De Bruijn graph

最后发布时间:2023-04-03 23:42:23 浏览量:

def de_bruijn_ize(st, k ):
    edges = []
    nodes = set()
    for i in range(len(st) -k +1):
        edges.append((st[i:i+k-1], st[i+1:i+k]))
        nodes.add(st[i:i+k-1])
        nodes.add(st[i+1:i+k])
    return nodes, edges
nodes, edges = de_bruijn_ize("ACGCGTCG", 3)
print(nodes)
print(edges)

{'GT', 'AC', 'CG', 'GC', 'TC'}
[('AC', 'CG'), ('CG', 'GC'), ('GC', 'CG'), ('CG', 'GT'), ('GT', 'TC'), ('TC', 'CG')]

def visualize_de_bruijn(st, k):
    nodes,edges = de_bruijn_ize(st, k)
    dot_str = 'digraph "DeBruijn graph" {\n'
    for node in nodes:
        dot_str += ' %s[label="%s"] ;\n' % (node, node)
    for src, dst in edges:
        dot_str +=  ' %s -> %s ;\n' % (src,dst)
    return dot_str + '}\n'
visualize_de_bruijn("ACGCGTCG", 3)