diff --git a/debruijn/debruijn.py b/debruijn/debruijn.py index 1aa2b20..54eeeeb 100644 --- a/debruijn/debruijn.py +++ b/debruijn/debruijn.py @@ -286,12 +286,15 @@ 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: - while graph.in_degree(node) >= 2: # if 2 or more ancestor add node + 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) + + return graph def solve_entry_tips(): @@ -302,7 +305,6 @@ def solve_out_tips(): pass def main(): - print(sys.argv[1]) fichier = str(sys.argv[1]) k = int(sys.argv[2]) hash_table = build_kmer_dict(fichier, k)