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test_nibblestorage.py
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test_nibblestorage.py
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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 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
import random
from khmer import SmallCounttable
from . import khmer_tst_utils as utils
# This mostly tests the underlying NibbleStorage class
def test_single_add():
sct = SmallCounttable(4, 1e6, 4)
sct.add("AAAA")
assert sct.get("AAAA") == 1
def test_split_byte_murmur():
# check the byte is correctly split when using murmur hash
sct = SmallCounttable(4, 4, 1)
# these kmers were carefully chosen to have hash values that produce
# consecutive indices in the count table.
a = "AAAC"
b = "AAAG"
assert sct.get_kmer_hashes(a) == [11898086063751343884]
assert sct.get_kmer_hashes(b) == [10548630838975263317]
sct.add(a)
assert sct.get(a) == 1
assert sct.get(b) == 0
def test_overflow():
# check that we do not overflow into other part of the byte
sct = SmallCounttable(4, 1e6, 4)
a = "AAAA"
b = "AAAT"
# try to overflow our 4bit counter
for n in range(17):
sct.add(a)
assert sct.get(a) == 15
assert sct.get(b) == 0
# repeat with the other kmer that hashes to the other half of the byte
sct = SmallCounttable(4, 1e6, 4)
a = "AAAA"
b = "AAAT"
# try to overflow our 4bit counter
for n in range(17):
sct.add(b)
assert sct.get(b) == 15
assert sct.get(a) == 0
def test_random_kmers():
# check for out-of-bounds errors and similar with random kmers
rng = random.Random(1)
sct = SmallCounttable(20, 1e2, 4)
kmers = ["".join(rng.choice("ACGT") for _ in range(20))
for n in range(400)]
for kmer in kmers:
sct.add(kmer)
for kmer in kmers:
sct.get(kmer)
def test_read_write():
rng = random.Random(1)
sct = SmallCounttable(20, 1e2, 4)
kmers = ["".join(rng.choice("ACGT") for _ in range(20))
for n in range(400)]
for kmer in kmers:
sct.add(kmer)
fname = utils.get_temp_filename('zzz')
sct.save(fname)
# on purpose choose parameters that are different from sct
sct2 = SmallCounttable.load(fname)
assert sct.ksize() == sct2.ksize()
for kmer in kmers:
assert sct.get(kmer) == sct2.get(kmer)