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# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 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 University of California 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,missing-docstring,no-member,protected-access
from __future__ import print_function
from __future__ import absolute_import
import khmer
import pytest
from . import khmer_tst_utils as utils
def test_get_kmer_hashes():
s = "ATGGATATGGAGGACAAGTATATGGAGGACAAGTATATGGAGGACAAGTAT"
a = khmer.Counttable(33, 1e6, 3)
assert a.get_kmer_hashes(s[:33]) == [4743239192574154715]
assert a.get_kmer_hashes(s[:34]) == [4743239192574154715,
2122462908541313313]
assert a.get_kmer_hashes(s[0:33]) == [4743239192574154715]
assert a.get_kmer_hashes(s[1:34]) == [2122462908541313313]
@pytest.mark.parametrize('kmer', [
('GATTACA' * 3),
('ATG' * 7),
('AGGACAAGTATATGGAGGACA'),
])
def test_kmer_revcom_hash(kmer):
a = khmer.Counttable(21, 1e4, 3)
assert a.hash(kmer) == a.hash(khmer.reverse_complement(kmer))
@pytest.mark.parametrize('ksize,sketch_allocator', [
(21, khmer.Nodetable),
(21, khmer.Counttable),
(21, khmer.SmallCounttable),
(49, khmer.Nodetable),
(49, khmer.Counttable),
(49, khmer.SmallCounttable),
])
def test_reverse_hash(ksize, sketch_allocator):
multiplier = int(ksize / len('GATTACA'))
kmer = 'GATTACA' * multiplier
sketch = sketch_allocator(ksize, 1e4, 4)
kmer_hash = sketch.hash(kmer)
with pytest.raises(ValueError) as ve:
_ = sketch.reverse_hash(kmer_hash)
assert 'not implemented' in str(ve)
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