def setUp(self):
"""Setup for NeedlemanWunschMatrix tests."""
self.nw_matrix = NeedlemanWunschMatrix('ACGU', 'CAGU')
#Since _init_first_row, _init_first_col and _init_first_cell are
#automatically called when NeedlemanWunschMatrix is initialized,
#need to change all elements in nw_matrix_empty to 0 to test
#that each _init works.
self.nw_matrix_empty = \
NeedlemanWunschMatrix('ACGU','CAGU')
for i in range(len(self.nw_matrix_empty)):
for j in range(len(self.nw_matrix_empty[i])):
self.nw_matrix_empty[i][j] = ScoreCell(0)
def setUp(self):
"""Setup for NeedlemanWunschMatrix tests."""
self.nw_matrix = NeedlemanWunschMatrix("ACGU", "CAGU")
# Since _init_first_row, _init_first_col and _init_first_cell are
# automatically called when NeedlemanWunschMatrix is initialized,
# need to change all elements in nw_matrix_empty to 0 to test
# that each _init works.
self.nw_matrix_empty = NeedlemanWunschMatrix("ACGU", "CAGU")
for i in range(len(self.nw_matrix_empty)):
for j in range(len(self.nw_matrix_empty[i])):
self.nw_matrix_empty[i][j] = ScoreCell(0)
class NeedlemanWunschMatrixTests(TestCase):
"""Tests for NeedlemanWunschMatrix class.
"""
def setUp(self):
"""Setup for NeedlemanWunschMatrix tests."""
self.nw_matrix = NeedlemanWunschMatrix('ACGU', 'CAGU')
#Since _init_first_row, _init_first_col and _init_first_cell are
#automatically called when NeedlemanWunschMatrix is initialized,
#need to change all elements in nw_matrix_empty to 0 to test
#that each _init works.
self.nw_matrix_empty = \
NeedlemanWunschMatrix('ACGU','CAGU')
for i in range(len(self.nw_matrix_empty)):
for j in range(len(self.nw_matrix_empty[i])):
self.nw_matrix_empty[i][j] = ScoreCell(0)
def test_init_first_row(self):
"""Tests for NeedlemanWunschMatrix _init_first_row function."""
nw_matrix_empty = copy(self.nw_matrix_empty)
#Init first row
nw_matrix_empty._init_first_row()
#matrix after first row init
matrix_scores_first_row_init = [[0, -1, -2, -3, -4], [0, 0, 0, 0, 0],
[0, 0, 0, 0, 0], [0, 0, 0, 0, 0],
[0, 0, 0, 0, 0]]
for i in range(len(nw_matrix_empty)):
for j in range(len(nw_matrix_empty[i])):
self.assertEqual(nw_matrix_empty[i][j].Score,\
matrix_scores_first_row_init[i][j])
def test_init_first_col(self):
"""Tests for NeedlemanWunschMatrix _init_first_col function."""
nw_matrix_empty = copy(self.nw_matrix_empty)
#Init first row
nw_matrix_empty._init_first_col()
#matrix after first row init
matrix_scores_first_row_init = [[0, 0, 0, 0, 0], [-1, 0, 0, 0, 0],
[-2, 0, 0, 0, 0], [-3, 0, 0, 0, 0],
[-4, 0, 0, 0, 0]]
for i in range(len(nw_matrix_empty)):
for j in range(len(nw_matrix_empty[i])):
self.assertEqual(nw_matrix_empty[i][j].Score,\
matrix_scores_first_row_init[i][j])
def test_init_first_cell(self):
"""Tests for NeedlemanWunschMatrix _init_first_cell function."""
nw_matrix_empty = copy(self.nw_matrix_empty)
#Init first row
nw_matrix_empty._init_first_cell()
self.assertEqual(nw_matrix_empty[0][0].Score, 0)
def test_initialized_matrix(self):
"""Tests for NeedlemanWunschMatrix after full initialization."""
matrix_scores_first_row_init = [[0, -1, -2, -3, -4], [-1, 0, 0, 0, 0],
[-2, 0, 0, 0, 0], [-3, 0, 0, 0, 0],
[-4, 0, 0, 0, 0]]
for i in range(len(self.nw_matrix)):
for j in range(len(self.nw_matrix[i])):
self.assertEqual(self.nw_matrix[i][j].Score,\
matrix_scores_first_row_init[i][j])
def test_fill(self):
"""Tests for NeedlemanWunschMatrix fill function."""
filled_nw_matrix = copy(self.nw_matrix)
filled_nw_matrix.fill()
matrix_scores_filled = [[0, -1, -2, -3, -4], [-1, -1, 0, -1, -2],
[-2, 0, -1, -1, -2], [-3, -1, -1, 0, -1],
[-4, -2, -2, -1, 1]]
matrix_pointers_filled = [[None, 'left', 'left', 'left', 'left'],
['up', 'diag', 'diag', 'left', 'left'],
['up', 'diag', 'up', 'diag', 'diag'],
['up', 'up', 'diag', 'diag', 'left'],
['up', 'up', 'up', 'up', 'diag']]
self.assertEqual(filled_nw_matrix.Filled, True)
for i in range(len(filled_nw_matrix)):
for j in range(len(filled_nw_matrix[i])):
self.assertEqual(filled_nw_matrix[i][j].Score,\
matrix_scores_filled[i][j])
self.assertEqual(filled_nw_matrix[i][j].Pointer,\
matrix_pointers_filled[i][j])
self.assertEqual(filled_nw_matrix.MaxScore, (1, 4, 4))
def test_traceback(self):
"""Tests for NeedlemanWunschMatrix traceback function."""
