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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) 2015-2016, 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=missing-docstring,invalid-name,no-member
"""
Build a counting Bloom filter from the given sequences, save in <countgraph>.
% load-into-counting.py <countgraph> <data1> [ <data2> <...> ]
Use '-h' for parameter help.
"""
from __future__ import print_function, unicode_literals
import json
import os
import sys
import threading
import textwrap
import khmer
from khmer import khmer_args
from khmer.khmer_args import (build_counting_args, report_on_config, info,
add_threading_args, calculate_graphsize,
sanitize_help)
from khmer.kfile import check_file_writable
from khmer.kfile import check_input_files
from khmer.kfile import check_space_for_graph
from khmer.khmer_logger import (configure_logging, log_info, log_error,
log_warn)
def get_parser():
epilog = """\
Note: with :option:`-b`/:option:`--no-bigcount` the output will be the
exact size of the k-mer countgraph and this script will use a constant
amount of memory. In exchange k-mer counts will stop at 255. The memory
usage of this script with :option:`-b` will be about 1.15x the product of
the :option:`-x` and :option:`-N` numbers.
Example::
load-into-counting.py -k 20 -x 5e7 out data/100k-filtered.fa
Multiple threads can be used to accelerate the process, if you have extra
cores to spare.
Example::
load-into-counting.py -k 20 -x 5e7 -T 4 out data/100k-filtered.fa
"""
parser = build_counting_args("Build a k-mer countgraph from the given"
" sequences.", epilog=textwrap.dedent(epilog),
citations=['counting', 'SeqAn'])
add_threading_args(parser)
parser.add_argument('output_countgraph_filename', help="The name of the"
" file to write the k-mer countgraph to.")
parser.add_argument('input_sequence_filename', nargs='+',
help="The names of one or more FAST[AQ] input "
"sequence files.")
parser.add_argument('-b', '--no-bigcount', dest='bigcount', default=True,
action='store_false', help="The default behaviour is "
"to count past 255 using bigcount. This flag turns "
"bigcount off, limiting counts to 255.")
parser.add_argument('-s', '--summary-info', type=str, default=None,
metavar="FORMAT", choices=[str('json'), str('tsv')],
help="What format should the machine readable run "
"summary be in? (`json` or `tsv`, disabled by"
" default)")
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
parser.add_argument('-q', '--quiet', dest='quiet', default=False,
action='store_true')
return parser
def main():
args = sanitize_help(get_parser()).parse_args()
configure_logging(args.quiet)
report_on_config(args)
base = args.output_countgraph_filename
filenames = args.input_sequence_filename
for name in args.input_sequence_filename:
check_input_files(name, args.force)
tablesize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(args.output_countgraph_filename, tablesize,
args.force)
info_filename = base + ".info"
check_file_writable(base)
check_file_writable(info_filename)
log_info('Saving k-mer countgraph to {base}', base=base)
log_info('Loading kmers from sequences in {filenames}',
filenames=repr(filenames))
# clobber the '.info' file now, as we always open in append mode below
with open(info_filename, 'w') as info_fp:
print('khmer version:', khmer.__version__, file=info_fp)
log_info('making countgraph')
countgraph = khmer_args.create_countgraph(args)
filename = None
total_num_reads = 0
for index, filename in enumerate(filenames):
rparser = khmer.ReadParser(filename)
threads = []
log_info('consuming input {input}', input=filename)
for _ in range(args.threads):
cur_thrd = \
threading.Thread(
target=countgraph.consume_seqfile_with_reads_parser,
args=(rparser, )
)
threads.append(cur_thrd)
cur_thrd.start()
for thread in threads:
thread.join()
if index > 0 and index % 10 == 0:
tablesize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(base, tablesize, args.force)
log_info('mid-save {base}', base=base)
countgraph.save(base)
with open(info_filename, 'a') as info_fh:
print('through', filename, file=info_fh)
total_num_reads += rparser.num_reads
n_kmers = countgraph.n_unique_kmers()
log_info('Total number of unique k-mers: {nk}', nk=n_kmers)
with open(info_filename, 'a') as info_fp:
print('Total number of unique k-mers:', n_kmers, file=info_fp)
log_info('saving {base}', base=base)
countgraph.save(base)
# Change max_false_pos=0.2 only if you really grok it. HINT: You don't
fp_rate = \
khmer.calc_expected_collisions(
countgraph, args.force, max_false_pos=.2)
with open(info_filename, 'a') as info_fp:
print('fp rate estimated to be %1.3f\n' % fp_rate, file=info_fp)
if args.summary_info:
mr_fmt = args.summary_info.lower()
mr_file = base + '.info.' + mr_fmt
log_info("Writing summmary info to {mr_file}", mr_file=mr_file)
with open(mr_file, 'w') as mr_fh:
if mr_fmt == 'json':
mr_data = {
"ht_name": os.path.basename(base),
"fpr": fp_rate,
"num_kmers": n_kmers,
"files": filenames,
"mrinfo_version": "0.2.0",
"num_reads": total_num_reads,
}
json.dump(mr_data, mr_fh)
mr_fh.write('\n')
elif mr_fmt == 'tsv':
mr_fh.write("ht_name\tfpr\tnum_kmers\tnum_reads\tfiles\n")
vals = [
os.path.basename(base),
"{:1.3f}".format(fp_rate),
str(n_kmers),
str(total_num_reads),
";".join(filenames),
]
mr_fh.write("\t".join(vals) + "\n")
log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
log_info('DONE.')
log_info('wrote to: {filename}', filename=info_filename)
if __name__ == '__main__':
main()
# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
# vim: set textwidth=79:
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