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test_ssw.py
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test_ssw.py
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# Copyright (C) 2023 Nick Conway
# Copyright (C) 2014-2018, Nick Conway; Wyss Institute Harvard University
#
# The MIT License
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
# http://www.opensource.org/licenses/mit-license.php
'''
tests.test_ssw
~~~~~~~~~~~~~~
Tests for the ssw-py
'''
import unittest
from ssw import ( # type: ignore
AlignmentMgr,
BitwiseAlignmentFlag,
force_align,
format_force_align,
)
# Reference sequence
REF_SEQ = ''.join([
'C', 'A', 'G', 'C', 'C', 'T', 'T', 'T',
'C', 'T', 'G', 'A', 'C', 'C', 'C', 'G',
'G', 'A', 'A', 'A', 'T', 'C', 'A', 'A',
'A', 'A', 'T', 'A', 'G', 'G', 'C', 'A',
'C', 'A', 'A', 'C', 'A', 'A', 'A',
])
# Read sequence
READ_SEQ = ''.join([
'C', 'T', 'G', 'A', 'G', 'C', 'C', 'G',
'G', 'T', 'A', 'A', 'A', 'T', 'C',
])
class TestAlignmentMgr(unittest.TestCase):
'''Tests for the AlignmentMgr class
'''
def setUp(self):
self.align_mgr = AlignmentMgr(
match_score=2,
mismatch_penalty=2,
)
def test_deprecation(self):
'''Test camelCase Deprecation'''
with self.assertWarns(UserWarning):
self.align_mgr.setRead(b'ACGT')
with self.assertWarns(UserWarning):
self.align_mgr.setReference(b'ACGT')
def test_exact(self):
a = self.align_mgr
a.set_read(b'ACGT')
ref = b'TTTTACGTCCCCC'
a.set_reference(b'TTTTACGTCCCCC')
res = a.align()
self.assertEqual(res.optimal_score, 8)
self.assertEqual(res.sub_optimal_score, 0)
self.assertEqual(res.reference_start, 4)
self.assertEqual(res.reference_end, 7)
self.assertEqual(res.read_start, 0)
self.assertEqual(res.read_end, 3)
# a.print_result(res)
with self.assertWarns(UserWarning):
a.setReference(ref)
def test_deletion(self):
a = self.align_mgr
a.set_read(b'ACGT')
a.set_reference(b'TTTTACAGTCCCCC')
res = a.align()
self.assertEqual(res.optimal_score, 5)
self.assertEqual(res.sub_optimal_score, 0)
self.assertEqual(res.reference_start, 4)
self.assertEqual(res.reference_end, 8)
self.assertEqual(res.read_start, 0)
self.assertEqual(res.read_end, 3)
# a.print_result(res)
def test_insertion_with_gap_open(self):
a = self.align_mgr
a.set_read(b'ACGT')
a.set_reference(b'TTTTACTCCCCC')
res = a.align(gap_open=3)
self.assertEqual(res.optimal_score, 4)
self.assertEqual(res.sub_optimal_score, 0)
self.assertEqual(res.reference_start, 4)
self.assertEqual(res.reference_end, 5)
self.assertEqual(res.read_start, 0)
self.assertEqual(res.read_end, 1)
# a.print_result(res)
def test_insertion_with_no_gap_open_penalty(self):
a = self.align_mgr
a.set_read(b'ACGT')
a.set_reference(b'TTTTACTCCCCC')
res = a.align(gap_open=0)
self.assertEqual(res.optimal_score, 6)
self.assertEqual(res.sub_optimal_score, 0)
self.assertEqual(res.reference_start, 4)
self.assertEqual(res.reference_end, 6)
self.assertEqual(res.read_start, 0)
self.assertEqual(res.read_end, 3)
# a.print_result(res)
def test_start_idx_test(self):
a = self.align_mgr
a.set_read(b'ACTG')
a.set_reference(b'ACTCACTG')
res = a.align(start_idx=4)
self.assertEqual(res.optimal_score, 8)
self.assertEqual(res.sub_optimal_score, 0)
self.assertEqual(res.reference_start, 0)
self.assertEqual(res.reference_end, 3)
self.assertEqual(res.read_start, 0)
self.assertEqual(res.read_end, 3)
# a.print_result(res, start_idx=4)
def test_force_align(self):
read = b'ACTG'
ref = b'TTTTCTGCCCCCACG'
res = force_align(read, ref)
self.assertEqual(res.optimal_score, 6)
self.assertEqual(res.sub_optimal_score, 0)
self.assertEqual(res.reference_start, 4)
self.assertEqual(res.reference_end, 6)
self.assertEqual(res.read_start, 1)
self.assertEqual(res.read_end, 3)
# self.a.set_read(read)
# self.a.set_reference(ref)
# self.a.print_result(res)
out = format_force_align(read, ref, res)
