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))
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))
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))
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))
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))
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))
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))
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))