def test_needleman_comparison_equal():
'''
Tests score comparison of equal alignments
'''
seq1 = "GCATGCU"
seq2 = "GATTACA"
needle1 = minineedle.NeedlemanWunsch(seq1, seq2)
needle1.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle1.align()
needle2 = minineedle.NeedlemanWunsch(seq1, seq2)
needle2.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle2.align()
assert (needle1 == needle2)
def test_needleman_comparison_lower():
'''
Tests score comparison of different alignments
'''
seq1 = "GCATGCU"
seq2 = "GATTACA"
seq3 = "LLLLLLL"
needle1 = minineedle.NeedlemanWunsch(seq1, seq2)
needle1.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle1.align()
needle2 = minineedle.NeedlemanWunsch(seq1, seq3)
needle2.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle2.align()
assert (needle1 > needle2)
def nwalign_and_compute_nw_score_naive(line_numbers_model, line_numbers_gaze):
if not line_numbers_model:
return 0
model = transform_line_order_to_sequence(line_numbers_model)
gaze = transform_line_order_to_sequence(line_numbers_gaze)
seq_model = ms.Sequence('Model', model)
seq_gaze = ms.Sequence('Actual', gaze)
alignment = minineedle.NeedlemanWunsch(seq_model, seq_gaze)
alignment.change_matrix(minineedle.ScoreMatrix(match=3, miss=-3, gap=-2))
try:
alignment.align()
#print(alignment)
score = alignment.get_score()
#print('score: ', str(score))
except ZeroDivisionError as e:
print('ZeroDivisionError when comparing the following numbers')
print('repeated ', line_numbers_model)
print('gaze ', line_numbers_gaze)
score = 0
return score
def test_strange_alignment():
seq1 = "TG--TA--CTA"
seq2 = "GG--TGA--CTA"
needle = minineedle.NeedlemanWunsch(seq1, seq2)
needle.change_matrix(minineedle.ScoreMatrix(2, -2, -3))
needle.align()
needle.gap_character = "+"
assert (needle.get_aligned_sequences("str")[0] == "TG--T+A--CTA")
def test_matrix_parameters():
'''
Checks if ScoreMatrix object rejects non-integer parameters.
'''
try:
matrix = minineedle.ScoreMatrix(1, 2, "b")
assert (1 == 0)
except ValueError:
assert (1 == 1)
def test_gap_change_alignment_before():
seq1 = "TGTTACGG"
seq2 = "GGTTGACTA"
needle = minineedle.NeedlemanWunsch(seq1, seq2)
needle.change_matrix(minineedle.ScoreMatrix(3, -3, -2))
needle.gap_character = "-gap-"
needle.align()
seq1, _ = needle.get_aligned_sequences(sequence_format="str")
assert (seq1 == "TGTT-gap-ACGG")
def test_smith_alignment_score():
'''
Checks if align method works
'''
seq1 = "TGTTACGG"
seq2 = "GGTTGACTA"
smith = minineedle.SmithWaterman(seq1, seq2)
smith.change_matrix(minineedle.ScoreMatrix(3, -3, -2))
smith.align()
assert (smith.get_score() == 13)
def test_needleman_alignment_identity():
'''
Tests if score is correctly computed.
'''
seq1 = "GCATGCU"
seq2 = "GATTACA"
needle = minineedle.NeedlemanWunsch(seq1, seq2)
needle.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle.align()
assert (needle.get_identity() == 50.0)
def test_needleman_alignment_integers():
'''
Tests if algorithm can handle integers
'''
seq1 = [1, 2, 3, 5, 1]
seq2 = [1, 2, 9, 9, 9, 3, 5, 1]
needle = minineedle.NeedlemanWunsch(seq1, seq2)
needle.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle.align()
assert (needle.get_score() == 2)
def test_needleman_alignment_score_different():
'''
Tests if score is correctly computed.
'''
seq1 = ["G", "C", "A", "T", "G", "C", "U"]
seq2 = "GATTACA"
needle = minineedle.NeedlemanWunsch(seq1, seq2)
needle.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle.align()
assert (needle.get_score() == 0)
def test_smith_alignment():
'''
Checks if align method works
'''
seq1 = "TGTTACGG"
seq2 = "GGTTGACTA"
smith = minineedle.SmithWaterman(seq1, seq2)
smith.change_matrix(minineedle.ScoreMatrix(3, -3, -2))
smith.align()
assert (smith.get_aligned_sequences()[0] == [
"G", "T", "T", minineedle.Gap(), "A", "C"
])
assert (smith.get_aligned_sequences()[1] == ["G", "T", "T", "G", "A", "C"])
def test_needleman_to_string():
'''
Tests string formatting of alignment object.
