neighbor_joining.py

#!/usr/bin/env python
# File created on 09 Mar 2011
from __future__ import division

__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"


from qiime.util import parse_command_line_parameters
from qiime.util import make_option
from qiime.hierarchical_cluster import single_file_nj, multiple_file_nj
import os

script_info = {}
script_info[
    'brief_description'] = """Build a neighbor joining tree comparing samples"""
script_info[
    'script_description'] = """The input to this step is a distance matrix (i.e. resulting file from beta_diversity.py)."""
script_info['script_usage'] = []
script_info['script_usage'].append(
    ("""neighbor joining (nj) cluster (Single File):""",
     """To perform nj clustering on a single distance matrix (e.g.: beta_div.txt, a result file from beta_diversity.py) use the following idiom:""",
     """%prog -i beta_div.txt -o beta_div_cluster.tre"""))
script_info['script_usage'].append(
    ("""neighbor joining (Multiple Files):""",
     """The script also functions in batch mode if a folder is supplied as input. This script operates on every file in the input directory and creates a corresponding neighbor joining tree file in the output directory, e.g.:""",
     """%prog -i beta_div_weighted_unifrac/ -o beta_div_weighted_clusters/"""))
script_info[
    'output_description'] = """The output is a newick formatted tree compatible with most standard tree viewing programs. Batch processing is also available, allowing the analysis of an entire directory of distance matrices."""
script_info['required_options'] = [
    make_option('-i', '--input_path', type='existing_path',
                help='input path.  directory for batch processing, ' +
                'filename for single file operation'),


    make_option('-o', '--output_path', type='new_path',
                help='output path. directory for batch processing, ' +
                'filename for single file operation'),
]
script_info['optional_options'] = []
script_info['version'] = __version__


def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)
    if os.path.isdir(opts.input_path):
        multiple_file_nj(opts.input_path, opts.output_path)
    elif os.path.isfile(opts.input_path):
        single_file_nj(opts.input_path, opts.output_path)
    else:
        print("io error, check input file path")
        exit(1)

if __name__ == "__main__":
    main()