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#!/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", "Jose Antonio Navas Molina"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
import warnings
warnings.filterwarnings('ignore', 'Not using MPI as mpi4py not found')
from qiime.util import (parse_command_line_parameters,
get_options_lookup,
make_option,
load_qiime_config)
from qiime.align_seqs import pairwise_alignment_methods
from qiime.parallel.align_seqs import ParallelAlignSeqsPyNast
qiime_config = load_qiime_config()
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""Parallel sequence alignment using PyNAST"""
script_info['script_description']="""A wrapper for the align_seqs.py PyNAST option, intended to make use of multicore/multiprocessor environments to perform analyses in parallel."""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Example""","""Align the input file (-i) against using PyNAST and write the output (-o) to $PWD/pynast_aligned_seqs/. 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 -o $PWD/pynast_aligned_seqs/"""))
script_info['output_description']="""This results in a multiple sequence alignment (FASTA-formatted)."""
script_info['required_options'] = [\
options_lookup['fasta_as_primary_input'],\
options_lookup['output_dir']
]
pairwise_alignment_method_choices = pairwise_alignment_methods.keys()
blast_db_default_help =\
qiime_config['pynast_template_alignment_blastdb'] or \
'created on-the-fly from template_alignment'
script_info['optional_options'] = [\
make_option('-a','--pairwise_alignment_method',\
type='choice',help='Method to use for pairwise alignments'+\
' [default: %default]',\
default='uclust',choices=pairwise_alignment_method_choices),\
make_option('-d','--blast_db',type='blast_db',\
dest='blast_db',help='Database to blast against'+\
' [default: %s]' % blast_db_default_help,
default=qiime_config['pynast_template_alignment_blastdb']),\
make_option('-e','--min_length',\
type='int',help='Minimum sequence '+\
'length to include in alignment [default: 75% of the'+\
' median input sequence length]',\
default=-1),
make_option('-p','--min_percent_id',action='store',\
type='float',help='Minimum percent '+\
'sequence identity to closest blast hit to include sequence in'+\
' alignment [default: %default]',default=75.0),\
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']
]
script_info['version'] = __version__
# pynast_template_alignment_fp is required only if it is not
# provided in qiime_config
if qiime_config['pynast_template_alignment_fp']:
script_info['optional_options'].append(make_option('-t','--template_fp',\
type='string',dest='template_fp',help='Filepath for '+\
'template against [default: %default]',
default=qiime_config['pynast_template_alignment_fp']))
else:
script_info['required_options'].append(make_option('-t','--template_fp',\
type='string',dest='template_fp',\
help='Filepath for template against',
default=qiime_config['pynast_template_alignment_fp']))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# create dict of command-line options
params = eval(str(opts))
parallel_runner = ParallelAlignSeqsPyNast(
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,
opts.output_dir,
params,
job_prefix=opts.job_prefix,
poll_directly=opts.poll_directly,
suppress_submit_jobs=False)
if __name__ == "__main__":
main()
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