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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 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_qiime_scripts_dir, get_options_lookup
from qiime.parallel.multiple_rarefactions import get_job_commands
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""Parallel multiple file rarefaction"""
script_info['script_description']="""This script performs like the multiple_rarefactions.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""","""Build rarefied otu tables containing 100 (-m) to 2000 (-x) sequences in steps of 100 (-s) with 5 (-n) repetions per number of sequences, from /home/qiime_user/otu_table.txt (-i). Write the output files to the /home/qiime_user/rare directory (-o, will be created if it doesn't exist). The name of the output files will be of the form /home/qiime_user/rare/rarefaction_<num_seqs>_<reptition_number>.txt""","""%prog -o /home/qiime_user/rare -m 100 -x 2000 -s 100 -n 5 -i /home/qiime_user/otu_table.txt"""))
script_info['script_usage'].append(("""Example 2""","""Build 8 rarefied otu tables each containing exactly 100 sequences per sample (even depth rarefaction).""","""%prog -o /home/qiime_user/rare -m 100 -x 100 -s 100 -n 8 -i /home/qiime_user/otu_table.txt"""))
script_info['output_description']="""The result of parallel_multiple_rarefactions.py consists of a number of files, which depend on the minimum/maximum number of sequences per samples, steps and iterations. The files have the same otu table format as the input otu_table.txt, and are named in the following way: rarefaction_100_0.txt, where "100" corresponds to the sequences per sample and "0" for the iteration."""
script_info['required_options'] = [\
make_option('-i', '--input_path',
help='input filepath, (the otu table) [REQUIRED]'),\
make_option('-o', '--output_path',
help="write output rarefied otu tables here makes dir if it doesn't exist [REQUIRED]"),\
make_option('-m', '--min', type=int,help='min seqs/sample [REQUIRED]'),\
make_option('-x', '--max', type=int,\
help='max seqs/sample (inclusive) [REQUIRED]'),\
]
script_info['optional_options'] = [\
make_option('-n', '--num-reps', dest='num_reps', default=10, type=int,
help='num iterations at each seqs/sample level [default: %default]'),\
make_option('--lineages_included', action='store_true', default=True,
help='Deprecated: lineages are now included by default. Pass' +\
' --supress_lineages_included to prevent output OTU tables' +\
' from including taxonomic (lineage) information for each OTU. Note:' +\
' this will only work if lineage information is in the input OTU' +\
' table.'),
make_option('--suppress_lineages_included', default=True,
action="store_false",dest='lineages_included',
help='Exclude taxonomic (lineage) information for each OTU.'),
make_option('-N','--single_rarefaction_fp',action='store',\
type='string',help='full path to scripts/single_rarefaction.py [default: %default]',\
default=join(get_qiime_scripts_dir(),'single_rarefaction.py')),\
make_option('-s', '--step', type=int, default=1,\
help='levels: min, min+step... for level <= max [default: %default]'),\
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']
]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# create local copies of command-line options
input_path = opts.input_path
output_dir = opts.output_path
min_seqs = opts.min
max_seqs = opts.max
step = opts.step
if not step > 0:
print "Error: step size must be greater than 0."
print "If min = max, just leave step size at 1."
exit(-1)
num_reps = opts.num_reps
lineages_included = opts.lineages_included
single_rarefaction_fp = opts.single_rarefaction_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 = []
# 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('RARIF')
# 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)
# generate the list of commands to be pushed out to nodes
commands, job_result_filepaths = \
get_job_commands(python_exe_fp,single_rarefaction_fp,job_prefix,\
input_path,output_dir,working_dir,min_seqs,max_seqs,step,num_reps,
lineages_included,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 even though no merging is necessary
# (get_poller_command requires this, but a future version won't)
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)
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(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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