time optimization for evaluate method

deconvolution/main/evaluate.py

@@ -180,7 +180,7 @@ def print_dgraphs_summary(frequencies, light_print=False):
 
 def str_to_udg_lists(s):
     udg = s.replace("]", "").replace(' [', '[')
-    return udg.split('[')
+    return udg.split('[')[1:]
 
 def parse_dg_name(gr, name):
     udg = nx.get_node_attributes(gr, 'udg')[name]
@@ -247,20 +247,24 @@ def print_d2_summary(connected_components, longest_path, covered_vars={}, light_
 
 
 def compute_next_nodes(d2_component):
+    # First parse dg names
+    dg_names = {}
+    for node in d2_component.nodes():
+        dg_names[node] = parse_dg_name(d2_component,node)
+
     next_nodes = {}
 
     for node in d2_component.nodes():
         # Parse the current node name
-        head, h1, h2 = parse_dg_name(d2_component,node)
+        head, h1, h2 = dg_names[node]
         next_nodes[node] = {}
-        neighbors = list(d2_component.neighbors(node))
 
         # Get the current molecule idxs
         molecule_idxs = mols_from_node(head[1])
         for mol_idx in molecule_idxs:
             nexts = []
-            for neighbor in neighbors:
-                nei_head, _, _ = parse_dg_name(d2_component,neighbor)
+            for neighbor in d2_component[node]:
+                nei_head, _, _ = dg_names[neighbor]
                 nei_mols = mols_from_node(nei_head[1])
                 nei_mols = [x for x in nei_mols if x > mol_idx]
                 
@@ -406,7 +410,7 @@ def verify_graph_edges(d2_component):
             for c in [c1,c2]:
                 for c_node in c:
                     nei_mols = mols_from_node(c_node.split()[0])
-                    nei_mols = [x for x in nei_mols if x > mol_idx] # fixme: also look at the <= molecules for more robustness
+                    nei_mols = [x for x in nei_mols if x > mol_idx]  # fixme: also look at the <= molecules for more robustness
                     
                     # If there are molecule next
                     if len(nei_mols) > 0: