コード例 #1
0
 def test_single_location_two_segments_uneven(self):
     mother = MagicMock()
     mother.starts = np.array([0, 5], dtype = np.uint32)
     mother.end = 20
     mother.founder = np.array([1, 2], dtype = np.uint32)
     father = MagicMock()
     father.starts = np.array([0, 10], dtype = np.uint32)
     father.end = 20
     father.founder = np.array([3, 4], dtype = np.uint32)
     locations = [(2, 11)]
     new_mother, new_father = recomb_genome._swap_at_locations(mother,
                                                               father,
                                                               locations)
     np.testing.assert_array_equal(new_mother.starts,
                                   np.array([0, 2, 10, 11],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_mother.founder,
                                   np.array([1, 3, 4, 2],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_father.starts,
                                   np.array([0, 2, 5, 11],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_father.founder,
                                   np.array([3, 1, 2, 4],
                                            dtype = np.uint32))
コード例 #2
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 def test_single_location_two_segments_uneven(self):
     mother = MagicMock()
     mother.starts = np.array([0, 5], dtype = np.uint32)
     mother.end = 20
     mother.founder = np.array([1, 2], dtype = np.uint32)
     father = MagicMock()
     father.starts = np.array([0, 10], dtype = np.uint32)
     father.end = 20
     father.founder = np.array([3, 4], dtype = np.uint32)
     locations = [(2, 11)]
     new_mother, new_father = recomb_genome._swap_at_locations(mother,
                                                               father,
                                                               locations)
     np.testing.assert_array_equal(new_mother.starts,
                                   np.array([0, 2, 10, 11],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_mother.founder,
                                   np.array([1, 3, 4, 2],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_father.starts,
                                   np.array([0, 2, 5, 11],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_father.founder,
                                   np.array([3, 1, 2, 4],
                                            dtype = np.uint32))
コード例 #3
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 def test_two_locations_at_boundary_two_segments (self):
     mother = MagicMock()
     mother.starts = np.array([0, 10], dtype = np.uint32)
     mother.end = 20
     mother.founder = np.array([1, 2], dtype = np.uint32)
     father = MagicMock()
     father.starts = np.array([0, 10], dtype = np.uint32)
     father.end = 20
     father.founder = np.array([3, 4], dtype = np.uint32)
     locations = [(0, 5), (15, 20)]
     new_mother, new_father = recomb_genome._swap_at_locations(mother,
                                                               father,
                                                               locations)
     np.testing.assert_array_equal(new_mother.starts,
                                   np.array([0, 5, 10, 15],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_mother.founder,
                                   np.array([3, 1, 2, 4],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_father.starts,
                                   np.array([0, 5, 10, 15],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_father.founder,
                                   np.array([1, 3, 4, 2],
                                            dtype = np.uint32))
コード例 #4
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 def test_two_locations_at_boundary_two_segments (self):
     mother = MagicMock()
     mother.starts = np.array([0, 10], dtype = np.uint32)
     mother.end = 20
     mother.founder = np.array([1, 2], dtype = np.uint32)
     father = MagicMock()
     father.starts = np.array([0, 10], dtype = np.uint32)
     father.end = 20
     father.founder = np.array([3, 4], dtype = np.uint32)
     locations = [(0, 5), (15, 20)]
     new_mother, new_father = recomb_genome._swap_at_locations(mother,
                                                               father,
                                                               locations)
     np.testing.assert_array_equal(new_mother.starts,
                                   np.array([0, 5, 10, 15],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_mother.founder,
                                   np.array([3, 1, 2, 4],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_father.starts,
                                   np.array([0, 5, 10, 15],
                                            dtype = np.uint32))
