def test_create_bucket():
seq = "banana"
bwt = BwtManberMyers(seq)
stage = 1
assert bwt._create_bucket([0, 1, 2, 3, 4, 5, 6], seq, stage) == {
'b': [0],
'a': [1, 3, 5],
'n': [2, 4],
'': [6]
}
seq = "abracadabra"
bwt = BwtManberMyers(seq)
stage = 1
assert bwt._create_bucket([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11], seq,
stage) == {
'a': [0, 3, 5, 7, 10],
'b': [1, 8],
'r': [2, 9],
'c': [4],
'd': [6],
'': [11]
}
seq = "STETSTESTE$"
bwt = BwtManberMyers(seq)
stage = 1
assert bwt._create_bucket([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10], seq,
stage) == {
'E': [2, 6, 9],
'S': [0, 4, 7],
'T': [1, 3, 5, 8],
'$': [10]
}
def main():
# Example usage
seq = "STETSTESTE"
bwt = BwtManberMyers(seq, debug=True)
print(f"Transforming {bwt.seq} using BWT:")
transformed_seq = bwt.transform()
print(f"Transformed sequence: {transformed_seq}")
suffix_array = bwt.suffixes
print(f"Corresponding suffix array: {suffix_array}")
print(f"\nRetransforming {transformed_seq}:")
retransformed_seq = bwt.retransform(transformed_seq, suffix_array)
print(f"Original sequence: {retransformed_seq}")
def test_retransform():
bwt = BwtManberMyers("")
bwt_seq = "annb$aa"
suffixes = [6, 5, 3, 1, 0, 4, 2]
assert bwt.retransform(bwt_seq, suffixes) == "banana$"
bwt_seq = "ard$rcaaaabb"
suffixes = [11, 10, 7, 0, 3, 5, 8, 1, 4, 6, 9, 2]
assert bwt.retransform(bwt_seq, suffixes) == "abracadabra$"
bwt_seq = "ETTTET$SSSE"
suffixes = [10, 9, 6, 2, 7, 4, 0, 8, 5, 1, 3]
assert bwt.retransform(bwt_seq, suffixes) == "STETSTESTE$"
def test_transform():
seq = "banana"
bwt = BwtManberMyers(seq)
assert bwt.transform() == "annb$aa"
seq = "abracadabra"
bwt = BwtManberMyers(seq)
assert bwt.transform() == "ard$rcaaaabb"
seq = "STETSTESTE$"
bwt = BwtManberMyers(seq)
assert bwt.transform() == "ETTTET$SSSE"
def test_get_bwt_seq():
seq = "banana$"
bwt = BwtManberMyers(seq)
suffixes = [6, 5, 3, 1, 0, 4, 2]
assert bwt._get_bwt_seq(seq, suffixes) == "annb$aa"
seq = "abracadabra$"
bwt = BwtManberMyers(seq)
suffixes = [11, 10, 7, 0, 3, 5, 8, 1, 4, 6, 9, 2]
assert bwt._get_bwt_seq(seq, suffixes) == "ard$rcaaaabb"
seq = "STETSTESTE$"
bwt = BwtManberMyers(seq)
suffixes = [10, 9, 6, 2, 7, 4, 0, 8, 5, 1, 3]
assert bwt._get_bwt_seq(seq, suffixes) == "ETTTET$SSSE"
def test_get_manber_myers_suffixes():
seq = "banana"
bwt = BwtManberMyers(seq)
assert bwt._get_manber_myers_suffixes(seq) == [5, 3, 1, 0, 4, 2]
seq = "abracadabra"
bwt = BwtManberMyers(seq)
assert bwt._get_manber_myers_suffixes(seq) == [
10, 7, 0, 3, 5, 8, 1, 4, 6, 9, 2
]
seq = "STETSTESTE$"
bwt = BwtManberMyers(seq)
assert bwt._get_manber_myers_suffixes(seq) == [
10, 9, 6, 2, 7, 4, 0, 8, 5, 1, 3
]
def test_sort_manber_myers():
seq = "banana"
bwt = BwtManberMyers(seq)
assert bwt._sort_manber_myers([0, 1, 2, 3, 4, 5,
6]) == [6, 5, 3, 1, 0, 4, 2]
seq = "abracadabra"
bwt = BwtManberMyers(seq)
assert bwt._sort_manber_myers(
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11]) == [11, 10, 7, 0, 3, 5, 8, 1, 4, 6, 9, 2]
seq = "STETSTESTE$"
bwt = BwtManberMyers(seq)
assert bwt._sort_manber_myers([0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
10]) == [10, 9, 6, 2, 7, 4, 0, 8, 5, 1, 3]
def test_validate_input_sequence():
bwt = BwtManberMyers("")
assert bwt._validate_input_sequence("banana") == "banana$"
assert bwt._validate_input_sequence("banana$") == "banana$"
with pytest.raises(ValueError, match=r".*$.*"):
bwt._validate_input_sequence("ban$ana")