How to use the kipoiseq.transforms.functional.fixed_len function in kipoiseq

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github kipoi / kipoiseq / tests / test_0_transforms_functional.py View on Github external
def test_pad_sequences():
    seq = 'CTTACTCAGA'
    assert fixed_len(seq, 4, anchor="center", value="N") == 'ACTC'
    assert fixed_len(seq, 9, anchor="start", value="N") == 'CTTACTCAG'

    assert fixed_len(seq, 10, anchor="start", value="N") == seq
    assert fixed_len(seq, 10, anchor="end", value="N") == 'CTTACTCAGA'
github kipoi / kipoiseq / tests / test_0_transforms_functional.py View on Github external
def test_pad_sequences():
    seq = 'CTTACTCAGA'
    assert fixed_len(seq, 4, anchor="center", value="N") == 'ACTC'
    assert fixed_len(seq, 9, anchor="start", value="N") == 'CTTACTCAG'

    assert fixed_len(seq, 10, anchor="start", value="N") == seq
    assert fixed_len(seq, 10, anchor="end", value="N") == 'CTTACTCAGA'
github kipoi / kipoiseq / tests / test_0_transforms_functional.py View on Github external
def test_fixed_len():
    seq = "ACGTTTATNT"
    assert len(fixed_len(seq, 20, value="N", anchor="end")) is 20
    assert fixed_len([1, 2, 3, 4], 6, value=[0],
                     anchor="end") == [0, 0, 1, 2, 3, 4]
    assert fixed_len([1, 2, 3, 4], 2, value=[0], anchor="end") == [3, 4]

    # expect error
    assert fixed_len(seq, length=3, value="NNN", anchor="end") == "TNT"
github kipoi / kipoiseq / tests / test_0_transforms_functional.py View on Github external
def test_fixed_len():
    seq = "ACGTTTATNT"
    assert len(fixed_len(seq, 20, value="N", anchor="end")) is 20
    assert fixed_len([1, 2, 3, 4], 6, value=[0],
                     anchor="end") == [0, 0, 1, 2, 3, 4]
    assert fixed_len([1, 2, 3, 4], 2, value=[0], anchor="end") == [3, 4]

    # expect error
    assert fixed_len(seq, length=3, value="NNN", anchor="end") == "TNT"
github kipoi / kipoiseq / tests / test_0_transforms_functional.py View on Github external
def test_fixed_len():
    seq = "ACGTTTATNT"
    assert len(fixed_len(seq, 20, value="N", anchor="end")) is 20
    assert fixed_len([1, 2, 3, 4], 6, value=[0],
                     anchor="end") == [0, 0, 1, 2, 3, 4]
    assert fixed_len([1, 2, 3, 4], 2, value=[0], anchor="end") == [3, 4]

    # expect error
    assert fixed_len(seq, length=3, value="NNN", anchor="end") == "TNT"
github kipoi / kipoiseq / tests / test_0_transforms_functional.py View on Github external
def test_one_hot():

    seq = "ACGTTTATNT"
    assert len(seq) == 10

    assert one_hot_dna(seq).shape == (10, 4)
    assert one_hot(seq).shape == (10, 4)

    assert np.all(one_hot_dna(seq) == one_hot(seq))

    assert one_hot(pad(seq, 20)).shape == (20, 4)

    assert one_hot(fixed_len(seq, 20)).shape == (20, 4)
    assert one_hot(fixed_len(seq, 5)).shape == (5, 4)
    assert trim(seq, 5) == 'TTTAT'
    assert trim(seq, 5, 'start') == 'ACGTT'
    assert trim(seq, 5, 'end') == 'TATNT'
    with pytest.raises(Exception):
        assert pad(seq, 5, 'end') == 'TATNT'

    assert np.all(one_hot(seq)[0] == np.array([1, 0, 0, 0]))
    assert np.all(one_hot(seq)[1] == np.array([0, 1, 0, 0]))
    assert np.all(one_hot(seq)[2] == np.array([0, 0, 1, 0]))
    assert np.all(one_hot(seq)[3] == np.array([0, 0, 0, 1]))
    assert np.all(one_hot(seq)[4] == np.array([0, 0, 0, 1]))
    assert np.all(one_hot(seq)[-1] == np.array([0, 0, 0, 1]))
    assert np.all(one_hot(seq)[-2] == np.array([0.25, 0.25, 0.25, 0.25]))

    with pytest.raises(ValueError):
github kipoi / kipoiseq / tests / test_0_transforms_functional.py View on Github external
def test_fixed_len():
    seq = "ACGTTTATNT"
    assert len(fixed_len(seq, 20, value="N", anchor="end")) is 20
    assert fixed_len([1, 2, 3, 4], 6, value=[0],
                     anchor="end") == [0, 0, 1, 2, 3, 4]
    assert fixed_len([1, 2, 3, 4], 2, value=[0], anchor="end") == [3, 4]

    # expect error
    assert fixed_len(seq, length=3, value="NNN", anchor="end") == "TNT"
github kipoi / kipoiseq / tests / test_0_transforms_functional.py View on Github external
def test_pad_sequences():
    seq = 'CTTACTCAGA'
    assert fixed_len(seq, 4, anchor="center", value="N") == 'ACTC'
    assert fixed_len(seq, 9, anchor="start", value="N") == 'CTTACTCAG'

    assert fixed_len(seq, 10, anchor="start", value="N") == seq
    assert fixed_len(seq, 10, anchor="end", value="N") == 'CTTACTCAGA'