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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 glob import glob
from os import popen, system, mkdir, makedirs
from os.path import split, splitext, join
from subprocess import check_call, CalledProcessError
from qiime.util import get_tmp_filename
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_assign_taxonomy, merge_to_n_commands
from qiime.util import get_options_lookup, get_qiime_scripts_dir
from qiime.parallel.alpha_diversity import get_job_commands
script_info={}
script_info['brief_description']="""Parallel alpha diversity"""
script_info['script_description']="""This script performs like the alpha_diversity.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""","""Apply the observed_species, chao1, PD_whole_tree metrics (-m) to all otu tables in /home/qiime_user/rare/ (-i) and write the resulting output files to /home/qiime_user/out/ (-o, will be created if it doesn't exist). Use the tree file rep_set.tre (-t) when necessary.""","""%prog -i /home/qiime_user/rare/ -o /home/qiime_user/out -m observed_species,chao1,PD_whole_tree -t /home/qiime_user/rep_set.tre"""))
script_info['output_description'] ="""The resulting output will be the same number of files as supplied by the user. The resulting files are tab-delimited text files, where the columns correspond to alpha diversity metrics and the rows correspond to samples and their calculated diversity measurements. """
script_info['version'] = __version__
options_lookup = get_options_lookup()
script_info['required_options'] = [\
make_option('-i', '--input_path',
help='input path, must be directory [REQUIRED]'),\
make_option('-o', '--output_path',
help='output path, must be directory [REQUIRED]'),\
]
script_info['optional_options'] = [\
make_option('-t', '--tree_path',
help='path to newick tree file, required for phylogenetic metrics'+\
' [default: %default]'),\
make_option('-N','--alpha_diversity_fp',action='store',\
type='string',help='full path to '+\
'scripts/alpha_diversity.py [default: %default]',\
default=join(get_qiime_scripts_dir(),'alpha_diversity.py')),\
make_option('-m', '--metrics',
help='metrics to use, comma delimited',
default='PD_whole_tree,chao1,observed_species'),
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'],\
options_lookup['jobs_to_start']
]
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# create local copies of command-line options
input_dir = opts.input_path
output_dir = opts.output_path
metrics = opts.metrics
tree_fp = opts.tree_path
alpha_diversity_fp = opts.alpha_diversity_fp
python_exe_fp = opts.python_exe_fp
path_to_cluster_jobs = opts.cluster_jobs_fp
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
jobs_to_start = opts.jobs_to_start
created_temp_paths = []
input_fps = glob('%s/*' % input_dir)
# split the input filepath into directory and filename, base filename and
# extension
# input_dir, input_fn = split(input_path)
# input_file_basename, input_file_ext = splitext(input_fn)
# set the job_prefix either based on what the user passed in,
# or a random string beginning with ALDIV (ALphaDIVersity)
job_prefix = opts.job_prefix or get_random_job_prefix('ALDIV')
# 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
# build the filepath for the 'jobs script'
jobs_fp = '%s/%sjobs.txt' % (output_dir, job_prefix)
created_temp_paths.append(jobs_fp)
# Get the list of commands to be run and the expected result files
commands, job_result_filepaths = \
get_job_commands(python_exe_fp,alpha_diversity_fp,tree_fp,job_prefix,
metrics,input_fps,output_dir,working_dir,command_prefix=' ',
command_suffix=' ')
# Merge commands into jobs_to_start number of jobs
commands = merge_to_n_commands(commands,jobs_to_start)
# 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
open(merge_map_filepath,'w').close()
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,\
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(path_to_cluster_jobs,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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