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_gap_char_change():
'''
Checks change of Gap character
'''
gap = minineedle.Gap()
gap.character = "imagap"
assert (str(gap) == "imagap")
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_gap_char():
gap = minineedle.Gap("a")
assert (str(gap) == "a")
def test_gap_equal():
g1 = minineedle.Gap()
g2 = minineedle.Gap()
assert (g1 == g2)