'''
seq1 = "GCATGCU"
seq2 = "GATTACA"
needle = minineedle.NeedlemanWunsch(seq1, seq2)
needle.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle.align()
assert (
str(needle) ==
"""Alignment of SEQUENCE 1 and SEQUENCE 2:\n\tGCA-TGCU\n\tG-ATTACA\n"""
)
def test_needleman_alignment_residue_mix():
'''
Tests if algorithm can handle different types in list
'''
seq1 = [1, "C", "A", 2, "G", "C", "U"]
seq2 = ["G", "A", "T", "T", "A", "C", "A"]
needle = minineedle.NeedlemanWunsch(seq1, seq2)
needle.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle.align()
try:
assert (1 == 1)
except ValueError:
assert (1 == 0)
def test_change_matrix_true():
'''
Tests if ScoreMatrix object is accepted by NeedlemanWunsch's change_matrix
method.
'''
seq1 = "ACTG"
seq2 = "ACTG"
matrix = minineedle.ScoreMatrix(1, -1, -1)
needle = minineedle.NeedlemanWunsch(seq1, seq2)
try:
needle.change_matrix(matrix)
assert (1 == 1)
except ValueError:
assert (1 == 0)
def test_needleman_alignment():
'''
Checks if align method works
'''
seq1 = "GCATGCU"
seq2 = "GATTACA"
needle = minineedle.NeedlemanWunsch(seq1, seq2)
needle.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle.align()
assert (needle._alseq1 == [
"G", "C", "A", minineedle.Gap(), "T", "G", "C", "U"
])
assert (needle._alseq2 == [
"G", minineedle.Gap(), "A", "T", "T", "A", "C", "A"
])
def test_needleman_dynamic_matrix():
'''
Checks if alignment score matrix is correct.
'''
seq1 = "GCATGCU"
seq2 = "GATTACA"
needle = minineedle.NeedlemanWunsch(seq1, seq2)
needle.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle.align()
expected_matrix = [[0, -1, -2, -3, -4, -5, -6, -7],
[-1, 1, 0, -1, -2, -3, -4, -5],
[-2, 0, 0, 1, 0, -1, -2, -3],
[-3, -1, -1, 0, 2, 1, 0, -1],
[-4, -2, -2, -1, 1, 1, 0, -1],
[-5, -3, -3, -1, 0, 0, 0, -1],
[-6, -4, -2, -2, -1, -1, 1, 0],
[-7, -5, -3, -1, -2, -2, 0, 0]]
assert (needle._nmatrix == expected_matrix)
def test_smith_dynamic_matrix():
'''
Checks if alignment score matrix is correct.
'''
seq1 = "TGTTACGG"
seq2 = "GGTTGACTA"
smith = minineedle.SmithWaterman(seq1, seq2)
smith.change_matrix(minineedle.ScoreMatrix(3, -3, -2))
smith.align()
expected_matrix = [[0, 0, 0, 0, 0, 0, 0, 0,
0], [0, 0, 3, 1, 0, 0, 0, 3, 3],
[0, 0, 3, 1, 0, 0, 0, 3,
6], [0, 3, 1, 6, 4, 2, 0, 1, 4],
[0, 3, 1, 4, 9, 7, 5, 3,
2], [0, 1, 6, 4, 7, 6, 4, 8, 6],
[0, 0, 4, 3, 5, 10, 8, 6, 5],
[0, 0, 2, 1, 3, 8, 13, 11, 9],
[0, 3, 1, 5, 4, 6, 11, 10, 8],
[0, 1, 0, 3, 2, 7, 9, 8, 7]]
assert (smith._nmatrix == expected_matrix)
def test_needleman_pointer_matrix():
'''
Tests if pointer matrix is correct.
'''
seq1 = "GCATGCU"
seq2 = "GATTACA"
needle = minineedle.NeedlemanWunsch(seq1, seq2)
needle.change_matrix(minineedle.ScoreMatrix(1, -1, -1))
needle.align()
expected_matrix = [
[None, 'left', 'left', 'left', 'left', 'left', 'left', 'left'],
['up', 'diag', 'left', 'left', 'left', 'diag', 'left', 'left'],
['up', 'up', 'diag', 'diag', 'left', 'left', 'left', 'left'],
['up', 'up', 'diag', 'up', 'diag', 'left', 'left', 'left'],
['up', 'up', 'diag', 'up', 'diag', 'diag', 'diag', 'diag'],
['up', 'up', 'diag', 'diag', 'up', 'diag', 'diag', 'diag'],
['up', 'up', 'diag', 'up', 'up', 'diag', 'diag', 'left'],
['up', 'up', 'up', 'diag', 'left', 'diag', 'up', 'diag']
]
assert (needle._pmatrix == expected_matrix)
