/usr/lib/khmer/bin/extract-long-sequences.py is in khmer 2.1.2+dfsg-3.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 | #!/usr/bin/python3
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, 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
"""
Extract long sequences.
Write out lines of FASTQ and FASTA files that exceed an argument-specified
length.
% scripts/extract-long-sequences.py [-h] [-o OUTPUT] [-l LENGTH]
input_filenames [input_filenames ...]
Use '-h' for parameter help.
"""
from __future__ import print_function
import argparse
import screed
import textwrap
import sys
from khmer import __version__
from khmer.utils import write_record
from khmer.kfile import add_output_compression_type, get_file_writer
from khmer.khmer_args import sanitize_help, KhmerArgumentParser
def get_parser():
epilog = """\
Example::
extract-long-sequences.py --length 10 tests/test-data/paired-mixed.fa
"""
parser = KhmerArgumentParser(
description='Extract FASTQ or FASTA sequences longer than'
' specified length (default: 200 bp).',
epilog=textwrap.dedent(epilog))
parser.add_argument('input_filenames', help='Input FAST[AQ]'
' sequence filename.', nargs='+')
parser.add_argument('-o', '--output', help='The name of the output'
' sequence file.', default=sys.stdout,
metavar='output', type=argparse.FileType('wb'))
parser.add_argument('-l', '--length', help='The minimum length of'
' the sequence file.',
type=int, default=200)
add_output_compression_type(parser)
return parser
def main():
args = sanitize_help(get_parser()).parse_args()
outfp = get_file_writer(args.output, args.gzip, args.bzip)
for filename in args.input_filenames:
for record in screed.open(filename):
if len(record['sequence']) >= args.length:
write_record(record, outfp)
print('wrote to: ' + args.output.name, file=sys.stderr)
if __name__ == '__main__':
main()
|