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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"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from qiime.util import parse_command_line_parameters
from qiime.util import make_option
from os import makedirs, system
from os.path import exists, split, splitext
from subprocess import check_call, CalledProcessError
from optparse import OptionParser
from cogent.app.formatdb import build_blast_db_from_fasta_path
from qiime.parallel.util import split_fasta, get_random_job_prefix, write_jobs_file,\
submit_jobs, compute_seqs_per_file, build_filepaths_from_filepaths,\
get_poller_command, write_filepaths_to_file,\
write_merge_map_file_blast
from qiime.parallel.blast import get_commands
from qiime.util import load_qiime_config, get_options_lookup
qiime_config = load_qiime_config()
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""Parallel BLAST"""
script_info['script_description']="""This script for performing blast while making use of multicore/multiprocessor environments to perform analyses in parallel."""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Example""","""BLAST /home/qiime_user/10_seq.fasta (-i) via three (-O) independent jobs against a blast database created from /home/qiime_user/1000_seq.fasta (-r). Store the results in /home/qiime_user/bla_out/ (-o).""","""%prog -i /home/qiime_user/10_seq.fasta -r /home/qiime_user/1000_seq.fasta -O 3 -o /home/qiime_user/bla_out/"""))
script_info['output_description']=""" """
script_info['required_options'] = [\
make_option('-i','--infile_path',action='store',\
type='string',dest='infile_path',
help='Path of sequences to use as queries [REQUIRED]'),\
make_option('-r','--refseqs_path',action='store',\
type='string',
help='Path to fasta sequences to search against' +\
' [REQUIRED]'),\
make_option('-o', '--output_dir', \
help='name of output directory for blast jobs [REQUIRED]')
]
script_info['optional_options'] = [\
make_option('-c','--disable_low_complexity_filter',
default=False,action='store_true',
help='disable filtering of low-complexity sequences '
'(i.e., -F F is passed to blast) [default: %default]'),\
make_option('-e','--e_value',action='store',\
type='float', default=1e-30, dest='e_value',
help='E-value threshold for blasts [default: %default]'),\
make_option('-n','--num_hits',action='store',\
type='int', default=1, dest='num_hits',
help='number of hits per query for blast results [default: %default]'),\
make_option('-w','--word_size',action='store',\
type='int', default=30, dest='word_size',
help='word size for blast searches [default: %default]'),\
make_option('-D', '--suppress_format_blastdb', action='store_true',\
default=False,help='supress format of blastdb [default: %default]'),\
make_option('-a','--blastmat_dir',action='store',\
type='string',help='full path to directory containing '+\
'blastmat file [default: %default]',\
default=qiime_config['blastmat_dir']),\
make_option('-b','--blastall_fp',
default=qiime_config['blastall_fp'],
help='Path to blastall [default: %default]'),\
options_lookup['jobs_to_start'],\
options_lookup['poller_fp'],\
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['python_exe_fp'],\
options_lookup['seconds_to_sleep']\
]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# create local copies of command-line options
input_fasta_fp = opts.infile_path
refseqs_path = opts.refseqs_path
python_exe_fp = opts.python_exe_fp
num_jobs_to_start = opts.jobs_to_start
blastall_fp = opts.blastall_fp
blastmat_dir = opts.blastmat_dir
cluster_jobs_fp = opts.cluster_jobs_fp
e_value = opts.e_value
word_size = opts.word_size
num_hits = opts.num_hits
output_dir = opts.output_dir
suppress_format_blastdb = opts.suppress_format_blastdb
poller_fp = opts.poller_fp
retain_temp_files = opts.retain_temp_files
suppress_polling = opts.suppress_polling
seconds_to_sleep = opts.seconds_to_sleep
poll_directly = opts.poll_directly
disable_low_complexity_filter = opts.disable_low_complexity_filter
created_temp_paths = []
# split the input filepath into directory and filename, base filename and
# extension
input_dir, input_fasta_fn = split(input_fasta_fp)
input_file_basename, input_fasta_ext = splitext(input_fasta_fn)
# set the job_prefix either based on what the user passed in,
# or a random string beginning with BLAST
job_prefix = opts.job_prefix or get_random_job_prefix('BLAST')
