python - Convert csv to Newick tree

Question

So I have a csv file where each line represents hierarchical data in the form: 'Phylum','Class','Order','Family','Genus','Species','Subspecies','unique_gi'

I would like to convert this to the classic Newick tree format sans distances. Either a novel method or a python package would be amazing. Thank you!

Answer 1

You could use some simple Python to build out a tree from the CSV, and then write it out to a Newick tree. Not sure if this is what you're trying to do or not.

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)

Example output:

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

Also, this library seems cool, and lets you visualize your trees: http://biopython.org/wiki/Phylo