Beispiel #1
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)
Beispiel #2
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)
Beispiel #3
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'])
Beispiel #4
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"])