single_rarefaction.py

#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division

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

from cogent.maths.stats.rarefaction import subsample, subsample_multinomial
from qiime.util import parse_command_line_parameters
from qiime.util import make_option
from qiime.rarefaction import SingleRarefactionMaker

script_info={}
script_info['brief_description']="""Perform rarefaction on an otu table"""
script_info['script_description']="""To perform bootstrap, jackknife, and rarefaction analyses, the otu table must be subsampled (rarefied).  This script rarefies, or subsamples, an OTU table.  This does not provide curves of diversity by number of sequences in a sample. Rather it creates a subsampled OTU table by random sampling (without replacement) of the input OTU table.  Samples that have fewer sequences then the requested rarefaction depth are omitted from the ouput otu tables.  The pseudo-random number generator used for rarefaction by subsampling is NumPy's default - an implementation of the Mersenne twister PRNG."""

script_info['script_usage']=[]

script_info['script_usage'].append(("""Example:""","""subsample otu_table.biom (-i) at 100 seqs/sample (-d), write results to otu_table_even100.txt (-o).""","""%prog -i otu_table.biom -o otu_table_even100.biom -d 100"""))

script_info['output_description']="""The results of single_rarefaction.py consist of a single subsampled OTU table. The file has the same otu table format as the input otu_table.biom. note: if the output file would be empty, no file is written"""


script_info['required_options']=[
    make_option('-i', '--input_path',
        help='Input OTU table filepath.',
        type='existing_filepath'),
    make_option('-o', '--output_path',
        help='Output OTU table filepath.',
        type='new_filepath'),
    make_option('-d', '--depth', type='int',
        help='Number of sequences to subsample per sample.'),
]
script_info['optional_options']=[
    make_option('--lineages_included',
        help='Deprecated: lineages are now included by default. Pass' +\
        ' --supress_lineages_included to prevent output OTU tables' +\
        ' from including taxonomic (lineage) information for each OTU. Note:' +\
        ' this will only work if lineage information is in the input OTU' +\
        ' table.'),
    make_option('--suppress_lineages_included', default=True, 
        action="store_false",dest='lineages_included',
        help='Exclude taxonomic (lineage) information for each OTU.'),
    make_option('-k', '--keep_empty_otus', default=False, action='store_true',
        help='Retain OTUs of all zeros, which are usually omitted from' +\
        ' the output OTU tables. [default: %default]'),
    make_option('--subsample_multinomial',default=False,action='store_true',
        help='subsample using subsampling with replacement [default: %default]')
]
script_info['option_label']={'input_path':'OTU table filepath',
                             'output_path': 'Output filepath',
                             'depth': '# of seqs/sample',
                             'suppress_lineages_included':'Suppress lineages',
                             'lineages_included': 'Include lineages',
                             'keep_empty_otus':'Retain empty OTUs'}
script_info['version'] = __version__


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

    if opts.subsample_multinomial:
        subsample_f = subsample_multinomial
    else:
        subsample_f = subsample

    maker = SingleRarefactionMaker(opts.input_path, opts.depth)
    maker.rarefy_to_file(opts.output_path, False,
        include_lineages=opts.lineages_included,
        empty_otus_removed=(not opts.keep_empty_otus),subsample_f=subsample_f)

if __name__ == "__main__":
    main()