make_otu_table.py

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

__author__ = "Jesse Stombaugh"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Justin Kuczynski","Jesse Stombaugh", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.7.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
 
from sys import argv, exit, stderr, stdout
from os.path import splitext
from qiime.filter import (get_seq_ids_from_seq_id_file, 
                          get_seq_ids_from_fasta_file)
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.util import make_option
from qiime.parse import parse_taxonomy
from qiime.make_otu_table import make_otu_table

options_lookup = get_options_lookup()

script_info={}
script_info['brief_description']="""Make OTU table"""
script_info['script_description']="""The script make_otu_table.py tabulates the number of times an OTU is found in each sample, and adds the taxonomic predictions for each OTU in the last column if a taxonomy file is supplied."""
script_info['script_usage']=[]

script_info['script_usage'].append(("Make OTU table","""Make an OTU table from an OTU map (i.e., result from pick_otus.py) and a taxonomy assignment file (i.e., result from assign_taxonomy.py). Write the output file to otu_table.biom.""","""%prog -i otu_map.txt -t tax_assignments.txt -o otu_table.biom"""))

script_info['script_usage'].append(("Make OTU table, excluding OTU ids listed in a fasta file","""Make an OTU table, excluding the sequences listed in pynast_failures.fna. Note that the file pass as -e must end with either '.fasta' or '.fna'.""","%prog -i otu_map.txt -o otu_table_no_pynast_failures.biom -e pynast_failures.fna"))

script_info['script_usage'].append(("Make OTU table, excluding a list of OTU ids","""Make an OTU table, excluding the sequences listed in chimeric_seqs.txt""","%prog -i otu_map.txt -o otu_table_non_chimeric.biom -e chimeric_seqs.txt"))

script_info['output_description']="""The output of make_otu_table.py is a biom file, where the columns correspond to Samples and rows correspond to OTUs and the number of times a sample appears in a particular OTU."""

script_info['required_options']=[\
 options_lookup['otu_map_as_primary_input'],
  options_lookup['output_biom_fp'],
]

script_info['optional_options']=[ \
  make_option('-t', '--taxonomy', type='existing_filepath', dest='taxonomy_fname',
              help='Path to taxonomy assignment, containing the assignments of taxons to sequences (i.e., resulting txt file from assign_taxonomy.py) [default: %default]'),
  make_option('-e','--exclude_otus_fp',type='existing_filepath',
   help=("path to a file listing OTU identifiers that should not be included in the "
         "OTU table (e.g., the output of identify_chimeric_seqs.py) or a fasta "
         "file where seq ids should be excluded (e.g., failures fasta file from align_seqs.py)"))
]

script_info['version'] = __version__


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

    exclude_otus_fp = opts.exclude_otus_fp
    
    outfile = open(opts.output_biom_fp, 'w')
    
    if not opts.taxonomy_fname:
        otu_to_taxonomy = None
    else:
       infile = open(opts.taxonomy_fname,'U')
       otu_to_taxonomy = parse_taxonomy(infile)
    
    ids_to_exclude = []
    if exclude_otus_fp:
        if splitext(exclude_otus_fp)[1] in ('.fasta','.fna'):
            ids_to_exclude = \
             get_seq_ids_from_fasta_file(open(exclude_otus_fp,'U'))
        else:
            ids_to_exclude = \
             get_seq_ids_from_seq_id_file(open(exclude_otus_fp,'U'))
    biom_otu_table = make_otu_table(open(opts.otu_map_fp, 'U'), 
                               otu_to_taxonomy,
                               ids_to_exclude)
    outfile.write(biom_otu_table)
    

if __name__ == "__main__":
    main()