corrected most bugs !

debruijn/debruijn.py

@@ -2,6 +2,7 @@
 Small assembly module based on de bruijn graphs
 """
 import os
+import sys
 import statistics
 import networkx as nx
 from networkx import algorithms
@@ -259,6 +260,11 @@ def solve_bubble(graph, ancestor_node, descendent_node):
         graph, nx.DiGraph: the same graph without the bubble
     """
     paths = algorithms.all_simple_paths(graph, ancestor_node, descendent_node)
+    paths2= []
+    for p in paths:
+        paths2.append(p)
+
+    paths = paths2
 
     weights = []
     path_lens = []
@@ -294,3 +300,25 @@ def solve_entry_tips():
 
 def solve_out_tips():
     pass
+
+def main():
+    fichier = str(sys.argv[1])
+    k-size = int(sys.argv[2])
+    hash_table = build_kmer_dict(fichier, k-size)
+    G = build_graph(hash_table)
+    
+    nb = 0
+    for n in G:
+        if G.in_degree(n) > 1:
+            nb += 1
+    
+    print("il y a {} bulles dans le graphe\n".format(nb))
+    
+    simplify_bubbles(G)
+    
+    nb = 0
+    for n in G:
+        if G.in_degree(n) > 1:
+            nb += 1
+
+    print("il y a {} bulles dans le graphe\n".format(nb))