self.nw_matrix.traceback()
self.assertEqual(self.nw_matrix.FirstAlign, ['A', 'C', '-', 'G', 'U'])
self.assertEqual(self.nw_matrix.SecondAlign, ['-', 'C', 'A', 'G', 'U'])
class NeedlemanWunschMatrixTests(TestCase):
"""Tests for NeedlemanWunschMatrix class.
"""
def setUp(self):
"""Setup for NeedlemanWunschMatrix tests."""
self.nw_matrix = NeedlemanWunschMatrix("ACGU", "CAGU")
# Since _init_first_row, _init_first_col and _init_first_cell are
# automatically called when NeedlemanWunschMatrix is initialized,
# need to change all elements in nw_matrix_empty to 0 to test
# that each _init works.
self.nw_matrix_empty = NeedlemanWunschMatrix("ACGU", "CAGU")
for i in range(len(self.nw_matrix_empty)):
for j in range(len(self.nw_matrix_empty[i])):
self.nw_matrix_empty[i][j] = ScoreCell(0)
def test_init_first_row(self):
"""Tests for NeedlemanWunschMatrix _init_first_row function."""
nw_matrix_empty = copy(self.nw_matrix_empty)
# Init first row
nw_matrix_empty._init_first_row()
# matrix after first row init
matrix_scores_first_row_init = [
[0, -1, -2, -3, -4],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
]
for i in range(len(nw_matrix_empty)):
for j in range(len(nw_matrix_empty[i])):
self.assertEqual(nw_matrix_empty[i][j].Score, matrix_scores_first_row_init[i][j])
def test_init_first_col(self):
"""Tests for NeedlemanWunschMatrix _init_first_col function."""
nw_matrix_empty = copy(self.nw_matrix_empty)
# Init first row
nw_matrix_empty._init_first_col()
# matrix after first row init
matrix_scores_first_row_init = [
[0, 0, 0, 0, 0],
[-1, 0, 0, 0, 0],
[-2, 0, 0, 0, 0],
[-3, 0, 0, 0, 0],
[-4, 0, 0, 0, 0],
]
for i in range(len(nw_matrix_empty)):
for j in range(len(nw_matrix_empty[i])):
self.assertEqual(nw_matrix_empty[i][j].Score, matrix_scores_first_row_init[i][j])
def test_init_first_cell(self):
"""Tests for NeedlemanWunschMatrix _init_first_cell function."""
nw_matrix_empty = copy(self.nw_matrix_empty)
# Init first row
nw_matrix_empty._init_first_cell()
self.assertEqual(nw_matrix_empty[0][0].Score, 0)
def test_initialized_matrix(self):
"""Tests for NeedlemanWunschMatrix after full initialization."""
matrix_scores_first_row_init = [
[0, -1, -2, -3, -4],
[-1, 0, 0, 0, 0],
[-2, 0, 0, 0, 0],
[-3, 0, 0, 0, 0],
[-4, 0, 0, 0, 0],
]
for i in range(len(self.nw_matrix)):
for j in range(len(self.nw_matrix[i])):
self.assertEqual(self.nw_matrix[i][j].Score, matrix_scores_first_row_init[i][j])
def test_fill(self):
"""Tests for NeedlemanWunschMatrix fill function."""
filled_nw_matrix = copy(self.nw_matrix)
filled_nw_matrix.fill()
matrix_scores_filled = [
[0, -1, -2, -3, -4],
[-1, -1, 0, -1, -2],
[-2, 0, -1, -1, -2],
[-3, -1, -1, 0, -1],
[-4, -2, -2, -1, 1],
]
matrix_pointers_filled = [
[None, "left", "left", "left", "left"],
["up", "diag", "diag", "left", "left"],
["up", "diag", "up", "diag", "diag"],
["up", "up", "diag", "diag", "left"],
["up", "up", "up", "up", "diag"],
]
self.assertEqual(filled_nw_matrix.Filled, True)
for i in range(len(filled_nw_matrix)):
for j in range(len(filled_nw_matrix[i])):
self.assertEqual(filled_nw_matrix[i][j].Score, matrix_scores_filled[i][j])
self.assertEqual(filled_nw_matrix[i][j].Pointer, matrix_pointers_filled[i][j])
self.assertEqual(filled_nw_matrix.MaxScore, (1, 4, 4))
def test_traceback(self):
"""Tests for NeedlemanWunschMatrix traceback function."""
self.nw_matrix.traceback()
self.assertEqual(self.nw_matrix.FirstAlign, ["A", "C", "-", "G", "U"])
self.assertEqual(self.nw_matrix.SecondAlign, ["-", "C", "A", "G", "U"])