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test_augment.py
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test_augment.py
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import numpy as np
from grelu.data.augment import Augmenter
from grelu.sequence.format import convert_input_type
seq = convert_input_type("ACGTAC", "indices")
label = np.array([0, 1, 2, 3, 4, 5], dtype=np.float32)
def test_augmenter_base():
aug = Augmenter(
rc=False, max_seq_shift=0, max_pair_shift=0, n_mutated_seqs=0, seed=0
)
assert len(aug) == 1
assert aug.max_values == [1, 1, 1, 1]
assert np.allclose(aug.products, [1, 1, 1, 1])
aug.mode = "serial"
for i in range(4):
assert aug._split(i) == [0, 0, 0, 0]
x = aug(seq=seq, idx=i)
assert np.allclose(x, seq)
x, y = aug(seq=seq, label=label, idx=i)
assert np.allclose(x, seq)
assert np.allclose(y, label)
aug.mode = "random"
for i in range(4):
assert aug._get_random_idxs() == [0, 0, 0, 0]
x = aug(seq=seq, idx=i)
assert np.allclose(x, seq)
x, y = aug(seq=seq, label=label, idx=i)
assert np.allclose(x, seq)
assert np.allclose(y, label)
def test_augmenter_rc():
aug = Augmenter(
rc=True,
max_seq_shift=0,
max_pair_shift=0,
n_mutated_seqs=0,
seed=0,
)
assert len(aug) == 2
assert aug.max_values == [2, 1, 1, 1]
assert np.allclose(aug.products, [1, 1, 1, 1])
# Cycle
aug.mode = "serial"
expected_seqs = [
"ACGTAC",
"GTACGT",
"ACGTAC",
"GTACGT",
]
xs = [aug(seq=seq, idx=i) for i in range(4)]
xs = [convert_input_type(x, "strings") for x in xs]
assert xs == expected_seqs
xs, ys = list(zip(*[aug(seq=seq, label=label, idx=i) for i in range(4)]))
xs = [convert_input_type(x, "strings") for x in xs]
assert xs == expected_seqs
assert np.allclose(
ys,
[
[0, 1, 2, 3, 4, 5],
[5, 4, 3, 2, 1, 0],
[0, 1, 2, 3, 4, 5],
[5, 4, 3, 2, 1, 0],
],
)
# Random
aug.mode = "random"
xs = [aug(seq=seq, idx=i) for i in range(4)]
xs = [convert_input_type(x, "strings") for x in xs]
assert xs == ["ACGTAC", "GTACGT", "GTACGT", "ACGTAC"]
xs, ys = list(zip(*[aug(seq=seq, label=label, idx=i) for i in range(4)]))
xs = [convert_input_type(x, "strings") for x in xs]
assert xs == ["GTACGT"] * 4
assert np.allclose(
ys,
[
[5, 4, 3, 2, 1, 0],
[5, 4, 3, 2, 1, 0],
[5, 4, 3, 2, 1, 0],
[5, 4, 3, 2, 1, 0],
],
)
def test_augmenter_seq_shift():
# Only seq shift
aug = Augmenter(
rc=False,
max_seq_shift=2,
max_pair_shift=0,
n_mutated_seqs=0,
seq_len=2,
)
assert len(aug) == 5
assert aug.max_values == [1, 5, 1, 1]
assert np.allclose(aug.products, [5, 1, 1, 1])
assert [aug._split(i) for i in range(5)] == [
[0, 0, 0, 0],
[0, 1, 0, 0],
[0, 2, 0, 0],
[0, 3, 0, 0],
[0, 4, 0, 0],
]
expected_seqs = ["AC", "CG", "GT", "TA", "AC"]
assert [
convert_input_type(aug(seq=seq, idx=i), "strings") for i in range(5)
] == expected_seqs
pairs = [aug(seq=seq, label=label, idx=i) for i in range(5)]
assert [convert_input_type(pair[0], "strings") for pair in pairs] == expected_seqs
assert np.allclose([pair[1] for pair in pairs], [[0, 1, 2, 3, 4, 5]] * 5)
def test_augmenter_pair_shift():
# Only pair shift
aug = Augmenter(
rc=False,
max_seq_shift=0,
