parallel_assign_taxonomy_blast.py

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

__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Jai Ram Rideout", "Jose Antonio Navas Molina"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
 
from os.path import join, abspath
from qiime.util import (get_options_lookup, get_qiime_scripts_dir,
                        load_qiime_config, make_option,
                        parse_command_line_parameters)
from qiime.parallel.assign_taxonomy import ParallelBlastTaxonomyAssigner

qiime_config = load_qiime_config()
options_lookup = get_options_lookup()

default_reference_seqs_fp = qiime_config['assign_taxonomy_reference_seqs_fp']
default_id_to_taxonomy_fp = qiime_config['assign_taxonomy_id_to_taxonomy_fp']

script_info={}

script_info['brief_description']="""Parallel taxonomy assignment using BLAST"""
script_info['script_description']="""This script performs like the assign_taxonomy.py script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel."""

script_info['script_usage']=[]
script_info['script_usage'].append(("""Example""","""Assign taxonomy to all sequences in the input file (-i) using BLAST with the id to taxonomy mapping file (-t) and reference sequences file (-r), and write the results (-o) to $PWD/blast_assigned_taxonomy/. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).""","""%prog -i $PWD/inseqs.fasta -t $PWD/id_to_tax.txt -r $PWD/refseqs.fasta -o $PWD/blast_assigned_taxonomy/"""))

script_info['output_description']="""Mapping of sequence identifiers to taxonomy and quality scores."""

script_info['required_options'] = [
 make_option('-i','--input_fasta_fp',
           type='existing_filepath',help='full path to '+\
           'input_fasta_fp [REQUIRED]'),
 make_option('-o','--output_dir',action='store',
           type='new_dirpath',help='full path to store output files '+\
           '[REQUIRED]')
]

script_info['optional_options'] = [\
 make_option('-r','--reference_seqs_fp',type='existing_filepath',\
        help='Ref seqs to blast against.  Must provide either --blast_db or '
        '--reference_seqs_db for assignment with blast [default: %s]' \
        % default_reference_seqs_fp,
        default=default_reference_seqs_fp),\
 make_option('-b', '--blast_db', type='blast_db',
        help='Database to blast against.  Must provide either --blast_db or '
        '--reference_seqs_db for assignment with blast [default: %default]'),\
 make_option('-e', '--e_value', type='float',
        help='Maximum e-value to record an assignment, only used for blast '
        'method [default: %default]',default=0.001),\
 make_option('-B','--blastmat_dir',action='store',\
           type='string',help='full path to directory containing '+\
           'blastmat file [default: %default]',\
           default=qiime_config['blastmat_dir']),\
 options_lookup['jobs_to_start'],
 options_lookup['retain_temp_files'],
 options_lookup['suppress_submit_jobs'],
 options_lookup['poll_directly'],
 options_lookup['cluster_jobs_fp'],
 options_lookup['suppress_polling'],
 options_lookup['job_prefix'],
 options_lookup['seconds_to_sleep']
]

if default_id_to_taxonomy_fp:
    script_info['optional_options'].append(\
     make_option('-t','--id_to_taxonomy_fp',action='store',\
           type='existing_filepath',help='full path to '+\
           'id_to_taxonomy mapping file [default: %s]' % default_id_to_taxonomy_fp,
           default=default_id_to_taxonomy_fp))
else:
    script_info['required_options'].append(\
     make_option('-t','--id_to_taxonomy_fp',action='store',\
           type='existing_filepath',help='full path to '+\
           'id_to_taxonomy mapping file [REQUIRED]'))

script_info['version'] = __version__ 

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)
            
    if not (opts.reference_seqs_fp or opts.blast_db):
        option_parser.error('Either a blast db (via -b) or a collection of '
                     'reference sequences (via -r) must be passed to '
                     'assign taxonomy using blast.')

    # create dict of command-line options
    params = eval(str(opts))

    parallel_runner = ParallelBlastTaxonomyAssigner(
            cluster_jobs_fp=opts.cluster_jobs_fp,
            jobs_to_start=opts.jobs_to_start,
            retain_temp_files=opts.retain_temp_files,
            suppress_polling=opts.suppress_polling,
            seconds_to_sleep=opts.seconds_to_sleep)

    parallel_runner(opts.input_fasta_fp,
                    abspath(opts.output_dir),
                    params,
                    job_prefix=opts.job_prefix,
                    poll_directly=opts.poll_directly,
                    suppress_submit_jobs=opts.suppress_submit_jobs)


if __name__ == "__main__":
    main()