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# 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=C0111,C0103
"""
Test code that verifies current script output md5 hashes against recorded
hashes, to ensure that script function isn't changing.
"""
from __future__ import print_function
from __future__ import absolute_import
import khmer
from . import khmer_tst_utils as utils
#
# hashes recorded as of git commit 799039ffcf15d2a3ac6902ae62ae2da81030e8d2
# (for trim-low-abund without --diginorm behavior) and
# b939a34b565ce973224abdd0eeb53d6b52833c01 (for trim-low-abund updates).
#
def test_normalize_by_median_k21_C20_M1e7():
infile = utils.get_test_data('simple-genome-reads.fa')
outfile = utils.get_temp_filename('out')
utils.runscript('normalize-by-median.py', ['-C', '20', '-k', '21',
'-M', '1e7', '-o', outfile,
infile])
hash = utils._calc_md5(open(outfile, 'rb'))
assert hash == '942e9024c25a8d85033d755d86aba4a3', hash
def test_normalize_by_median_k21_C15_M1e7():
infile = utils.get_test_data('simple-genome-reads.fa')
outfile = utils.get_temp_filename('out')
utils.runscript('normalize-by-median.py', ['-C', '15', '-k', '21',
'-M', '1e7', '-o', outfile,
infile])
hash = utils._calc_md5(open(outfile, 'rb'))
assert hash == '0d1b4b9d4c76cb8cdeee5a98f6e70163', hash
def test_trim_low_abund_k21_C0_M1e7_diginorm():
# should be same as normalize-by-median -C 20 -k 21 -M 1e7
infile = utils.get_test_data('simple-genome-reads.fa')
outfile = utils.get_temp_filename('out')
utils.runscript('trim-low-abund.py', ['-C', '0', '-k', '21',
'--diginorm',
'--diginorm-coverage', '20',
'-M', '1e7', '-o', outfile,
infile])
hash = utils._calc_md5(open(outfile, 'rb'))
assert hash == '942e9024c25a8d85033d755d86aba4a3', hash
def test_trim_low_abund_k21_C0_M1e7_diginorm_dn15():
# should be same as normalize-by-median -C 15 -k 21 -M 1e7
infile = utils.get_test_data('simple-genome-reads.fa')
outfile = utils.get_temp_filename('out')
utils.runscript('trim-low-abund.py', ['-C', '0', '-k', '21',
'--diginorm',
'--diginorm-coverage', '15',
'-M', '1e7', '-o', outfile,
infile])
hash = utils._calc_md5(open(outfile, 'rb'))
assert hash == '0d1b4b9d4c76cb8cdeee5a98f6e70163', hash
def test_trim_low_abund_k21_C2_M1e7_diginorm_dn15():
# should be same as normalize-by-median -C 15 -k 21 -M 1e7
infile = utils.get_test_data('simple-genome-reads.fa')
outfile = utils.get_temp_filename('out')
utils.runscript('trim-low-abund.py', ['-C', '2', '-k', '21',
'--diginorm',
'--diginorm-coverage', '15',
'-M', '1e7', '-o', outfile,
infile])
hash = utils._calc_md5(open(outfile, 'rb'))
assert hash == 'fa09d094a9e623639a34f772b04d766c', hash
def test_trim_low_abund_k21_M1e7_C2():
infile = utils.get_test_data('simple-genome-reads.fa')
outfile = utils.get_temp_filename('out')
utils.runscript('trim-low-abund.py', ['-C', '2', '-k', '21',
'-M', '1e7', '-o', outfile,
infile])
hash = utils._calc_md5(open(outfile, 'rb'))
assert hash == '9495801b282ff6b08961b685d12a954c', hash
def test_trim_low_abund_k21_M1e7_C3():
infile = utils.get_test_data('simple-genome-reads.fa')
outfile = utils.get_temp_filename('out')
utils.runscript('trim-low-abund.py', ['-C', '3', '-k', '21',
'-M', '1e7', '-o', outfile,
infile])
hash = utils._calc_md5(open(outfile, 'rb'))
assert hash == 'da36ec64e7d001470c04dc19af5b8635', hash
def test_trim_low_abund_k21_M1e7_C4():
infile = utils.get_test_data('simple-genome-reads.fa')
outfile = utils.get_temp_filename('out')
utils.runscript('trim-low-abund.py', ['-C', '4', '-k', '21',
'-M', '1e7', '-o', outfile,
infile])
hash = utils._calc_md5(open(outfile, 'rb'))
assert hash == '65596253b87ed8d5aeb14dc8cf5a7406', hash
def test_trim_low_abund_k21_M1e7_C4_variable():
infile = utils.get_test_data('simple-genome-reads.fa')
outfile = utils.get_temp_filename('out')
utils.runscript('trim-low-abund.py', ['-C', '4', '-k', '21',
'-V',
'-M', '1e7', '-o', outfile,
infile])
hash = utils._calc_md5(open(outfile, 'rb'))
assert hash == '324871db807839f8bddd43548abcbeda', hash
def test_trim_low_abund_k21_M1e7_C4_variable_Z25():
infile = utils.get_test_data('simple-genome-reads.fa')
outfile = utils.get_temp_filename('out')
utils.runscript('trim-low-abund.py', ['-C', '4', '-k', '21',
'-V', '-Z', '25',
'-M', '1e7', '-o', outfile,
infile])
hash = utils._calc_md5(open(outfile, 'rb'))
assert hash == '6ec4f9874262f3eaf98cab4910c428f5', hash
def test_trim_low_abund_k21_M1e7_C4_variable_Z15():
infile = utils.get_test_data('simple-genome-reads.fa')
outfile = utils.get_temp_filename('out')
utils.runscript('trim-low-abund.py', ['-C', '4', '-k', '21',
'-V', '-Z', '15',
'-M', '1e7', '-o', outfile,
infile])
with open(outfile, 'rb') as output:
hashval = utils._calc_md5(output)
assert hashval == '393805ac92e8bed31a374de9ee89ead8', hash
|