max_pair_shift=2,
n_mutated_seqs=0,
seq_len=2,
label_len=2,
)
assert len(aug) == 5
assert aug.max_values == [1, 1, 5, 1]
assert np.allclose(aug.products, [5, 5, 1, 1])
assert [aug._split(i) for i in range(5)] == [
[0, 0, 0, 0],
[0, 0, 1, 0],
[0, 0, 2, 0],
[0, 0, 3, 0],
[0, 0, 4, 0],
]
expected_seqs = ["AC", "CG", "GT", "TA", "AC"]
assert [
convert_input_type(aug(seq=seq, idx=i), "strings") for i in range(5)
] == expected_seqs
pairs = [aug(seq=seq, label=label, idx=i) for i in range(5)]
assert [convert_input_type(pair[0], "strings") for pair in pairs] == expected_seqs
assert np.allclose(
[pair[1] for pair in pairs], [[0, 1], [1, 2], [2, 3], [3, 4], [4, 5]]
)
def test_augmenter_mutations():
# Only mutations
aug = Augmenter(
rc=False, max_seq_shift=0, max_pair_shift=0, n_mutated_seqs=2, n_mutated_bases=1
)
assert len(aug) == 2
assert aug.max_values == [1, 1, 1, 2]
assert np.allclose(aug.products, [2, 2, 2, 1])
assert [aug._split(i) for i in range(2)] == [
[0, 0, 0, 0],
[0, 0, 0, 1],
]
for i in range(2):
assert np.sum(aug(seq=seq, idx=i) != seq) == 1
x, y = aug(seq=seq, label=label, idx=i)
assert np.sum(x != seq) == 1
assert np.sum(y != label) == 0
# rc + seq shift
aug = Augmenter(
rc=True,
max_seq_shift=1,
max_pair_shift=0,
n_mutated_seqs=0,
seq_len=3,
)
assert len(aug) == 6
assert aug.max_values == [2, 3, 1, 1]
assert np.allclose(aug.products, [3, 1, 1, 1])
assert [aug._split(i) for i in range(6)] == [
[0, 0, 0, 0],
[0, 1, 0, 0],
[0, 2, 0, 0],
[1, 0, 0, 0],
[1, 1, 0, 0],
[1, 2, 0, 0],
]
expected_seqs = [
"ACG",
"CGT",
"GTA",
"CGT",
"ACG",
"TAC",
]
assert [
convert_input_type(aug(seq=seq[:-1], idx=i), "strings") for i in range(6)
] == expected_seqs
pairs = [aug(seq=seq, label=label, idx=i) for i in range(6)]
assert [convert_input_type(pair[0], "strings") for pair in pairs] == expected_seqs
assert np.allclose(
[pair[1] for pair in pairs],
[
[0, 1, 2, 3, 4, 5],
[0, 1, 2, 3, 4, 5],
[0, 1, 2, 3, 4, 5],
[5, 4, 3, 2, 1, 0],
[5, 4, 3, 2, 1, 0],
[5, 4, 3, 2, 1, 0],
],
)
def test_augmenter_composite():
# rc + seq shift + pair_shift
aug = Augmenter(
rc=True,
max_seq_shift=1,
max_pair_shift=1,
n_mutated_seqs=0,
seq_len=1,
label_len=1,
)
assert len(aug) == 18
assert aug.max_values == [2, 3, 3, 1]
assert np.allclose(aug.products, [9, 3, 1, 1])
assert [aug._split(i) for i in range(18)] == [
[0, 0, 0, 0],
[0, 0, 1, 0],
[0, 0, 2, 0],
[0, 1, 0, 0],
[0, 1, 1, 0],
[0, 1, 2, 0],
[0, 2, 0, 0],
[0, 2, 1, 0],
[0, 2, 2, 0],
[1, 0, 0, 0],
[1, 0, 1, 0],
[1, 0, 2, 0],
[1, 1, 0, 0],
[1, 1, 1, 0],
[1, 1, 2, 0],
[1, 2, 0, 0],
[1, 2, 1, 0],
[1, 2, 2, 0],
]
expected_seqs = [
"A",
"C",
"G",
"C",
"G",
"T",
"G",
"T",
"A",
"T",
"G",
"C",
"G",
"C",
"A",
"C",
"A",
"T",
]
assert [
convert_input_type(aug(seq=seq, idx=i), "strings") for i in range(18)
] == expected_seqs
pairs = [aug(seq=seq, label=label, idx=i) for i in range(18)]
assert [convert_input_type(pair[0], "strings") for pair in pairs] == expected_seqs
assert np.allclose(
np.concatenate([pair[1] for pair in pairs]).astype(int),
[
0,
1,
2,
0,
1,
2,
0,
1,
2,
0,
1,
2,
0,
1,
2,
0,
1,
2,
],
)