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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","Dan Knights"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from qiime.util import make_option
from qiime.util import parse_command_line_parameters,\
load_qiime_config, get_options_lookup, get_qiime_scripts_dir
from qiime.parallel.pick_otus_blast import get_job_commands,\
get_poller_command
from qiime.parallel.util import split_fasta, get_random_job_prefix,\
write_jobs_file,submit_jobs, compute_seqs_per_file,\
build_filepaths_from_filepaths, write_filepaths_to_file,\
write_merge_map_file_pick_otus
from os import popen, system, makedirs, mkdir
from os.path import split, splitext, join
from subprocess import check_call, CalledProcessError
from qiime.util import get_tmp_filename
from cogent.app.formatdb import build_blast_db_from_fasta_path
qiime_config = load_qiime_config()
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""Parallel pick otus using BLAST"""
script_info['script_description']="""This script performs like the pick_otus.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""","""Pick OTUs by blasting /home/qiime_user/inseqs.fasta against /home/qiime_user/refseqs.fasta and write the output to the /home/qiime_user/out/ directory.""","""%prog -i /home/qiime_user/inseqs.fasta -r /home/qiime_user/refseqs.fasta -o /home/qiime_user/out/"""))
script_info['output_description']="""The output consists of two files (i.e. seqs_otus.txt and seqs_otus.log). The .txt file is composed of tab-delimited lines, where the first field on each line corresponds to an (arbitrary) cluster identifier, and the remaining fields correspond to sequence identifiers assigned to that cluster. Sequence identifiers correspond to those provided in the input FASTA file. The resulting .log file contains a list of parameters passed to this script along with the output location of the resulting .txt file."""
script_info['required_options'] = [\
make_option('-i','--input_fasta_fp',action='store',\
type='string',help='full path to '+\
'input_fasta_fp'),\
make_option('-o','--output_dir',action='store',\
type='string',help='path to store output files')\
]
script_info['optional_options'] = [\
make_option('-e','--max_e_value',\
help='Max E-value '+\
'[default: %default]', default='1e-10'),\
make_option('-s','--similarity',action='store',\
type='float',help='Sequence similarity '+\
'threshold [default: %default]',default=0.97),\
make_option('-r','--refseqs_fp',action='store',\
type='string',help='full path to '+\
'template alignment [default: %default]'),\
make_option('-b','--blast_db',action='store',\
type='string',help='database to blast against '+\
'[default: %default]'),\
make_option('--min_aligned_percent',
help=('Minimum percent of query sequence that can be aligned '
'to consider a hit (BLAST OTU picker only) [default: %default]'),
default=0.50,type='float'),
#Define parallel-script-specific parameters
make_option('-N','--pick_otus_fp',action='store',\
type='string',help='full path to '+\
'scripts/pick_otus.py [default: %default]',\
default=join(get_qiime_scripts_dir(),'pick_otus.py')),\
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)
if opts.blast_db == None and opts.refseqs_fp == None:
option_parser.error('Either blast_db or refseqs_fp must be provided.')
# create local copies of command-line options
python_exe_fp = opts.python_exe_fp
pick_otus_fp = opts.pick_otus_fp
refseqs_fp = opts.refseqs_fp
cluster_jobs_fp = opts.cluster_jobs_fp
input_fasta_fp = opts.input_fasta_fp
jobs_to_start = opts.jobs_to_start
output_dir = opts.output_dir
poller_fp = opts.poller_fp
retain_temp_files = opts.retain_temp_files
suppress_polling = opts.suppress_polling
seconds_to_sleep = opts.seconds_to_sleep
max_e_value = opts.max_e_value
similarity = opts.similarity
poll_directly = opts.poll_directly
min_aligned_percent = opts.min_aligned_percent
created_temp_paths = []
if not opts.blast_db:
# Build the blast database from the reference_seqs_fp -- all procs
# will then access one db rather than create one per proc
blast_db, db_files_to_remove = \
build_blast_db_from_fasta_path(refseqs_fp)
created_temp_paths += db_files_to_remove
else:
blast_db = opts.blast_db
# 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 RDP
job_prefix = opts.job_prefix or get_random_job_prefix('POTU')
# 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,jobs_to_start)
# 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,working_dir=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 and the list of
# output files generated by each job
commands, job_result_filepaths = \
get_job_commands(python_exe_fp,pick_otus_fp,tmp_fasta_fps,
output_dir,blast_db,job_prefix,working_dir,max_e_value,similarity,
min_aligned_percent)
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
process_run_results_f =\
'qiime.parallel.pick_otus_blast.parallel_blast_process_run_results_f'
write_merge_map_file_pick_otus(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)
# Generate the command to run the poller, and the list of temp files
# created by the poller
if not poll_directly:
poller_command, poller_result_filepaths =\
get_poller_command(python_exe_fp,poller_fp,expected_files_filepath,\
merge_map_filepath,deletion_list_filepath,process_run_results_f,\
seconds_to_sleep=seconds_to_sleep)
created_temp_paths += poller_result_filepaths
# 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,process_run_results_f,\
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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