convert_otu_table_to_unifrac_sample_mapping.py

#! /usr/bin/env python

__author__ = "Cathy Lozupone"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Catherine Lozupone", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.7.0"
__maintainer__ = "Cathy Lozupone"
__email__ = "lozupone@colorado.edu"
__status__ = "Release"

from biom.parse import parse_biom_table
from qiime.util import make_option
from qiime.util import parse_command_line_parameters
from qiime.format import format_unifrac_sample_mapping


script_info={}
script_info['brief_description']="""Convert a QIIME OTU table to a UniFrac sample mapping file"""
script_info['script_description']="""This script allows users who have picked OTUs in QIIME to convert it to a sample mapping (environment) file for use with the Unifrac web interface."""

script_info['script_usage']=[]

script_info['script_usage'].append(("""Example:""","""Convert a biom-formatted OTU table to a unifrac sample mapping (environment) file: ""","""%prog -i otu_table.biom -o otu_table.sample_mapping.txt"""))

script_info['output_description']="""The result of this script is a sample mapping file for the UniFrac web interface."""
script_info['required_options']=[\
    make_option('-i', '--otu_table_fp',type='existing_filepath',help='path to the otu table'),
    make_option('-o', '--output_fp', type='new_filepath', help='path to output file')]

script_info['version'] = __version__

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

    otu_table_fp = opts.otu_table_fp
    output_fp = opts.output_fp
    verbose = opts.verbose
    
    otu_table = parse_biom_table(open(otu_table_fp, 'U'))
    result = format_unifrac_sample_mapping(otu_table.SampleIds,
                                           otu_table.ObservationIds,
                                           otu_table.iterObservationData())
    of = open(output_fp, 'w')
    of.write('\n'.join(result))
    of.close()

if __name__ == "__main__":
    main()