Construct Newick Tree from tab-delimited or csv file of phylogeny, preferably in Python

Question

[weslfield]

So I am looking for a way, preferably a Pythonic way (packages are ok), to convert a tab-delimited or csv of hierarchical phylogenies into the classic Newick format for tree visualization.

Each line of the file has ['Phylum','Class','Order','Family','Genus','Species','Subspecies','gi'] as values and I would like to create a Newick tree representaiton. Any help greatly appreciated. Thanks!

[Pierre Lindenbaum]

Hello weslfield!

It appears that your post has been cross-posted to another site: http://stackoverflow.com/questions/26146623

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[Asaf]

You can use dendropy.

The easiest way I can think of (without thinking too much) is for each line go from the phylum down to gi and create a child node or select a node you already created. Then you can export the tree in Newick format.

[weslfield]

Thanks Asaf, the code below in my answer addressed the problem using the node approach.

תודה רבה מטכניון :)

[Asaf]

ד"ש לרותי

Answer 2

[weslfield]

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)