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#!/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__ = "1.4.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"
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:""","""neighbor_joining.py -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.:""","""neighbor_joining.py -i beta_div_weighted_unifrac/ -o beta_div_weighted_clusters/"""))
script_info['script_usage'].append(('','',''))
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',
help='input path. directory for batch processing, '+\
'filename for single file operation'),\
make_option('-o', '--output_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()
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