cluster_quality.py

#!/usr/bin/env python
# File created on 10 Mar 2011
from __future__ import division

__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Justin Kuczynski"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
 

from qiime.util import parse_command_line_parameters
from qiime.util import make_option
from qiime.parse import parse_mapping_file_to_dict, parse_distmat
import os
import sys
import numpy

from qiime.cluster_quality import clust_qual_ratio

script_info={}
script_info['brief_description']="""compute the quality of a cluster"""
script_info['script_description']="""The input is a distance matrix (i.e. resulting file from beta_diversity.py)."""

script_info['script_usage']=[]

script_info['script_usage'].append(("""cluster quality based on the treatment category:""","""to compute the quality of clusters, and print to stdout, use the following idiom:""","""%prog -i weighted_unifrac_otu_table.txt -m Fasting_Map.txt -c Treatment"""))

script_info['script_usage'].append(("""cluster quality based on the DOB category:""","""to compute the quality of clusters, and print to stdout, use the following idiom:""","""%prog -i weighted_unifrac_otu_table.txt -m Fasting_Map.txt -c DOB"""))


script_info['output_description']="""The output is either a single number (with -s), or a more detailed output of the similarity between and within clusters."""
script_info['required_options']=[
make_option('-i', '--input_path', type='existing_filepath',
     help='input distance matrix file'),\

make_option('-m', '--map', type='existing_filepath',
     help='mapping file'),

make_option('-c', '--category', type='string',
     help='column of mapping file delimiting clusters'),



]
script_info['optional_options']=[

make_option('-o', '--output_path',default=None, type='new_filepath',
            help='output path, prints to stdout if omitted'),
make_option('-s', '--short',action="store_true",
            help='print only '+\
            'the ratio of mean dissimilarities between/within clusters'+\
            ' instead of more detailed output'),

make_option('--metric', default='ratio', type='choice',
     choices=['ratio'],
     help='choice of quality metric to apply. Currently only one option '+\
     'exists, the ratio of mean(distances between samples from different '+\
     'clusters) to mean(distances between samples from the same cluster) '+\
     'Default: %default'),
]
script_info['version'] = __version__


def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    if opts.output_path != None:
        outf = open(opts.output_path,'w')
    else:
        outf = sys.stdout

    dists = parse_distmat(open(opts.input_path,'U'))
    map_data = parse_mapping_file_to_dict(open(opts.map,'U'))
    diff_dists, same_dists = clust_qual_ratio(dists, map_data, opts.category)



    if opts.short:
        print >> outf, numpy.mean(diff_dists)/numpy.mean(same_dists)
    else:
        print >> outf, "dissimilarity ratio between/within (large for clustered data):"
        print >> outf, numpy.mean(diff_dists)/numpy.mean(same_dists)
        print >> outf, "dissimilarities between clusters: mean, std, num:"
        print >> outf, '\t'.join(map(str,[numpy.mean(diff_dists), numpy.std(diff_dists),
         len(diff_dists)]))
        print >> outf, "dissimilarities within clusters: mean, std, num:"
        print >> outf, '\t'.join(map(str,[numpy.mean(same_dists), numpy.std(same_dists),
         len(same_dists)]))



if __name__ == "__main__":
    main()