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'
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):
one_hot(['A', 'C'])
with pytest.raises(ValueError):
one_hot_dna(['A', 'C'])
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"