Python create_set_parts Examples

Example #1

File: test_parse_to_rates.py Project: brettc/partitionfinder

def test_axpi():
    set_parts = morph_tiger.create_set_parts(MORPH_ALIGN)
    axpi_0 = morph_tiger.axpi(set_parts[0], set_parts[1])
    assert axpi_0 == 0.5
    axpi_1 = morph_tiger.axpi(set_parts[0], set_parts[2])
    two_thirds = 2.0 / 3
    assert axpi_1 == two_thirds

Example #2

File: test_parse_to_rates.py Project: brettc/partitionfinder

def test_set_parts():
    set_parts = morph_tiger.create_set_parts(MORPH_ALIGN)
    assert set_parts == [
        [[0, 1, 3, 4]],
        [[3, 4], [0, 1, 2]],
        [[0, 1], [2], [3]],
        [[0, 1, 3, 4], [2]],
        [[3, 4], [0, 1, 2]],
        [[0, 1, 2], [3, 4]],
        [[0, 1], [3, 4]],
        [[0], [1, 2], [3], [4]],
        [[0, 1, 2, 3], [4]],
        [[0], [2, 3, 4]],
        [[1, 2, 3, 4], [0]],
        [[1, 3, 4], [0]],
        [[2, 3, 4], [0, 1]],
        [[2, 3], [0, 1, 4]],
        [[0, 1, 2, 3], [4]],
        [[1, 2, 3, 4], [0]],
        [[0, 1], [2, 3, 4]],
        [[2], [3], [0, 1, 4]],
        [[2], [0, 1, 3, 4]],
        [[2], [3], [0, 1, 4]],
        [[0], [3, 4]],
        [[0, 1, 2], [3, 4]],
        [[0, 1], [2, 3, 4]],
        [[0, 1, 2], [3, 4]],
        [[1], [0, 3, 4]],
    ]

Example #3

File: test_parse_to_rates.py Project: wangdang511/partitionfinder

def test_axpi():
    set_parts = morph_tiger.create_set_parts(MORPH_ALIGN)
    axpi_0 = morph_tiger.axpi(set_parts[0], set_parts[1])
    assert axpi_0 == 0.5
    axpi_1 = morph_tiger.axpi(set_parts[0], set_parts[2])
    two_thirds = 2.0 / 3
    assert axpi_1 == two_thirds

Example #4

File: test_parse_to_rates.py Project: wangdang511/partitionfinder

def test_set_parts():
    set_parts = morph_tiger.create_set_parts(MORPH_ALIGN)
    assert set_parts == [[[0, 1, 3, 4]], [[3, 4], [0, 1, 2]],
                         [[0, 1], [2], [3]], [[0, 1, 3, 4], [2]],
                         [[3, 4], [0, 1, 2]], [[0, 1, 2], [3, 4]],
                         [[0, 1], [3, 4]], [[0], [1, 2], [3], [4]],
                         [[0, 1, 2, 3], [4]], [[0], [2, 3, 4]],
                         [[1, 2, 3, 4], [0]], [[1, 3, 4], [0]],
                         [[2, 3, 4], [0, 1]], [[2, 3], [0, 1, 4]],
                         [[0, 1, 2, 3], [4]], [[1, 2, 3, 4], [0]],
                         [[0, 1], [2, 3, 4]], [[2], [3], [0, 1, 4]],
                         [[2], [0, 1, 3, 4]], [[2], [3], [0, 1, 4]],
                         [[0], [3, 4]], [[0, 1, 2], [3, 4]], [[0, 1],
                                                              [2, 3, 4]],
                         [[0, 1, 2], [3, 4]], [[1], [0, 3, 4]]]

Example #5

File: test_parse_to_rates.py Project: brettc/partitionfinder

def test_rates():
    set_parts = morph_tiger.create_set_parts(MORPH_ALIGN)
    rates = morph_tiger.calculate_rates(set_parts)
    print rates

Example #6

File: test_parse_to_rates.py Project: wangdang511/partitionfinder

def test_rates():
    set_parts = morph_tiger.create_set_parts(MORPH_ALIGN)
    rates = morph_tiger.calculate_rates(set_parts)
    print rates