以newick格式保存NetworkX樹

Question

我在networkx中創建了一個圖並獲取它的bfs樹。

G = nx.Graph() 

# build a graph 

tree = nx.bfs_tree(G, '1') 

現在我想將newick format中的樹保存到一個文件中。什麼是最好的方法來做到這一點？

Answer 1

通過this answer啓發，我做這樣的事情：

import networkx as nx 
import matplotlib.pyplot as plt 

def recursive_search(dict, key): 
    if key in dict: 
     return dict[key] 
    for k, v in dict.items(): 
     item = recursive_search(v, key) 
     if item is not None: 
      return item 

def bfs_edge_lst(graph, n): 
    return list(nx.bfs_edges(graph, n)) 

def load_graph(filename): 
    G = nx.Graph() 
    # build the graph 
    return G 

def tree_from_edge_lst(elst): 
    tree = {'1': {}} 
    for src, dst in elst: 
     subt = recursive_search(tree, src) 
     subt[dst] = {} 
    return tree 

def tree_to_newick(tree): 
    items = [] 
    for k in tree.keys(): 
     s = '' 
     if len(tree[k].keys()) > 0: 
      subt = tree_to_newick(tree[k]) 
      if subt != '': 
       s += '(' + subt + ')' 
     s += k 
     items.append(s) 
    return ','.join(items) 

g = load_graph('dataset.txt') 
elst = bfs_edge_lst(g, '1') 
tree = tree_from_edge_lst(elst) 
newick = tree_to_newick(tree) + ';'