final, buggy..

debruijn/debruijn.py

@@ -286,14 +286,17 @@ def simplify_bubbles(graph):
         graph, nx.DiGraph: a bubble-less de bruijn graph
     """
     fork_nodes = []# empty list containing nodes with 2 or more ancestors
-
-    for node in graph:
-        if graph.in_degree(node) >= 2: # if 2 or more ancestor add node
-            pred = [n for n in graph.predecessors(node)] 
-            ancestor = algorithms.lowest_common_ancestor(graph,pred[0], pred[1])
-            graph = solve_bubble(graph, ancestor, node)
-
-
+    f=1
+    while f == 1: 
+        for node in graph:
+            if graph.in_degree(node) >= 2: # if 2 or more ancestor add node
+                pred = [n for n in graph.predecessors(node)] 
+                if len(pred) > 2:
+                    f = 1
+                else:
+                    f = 0
+                ancestor = algorithms.lowest_common_ancestor(graph,pred[0], pred[1])
+                graph = solve_bubble(graph, ancestor, node)
 
     return graph