convert_count_to_shared.py

#!/usr/bin/env python


"""Converts a MOTHUR count file to a MOTHUR shared file

Usage:
    convert_count_to_shared [count_file]

Synopsis:
    The generation of OTUs are not always desired but many functions performed
    by MOTHUR require the OTU generation step. For users wishing to take
    advantage of these functions without OTU generation,
    convert_count_to_shared creates a '.shared' file from a '.count_table'
    file where each Representative Sequence is labeled as a unique OTU. This
    effectively bypasses OTU generation.

Required Arguments:
    count_file:     MOTHUR generated count table file to convert to a shared
                    file

Output:
    A MOTHUR formatted '[count_file].shared' file.

Copyright:

    convert_count_to_shared.py Convert MOTHUR count file to shared file
    Copyright (C) 2016  William Brazelton, Alex Hyer

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
"""

from __future__ import print_function
__version__ = '1.0.0'
__author__ = 'Alex Hyer, William Brazelton'

import argparse
import sys


def read_count_file(count_file):
    with open(count_file, 'rU') as count_handle:
        first_line = count_handle.readline()
        first_line = first_line.strip().split('\t')
        count_table = {header: [] for header in first_line}
        for line in count_handle:
            split_line = line.strip().split('\t')
            for column in enumerate(split_line):
                header = first_line[column[0]]
                count_table[header].append(column[1])
    return count_table


def main():
    parser = argparse.ArgumentParser(description=__doc__,
                                     formatter_class=argparse.
                                     RawDescriptionHelpFormatter)
    parser.add_argument('count_file', metavar='Count File',
                        help='MOTHUR count file to convert to shared file')
    args = parser.parse_args()

    count_file = open(args.count_file)
    out_name = count_file.name + '.shared'

    count_table = read_count_file(count_file.name)
    with open(out_name, 'w') as out_handle:
        new_first_line = 'label\tGroup\tnumOtus\t' + '\t'.join(
            [sequence for sequence in count_table['Representative_Sequence']])
        out_handle.write(new_first_line + '\n')
        for key in count_table.keys():
            if key == 'Representative_Sequence' or key == 'total':
                continue
            column_number = len(count_table[key])
            new_line = 'unique\t{0}\t{1}\t'.format(key, column_number) \
                       + '\t'.join(abundance for abundance in count_table[key])
            out_handle.write(new_line + '\n')

if __name__ == '__main__':
    main()
sys.exit(0)