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

import argparse

import anvio
import anvio.terminal as terminal
import anvio.clustering as clustering


__author__ = "A. Murat Eren"
__copyright__ = "Copyright 2015, The anvio Project"
__credits__ = []
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "a.murat.eren@gmail.com"
__status__ = "Development"


run = terminal.Run()
progress = terminal.Progress()

parser = argparse.ArgumentParser(description='Takes an observation matrix, returns a newick tree')
parser.add_argument('input_matrix', metavar = 'PATH', default = None,
                    help = 'Input matrix')
parser.add_argument('-o', '--output-file-name', metavar = 'PATH', default = None,
                    help = 'Output file name')

args = parser.parse_args()

if not args.output_file_name:
    args.output_file_name = args.input_matrix + '.newick'

run.info('Input matrix file', args.input_matrix)
progress.new('Analyzing input file')
clustering.get_newick_tree_data(args.input_matrix, args.output_file_name, progress = progress)
progress.end()
run.info('Output newick', args.output_file_name)
