#!/usr/bin/python
# -*- coding: utf-8 -*-

# --------------------------------------------------
# File Name: bio.py
# Purpose:
# Creation Date: 10-03-2017
# Last Modified: Fri, Mar 10, 2017 12:51:16 AM
# Author(s): Mike Stout 
# Copyright 2017 The Author(s) All Rights Reserved
# Credits: 
# --------------------------------------------------

from Bio import SeqIO
for r in SeqIO.parse("all.aligned.fasta", "fasta"):
    print r

'''

from Bio import AlignIO
alignments = AlignIO.parse("all.phy", "phylip")
for alignment in alignments:
    print alignment
    print

from Bio.Align.Applications import ClustalwCommandline
cline = ClustalwCommandline("clustalw2", infile="all.aligned.fasta")
print cline

exit()
'''
import pylab

from Bio import Phylo
tree = Phylo.read("seqs.phy", "newick")
#Phylo.draw_ascii(tree)

tree.rooted = True
Phylo.draw_graphiz(tree)

pylab.show()                    # Displays the tree in an interactive viewer
#pylab.savefig('phylo-dot.png')