python - 将 csv 转换为 Newick 树

Question

所以我有一个 csv 文件，其中每一行代表以下形式的分层数据:'门','类','目','科','属','种','亚种','unique_gi'

我想将其转换为经典 Newick tree format没有距离。无论是新颖的方法还是 python 包都会很棒。谢谢!

Answer 1

您可以使用一些简单的 Python 从 CSV 构建树，然后将其写入 Newick 树。不确定这是否是您想要做的。

import csv
from collections import defaultdict
from pprint import pprint

def tree(): return defaultdict(tree)

def tree_add(t, path):
  for node in path:
    t = t[node]

def pprint_tree(tree_instance):
    def dicts(t): return {k: dicts(t[k]) for k in t}
    pprint(dicts(tree_instance))

def csv_to_tree(input):
    t = tree()
    for row in csv.reader(input, quotechar='\''):
        tree_add(t, row)
    return t

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

def csv_to_weightless_newick(input):
    t = csv_to_tree(input)
    #pprint_tree(t)
    return tree_to_newick(t)

if __name__ == '__main__':
    # see https://docs.python.org/2/library/csv.html to read CSV file
    input = [
        "'Phylum','Class','Order','Family','Genus','Species','Subspecies','unique_gi'", 
        "'Phylum','Class','Order','example'",
        "'Another','Test'",
    ]

    print csv_to_weightless_newick(input)

示例输出:

$ python ~/tmp/newick_tree.py
(((example,((((unique_gi)Subspecies)Species)Genus)Family)Order)Class)Phylum,(Test)Another

此外，这个库看起来很酷，可以让您可视化您的树:http://biopython.org/wiki/Phylo