# A temporary output directory is created in output_dir named
# job_prefix. Output files are then moved from the temporary
# directory to the output directory when they are complete, allowing
# a poller to detect when runs complete by the presence of their
# output files.
working_dir = '%s/%s' % (output_dir,job_prefix)
try:
makedirs(working_dir)
created_temp_paths.append(working_dir)
except OSError:
# working dir already exists
pass
# compute the number of sequences that should be included in
# each file after splitting the input fasta file
num_seqs_per_file = compute_seqs_per_file(input_fasta_fp,num_jobs_to_start)
# Build the blast database if necessary
if not suppress_format_blastdb:
blast_db, db_files_to_remove = \
build_blast_db_from_fasta_path(refseqs_path)
created_temp_paths += db_files_to_remove
# split the fasta files and get the list of resulting files
tmp_fasta_fps =\
split_fasta(open(input_fasta_fp),num_seqs_per_file,job_prefix,output_dir)
created_temp_paths += tmp_fasta_fps
# build the filepath for the 'jobs script'
jobs_fp = '%s/%sjobs.txt' % (output_dir, job_prefix)
created_temp_paths.append(jobs_fp)
# generate the list of commands to be pushed out to nodes
commands, job_result_filepaths = get_commands(tmp_fasta_fps,refseqs_path,
blastall_fp,blastmat_dir,e_value,word_size,num_hits,output_dir,working_dir,
disable_low_complexity_filter=disable_low_complexity_filter,
command_prefix=None,command_suffix=None)
created_temp_paths += job_result_filepaths
# Set up poller apparatus if the user does not suppress polling
if not suppress_polling:
# Write the list of files which must exist for the jobs to be
# considered complete
expected_files_filepath = '%s/expected_out_files.txt' % working_dir
write_filepaths_to_file(job_result_filepaths,expected_files_filepath)
created_temp_paths.append(expected_files_filepath)
# Write the mapping file which described how the output files from
# each job should be merged into the final output files
merge_map_filepath = '%s/merge_map.txt' % working_dir
write_merge_map_file_blast(job_result_filepaths,output_dir,\
merge_map_filepath,input_file_basename)
created_temp_paths.append(merge_map_filepath)
# Create the filepath listing the temporary files to be deleted,
# but don't write it yet
deletion_list_filepath = '%s/deletion_list.txt' % working_dir
created_temp_paths.append(deletion_list_filepath)
if not poll_directly:
# Generate the command to run the poller, and the list of temp files
# created by the poller
poller_command, poller_result_filepaths =\
get_poller_command(python_exe_fp,poller_fp,expected_files_filepath,\
merge_map_filepath,deletion_list_filepath,\
seconds_to_sleep=seconds_to_sleep)
# append the poller command to the list of job commands
commands.append(poller_command)
else:
poller_command, poller_result_filepaths =\
get_poller_command(python_exe_fp,poller_fp,expected_files_filepath,\
merge_map_filepath,deletion_list_filepath,\
seconds_to_sleep=seconds_to_sleep,\
command_prefix='',command_suffix='')
created_temp_paths += poller_result_filepaths
if not retain_temp_files:
# If the user wants temp files deleted, now write the list of
# temp files to be deleted
write_filepaths_to_file(created_temp_paths,deletion_list_filepath)
else:
# Otherwise just write an empty file
write_filepaths_to_file([],deletion_list_filepath)
# write the commands to the 'jobs files'
write_jobs_file(commands,job_prefix=job_prefix,jobs_fp=jobs_fp)
# submit the jobs file using cluster_jobs, if not suppressed by the
# user
if not opts.suppress_submit_jobs:
submit_jobs(cluster_jobs_fp,jobs_fp,job_prefix)
if poll_directly:
try:
check_call(poller_command.split())
except CalledProcessError, e:
print '**Error occuring when calling the poller directly. '+\
'Jobs may have been submitted, but are not being polled.'
print str(e)
exit(-1)
if __name__ == "__main__":
main()
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