     np.testing.assert_array_equal(new_father.founder,
                                   np.array([1, 3, 4, 2],
                                            dtype = np.uint32))
コード例 #5
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 def test_multiple_locations_single_segment(self):
     mother = MagicMock()
     mother.starts = np.array([0], dtype = np.uint32)
     mother.end = 10
     mother.founder = np.array([1], dtype = np.uint32)
     father = MagicMock()
     father.starts = np.array([0], dtype = np.uint32)
     father.end = 10
     father.founder = np.array([2], dtype = np.uint32)
     locations = [(0, 4), (6, 10)]
     new_mother, new_father = recomb_genome._swap_at_locations(mother,
                                                               father,
                                                               locations)
     np.testing.assert_array_equal(new_mother.starts,
                                   np.array([0, 4, 6], dtype = np.uint32))
     np.testing.assert_array_equal(new_mother.founder,
                                   np.array([2, 1, 2], dtype = np.uint32))
     np.testing.assert_array_equal(new_father.starts,
                                   np.array([0, 4, 6], dtype = np.uint32))
     np.testing.assert_array_equal(new_father.founder,
                                   np.array([1, 2, 1], dtype = np.uint32))
コード例 #6
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 def test_single_location_middle_boundary(self):
     mother = MagicMock()
     mother.starts = np.array([0], dtype = np.uint32)
     mother.end = 10
     mother.founder = np.array([1], dtype = np.uint32)
     father = MagicMock()
     father.starts = np.array([0], dtype = np.uint32)
     father.end = 10
     father.founder = np.array([2], dtype = np.uint32)
     locations = [(2, 8)]
     new_mother, new_father = recomb_genome._swap_at_locations(mother,
                                                               father,
                                                               locations)
     np.testing.assert_array_equal(new_mother.starts,
                      np.array([0, 2, 8], dtype = np.uint32))
     np.testing.assert_array_equal(new_mother.founder,
                      np.array([1, 2, 1], dtype = np.uint32))
     np.testing.assert_array_equal(new_father.starts,
                      np.array([0, 2, 8], dtype = np.uint32))
     np.testing.assert_array_equal(new_father.founder,
                      np.array([2, 1, 2], dtype = np.uint32))
コード例 #7
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 def test_single_location_left_boundary(self):
     mother = MagicMock()
     mother.starts = np.array([0], dtype = np.uint32)
     mother.end = 10
     mother.founder = np.array([1], dtype = np.uint32)
     father = MagicMock()
     father.starts = np.array([0], dtype = np.uint32)
     father.end = 10
     father.founder = np.array([2], dtype = np.uint32)
     locations = [(0, 5)]
     new_mother, new_father = recomb_genome._swap_at_locations(mother,
                                                               father,
                                                               locations)
     np.testing.assert_array_equal(new_mother.starts,
                                   np.array([0, 5], dtype = np.uint32))
     np.testing.assert_array_equal(new_mother.founder,
                                   np.array([2, 1], dtype = np.uint32))
     np.testing.assert_array_equal(new_father.starts,
                                   np.array([0, 5], dtype = np.uint32))
     np.testing.assert_array_equal(new_father.founder,
                                   np.array([1, 2], dtype = np.uint32))
コード例 #8
0
 def test_multiple_locations_single_segment(self):
     mother = MagicMock()
     mother.starts = np.array([0], dtype = np.uint32)
     mother.end = 10
     mother.founder = np.array([1], dtype = np.uint32)
     father = MagicMock()
     father.starts = np.array([0], dtype = np.uint32)
     father.end = 10
     father.founder = np.array([2], dtype = np.uint32)
     locations = [(0, 4), (6, 10)]
     new_mother, new_father = recomb_genome._swap_at_locations(mother,
                                                               father,
                                                               locations)
     np.testing.assert_array_equal(new_mother.starts,
                                   np.array([0, 4, 6], dtype = np.uint32))
     np.testing.assert_array_equal(new_mother.founder,
                                   np.array([2, 1, 2], dtype = np.uint32))
     np.testing.assert_array_equal(new_father.starts,
                                   np.array([0, 4, 6], dtype = np.uint32))
     np.testing.assert_array_equal(new_father.founder,
                                   np.array([1, 2, 1], dtype = np.uint32))