ---")
     d2a.transitive_reduction(d2g)
 
     # Take the principal component
+    print("--- Extract and write the graph ---")
     components = [c for c in nx.connected_components(d2g) if len(c) > args.component_min_size]
     nodes = set()
     for comp in components: