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debruijn-tp
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final

master
nzimme 2019-10-24 21:47:14 +02:00
parent 096225c793
commit 1b9fe1030d
1 changed files with 4 additions and 2 deletions
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6
debruijn/debruijn.py
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@ -286,12 +286,15 @@ def simplify_bubbles(graph):
graph, nx.DiGraph: a bubble-less de bruijn graph graph, nx.DiGraph: a bubble-less de bruijn graph
""" """
fork_nodes = []# empty list containing nodes with 2 or more ancestors fork_nodes = []# empty list containing nodes with 2 or more ancestors
for node in graph: 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)] pred = [n for n in graph.predecessors(node)]
ancestor = algorithms.lowest_common_ancestor(graph,pred[0], pred[1]) ancestor = algorithms.lowest_common_ancestor(graph,pred[0], pred[1])
graph = solve_bubble(graph, ancestor, node) graph = solve_bubble(graph, ancestor, node)
return graph return graph
def solve_entry_tips(): def solve_entry_tips():
@ -302,7 +305,6 @@ def solve_out_tips():
pass pass
def main(): def main():
print(sys.argv[1])
fichier = str(sys.argv[1]) fichier = str(sys.argv[1])
k = int(sys.argv[2]) k = int(sys.argv[2])
hash_table = build_kmer_dict(fichier, k) hash_table = build_kmer_dict(fichier, k)