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#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2011-2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of the Michigan State University nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project@idyll.org
# pylint: disable=invalid-name, missing-docstring
"""
Partition a graph.
% python scripts/partition-graph.py <base>
This will output many <base>.subset.N.pmap files.
Use '-h' for parameter help.
"""
from __future__ import print_function
import threading
import gc
import os.path
import argparse
import textwrap
import sys
from khmer import __version__, load_nodegraph
from khmer.khmer_args import (add_threading_args, info, sanitize_help,
ComboFormatter, _VersionStdErrAction)
from khmer.kfile import check_input_files
# stdlib queue module was renamed on Python 3
try:
import queue
except ImportError:
import Queue as queue
DEFAULT_SUBSET_SIZE = int(1e5)
DEFAULT_N_THREADS = 4
def worker(tasks, basename, stop_big_traversals):
while True:
try:
(nodegraph, index, start, stop) = tasks.get(False)
except queue.Empty:
print('exiting', file=sys.stderr)
return
outfile = basename + '.subset.%d.pmap' % (index,)
if os.path.exists(outfile):
print('SKIPPING', outfile, ' -- already exists', file=sys.stderr)
continue
print('starting:', basename, index, file=sys.stderr)
# pay attention to stoptags when partitioning; take command line
# direction on whether or not to exhaustively traverse.
subset = nodegraph.do_subset_partition(start, stop, True,
stop_big_traversals)
print('saving:', basename, index, file=sys.stderr)
nodegraph.save_subset_partitionmap(subset, outfile)
del subset
gc.collect()
def get_parser():
epilog = """\
The resulting partition maps are saved as ``${basename}.subset.#.pmap``
files.
"""
parser = argparse.ArgumentParser(
description="Partition a sequence graph based upon waypoint "
"connectivity", epilog=textwrap.dedent(epilog),
formatter_class=ComboFormatter)
parser.add_argument('basename', help="basename of the input k-mer"
"nodegraph + tagset files")
parser.add_argument('--stoptags', '-S', metavar='filename', default='',
help="Use stoptags in this file during partitioning")
parser.add_argument('--subset-size', '-s', default=DEFAULT_SUBSET_SIZE,
type=float, help='Set subset size (usually 1e5-1e6 is '
'good)')
parser.add_argument('--no-big-traverse', action='store_true',
default=False, help='Truncate graph joins at big '
'traversals')
parser.add_argument('--version', action=_VersionStdErrAction,
version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
add_threading_args(parser)
return parser
def main():
info('partition-graph.py', ['graph'])
args = sanitize_help(get_parser()).parse_args()
basename = args.basename
filenames = [basename, basename + '.tagset']
for _ in filenames:
check_input_files(_, args.force)
print('--', file=sys.stderr)
print('SUBSET SIZE', args.subset_size, file=sys.stderr)
print('N THREADS', args.threads, file=sys.stderr)
if args.stoptags:
print('stoptag file:', args.stoptags, file=sys.stderr)
print('--', file=sys.stderr)
print('loading nodegraph %s' % basename, file=sys.stderr)
nodegraph = load_nodegraph(basename)
nodegraph.load_tagset(basename + '.tagset')
# do we want to load stop tags, and do they exist?
if args.stoptags:
print('loading stoptags from', args.stoptags, file=sys.stderr)
nodegraph.load_stop_tags(args.stoptags)
# do we want to exhaustively traverse the graph?
stop_big_traversals = args.no_big_traverse
if stop_big_traversals:
print('** This script brakes for lumps:',
' stop_big_traversals is true.', file=sys.stderr)
else:
print('** Traverse all the things:',
' stop_big_traversals is false.', file=sys.stderr)
#
# now, partition!
#
# divide the tags up into subsets
divvy = nodegraph.divide_tags_into_subsets(int(args.subset_size))
n_subsets = len(divvy)
divvy.append(0)
# build a queue of tasks:
worker_q = queue.Queue()
# break up the subsets into a list of worker tasks
for _ in range(0, n_subsets):
start = divvy[_]
end = divvy[_ + 1]
worker_q.put((nodegraph, _, start, end))
print('enqueued %d subset tasks' % n_subsets, file=sys.stderr)
open('%s.info' % basename, 'w').write('%d subsets total\n' % (n_subsets))
n_threads = args.threads
if n_subsets < n_threads:
n_threads = n_subsets
# start threads!
print('starting %d threads' % n_threads, file=sys.stderr)
print('---', file=sys.stderr)
threads = []
for _ in range(n_threads):
cur_thrd = threading.Thread(target=worker, args=(worker_q, basename,
stop_big_traversals))
threads.append(cur_thrd)
cur_thrd.start()
print('done starting threads', file=sys.stderr)
# wait for threads
for _ in threads:
_.join()
print('---', file=sys.stderr)
print('done making subsets! see %s.subset.*.pmap' %
(basename,), file=sys.stderr)
if __name__ == '__main__':
main()
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