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"