self.assertEqual(out, ('TTTTCTGCCCCCACG', ' ACTG'))
def test_bitwise_flag(self):
a = self.align_mgr
a.set_read(READ_SEQ)
a.set_reference(REF_SEQ)
# 1. Test BitwiseAlignmentFlag.best_idxs
res = a.align(
gap_open=3,
gap_extension=1,
bitwise_flag=BitwiseAlignmentFlag.best_idxs,
)
self.assertEqual(res.CIGAR, '9M1I5M')
self.assertEqual(res.optimal_score, 21)
self.assertEqual(res.sub_optimal_score, 8)
self.assertEqual(res.reference_start, 8)
self.assertEqual(res.reference_end, 21)
self.assertEqual(res.read_start, 0)
self.assertEqual(res.read_end, 14)
# 2. Test BitwiseAlignmentFlag.best_idxs_no_cigar
res = a.align(
gap_open=3,
gap_extension=1,
bitwise_flag=BitwiseAlignmentFlag.best_idxs_no_cigar,
)
self.assertEqual(res.CIGAR, '')
self.assertEqual(res.optimal_score, 21)
self.assertEqual(res.sub_optimal_score, 8)
self.assertEqual(res.reference_start, 8)
self.assertEqual(res.reference_end, 21)
self.assertEqual(res.read_start, 0)
self.assertEqual(res.read_end, 14)
# 3. Test BitwiseAlignmentFlag.end_idxs_only_no_cigar
res = a.align(
gap_open=3,
gap_extension=1,
bitwise_flag=BitwiseAlignmentFlag.end_idxs_only_no_cigar,
)
self.assertEqual(res.CIGAR, '')
self.assertEqual(res.optimal_score, 21)
self.assertEqual(res.sub_optimal_score, 8)
self.assertEqual(res.reference_start, -1)
self.assertEqual(res.reference_end, 21)
self.assertEqual(res.read_start, -1)
self.assertEqual(res.read_end, 14)
# 4. Test BitwiseAlignmentFlag.score_filter
# 4.a change ``score_cutoff`` to 0
res = a.align(
gap_open=3,
gap_extension=1,
bitwise_flag=BitwiseAlignmentFlag.score_filter,
score_cutoff=0,
)
self.assertEqual(res.CIGAR, '9M1I5M')
self.assertEqual(res.optimal_score, 21)
self.assertEqual(res.sub_optimal_score, 8)
self.assertEqual(res.reference_start, 8)
self.assertEqual(res.reference_end, 21)
self.assertEqual(res.read_start, 0)
self.assertEqual(res.read_end, 14)
# 4.b change ``score_cutoff`` to 22
res = a.align(
gap_open=3,
gap_extension=1,
bitwise_flag=BitwiseAlignmentFlag.score_filter,
score_cutoff=22,
)
self.assertEqual(res.CIGAR, '')
self.assertEqual(res.optimal_score, 21)
self.assertEqual(res.sub_optimal_score, 8)
self.assertEqual(res.reference_start, -1)
self.assertEqual(res.reference_end, 21)
self.assertEqual(res.read_start, -1)
self.assertEqual(res.read_end, 14)
# 5. Test BitwiseAlignmentFlag.distance_filter
# 5.a change ``distance_cutoff`` to 0
res = a.align(
gap_open=3,
gap_extension=1,
bitwise_flag=BitwiseAlignmentFlag.distance_filter,
distance_cutoff=0,
)
self.assertEqual(res.CIGAR, '')
self.assertEqual(res.optimal_score, 21)
self.assertEqual(res.sub_optimal_score, 8)
self.assertEqual(res.reference_start, 8)
self.assertEqual(res.reference_end, 21)
self.assertEqual(res.read_start, 0)
self.assertEqual(res.read_end, 14)
# 5.b change ``distance_cutoff`` to 13
# (equal to the READ_SEQ length - 2)
res = a.align(
gap_open=3,
gap_extension=1,
bitwise_flag=BitwiseAlignmentFlag.distance_filter,
distance_cutoff=13,
)
self.assertEqual(res.CIGAR, '')
self.assertEqual(res.optimal_score, 21)
self.assertEqual(res.sub_optimal_score, 8)
self.assertEqual(res.reference_start, 8)
self.assertEqual(res.reference_end, 21)
self.assertEqual(res.read_start, 0)
self.assertEqual(res.read_end, 14)
# 5.c change ``distance_cutoff`` to 14
# (equal to the READ_SEQ length - 1)
res = a.align(
gap_open=3,
gap_extension=1,
bitwise_flag=BitwiseAlignmentFlag.distance_filter,
distance_cutoff=len(READ_SEQ) - 1,
)
self.assertEqual(res.CIGAR, '9M1I5M')
self.assertEqual(res.optimal_score, 21)
self.assertEqual(res.sub_optimal_score, 8)
self.assertEqual(res.reference_start, 8)
self.assertEqual(res.reference_end, 21)
self.assertEqual(res.read_start, 0)
self.assertEqual(res.read_end, 14)