ViewTree

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# vim:fileencoding=utf-8

import os
import sys
import argparse
from Bio import Phylo

_LICENSE = """
http://www.github.org/jbpease/mixtape
MixTAPE: Mix of Tools for Analysis in Phylogenetics and Evolution

This file is part of MixTAPE.

MixTAPE is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

MixTAPE is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with MixTAPE.  If not, see <http://www.gnu.org/licenses/>.
"""


def generate_argparser():
    parser = argparse.ArgumentParser(
        description=__doc__,
        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
        epilog=_LICENSE)
    parser.add_argument('treefile', nargs='?', type=argparse.FileType('r'),
                        default=sys.stdin,
                        help="input newick tree file")
    parser.add_argument('--out', type=os.path.abspath,
                        default=sys.stdout, help="output fasta file")
    parser.add_argument('--figsize', type=float, nargs=2,
                        help="fixed height/width in inches for figure")
    return parser


def main(arguments=None):
    arguments = arguments if arguments is not None else sys.argv[1:]
    parser = generate_argparser()
    args = parser.parse_args(args=arguments)
    tree = Phylo.read(args.treefile, 'newick')
    tree.root_at_midpoint()
    tree.ladderize()
    if args.out.endswith(".pdf"):
        from matplotlib import pyplot as plt 
        if args.figsize is not None: 
            fig = plt.figure(figsize=(args.figsize[0], args.figsize[1]), )
        else:
            fig = plt.figure()
        ax1 = fig.add_subplot(111)
        Phylo.draw(tree, axes=ax1, do_show=False)
        fig.tight_layout()
        fig.savefig(args.out)
    else:
        Phylo.draw_ascii(tree)
    
    return ''


if __name__ == '__main__':
    main()