def test3():
# Insertions in middle of strings and strings are of different lengths
str1 = [('m', .5), ('M', .05), ('m', .4), ('M', .7), ('m', .3)]
str2 = [('m', .5), ('M', .75), ('m', .33)]
mat = sg.get_alignmentmat(str1, str2)
alignment = sg.get_bestalignment_index(str1, str2)
assert (alignment == ([('m', (0.5, 0.5)), ('M', (0.05, 0)),
('m', (0.4, 0)), ('M', (0.7, 0.75)),
('m', (0.3, 0.33))], [(0, 0), (1, 'None'),
(2, 'None'), (3, 1), (4, 2)]))
alignment_cost = sum((abs(alignment[0][i][1][0] - alignment[0][i][1][1]))
for i in range(len(alignment[0])))
assert (alignment_cost == mat[len(mat) - 1][len(mat[0]) - 1])
def test4():
# No diagonal moves in traceback
str1 = [('a', .5), ('b', .05), ('c', .6), ('d', .7), ('e', .3)]
str2 = [('f', .4), ('g', .75), ('h', .33)]
mat = sg.get_alignmentmat(str1, str2)
alignment = sg.get_bestalignment_index(str1, str2)
assert (alignment == ([('f', (0, 0.4)), ('g', (0, 0.75)), ('h', (0, 0.33)),
('a', (0.5, 0)), ('b', (0.05, 0)), ('c', (0.6, 0)),
('d', (0.7, 0)), ('e', (0.3, 0))], [('None', 0),
('None', 1),
('None', 2),
(0, 'None'),
(1, 'None'),
(2, 'None'),
(3, 'None'),
(4, 'None')]))
alignment_cost = sum((abs(alignment[0][i][1][0] - alignment[0][i][1][1]))
for i in range(len(alignment[0])))
assert (alignment_cost == mat[len(mat) - 1][len(mat[0]) - 1])
def test1():
# Insertions at ends
str1 = [('m', .5), ('M', .75), ('m', .9), ('M', .3)]
str2 = [('M', .25), ('m', .5), ('M', .7), ('m', .8)]
mat = sg.get_alignmentmat(str1, str2)
assert (mat == [[0, 0.25, 0.75, 1.45, 2.25], [0.5, 0.75, 0.25, 0.95, 1.75],
[1.25, 1.0, 1.0, 0.30000000000000004, 1.1],
[2.15, 1.9, 1.4, 1.2000000000000002, 0.4],
[
2.4499999999999997, 2.1999999999999997, 1.7,
1.5000000000000002, 0.7
]])
alignment = sg.get_bestalignment_index(str1, str2)
assert (alignment == ([('M', (0, 0.25)), ('m', (0.5, 0.5)),
('M', (0.75, 0.7)), ('m', (0.9, 0.8)),
('M', (0.3, 0))], [('None', 0), (0, 1), (1, 2),
(2, 3), (3, 'None')]))
alignment_cost = sum((abs(alignment[0][i][1][0] - alignment[0][i][1][1]))
for i in range(len(alignment[0])))
assert (alignment_cost == mat[len(mat) - 1][len(mat[0]) - 1])
def test2():
# Insertions at beginning & strings are of different lengths
# NOTE there are two optimal alignments in this example
str1 = [('m', .5), ('M', .05), ('m', .6), ('M', .7), ('m', .3)]
str2 = [('m', .4), ('M', .75), ('m', .33)]
mat = sg.get_alignmentmat(str1, str2)
assert (mat == [[0, 0.4, 1.15, 1.48],
[0.5, 0.09999999999999998, 0.85, 1.18],
[0.55, 0.14999999999999997, 0.7999999999999999, 1.13],
[1.15, 0.75, 1.4, 1.0699999999999998],
[1.8499999999999999, 1.45, 0.8, 1.1300000000000001],
[2.15, 1.75, 1.1, 0.8300000000000001]])
alignment = sg.get_bestalignment_index(str1, str2)
assert (alignment == ([('m', (0.5, 0)), ('M', (0.05, 0)),
('m', (0.6, 0.4)), ('M', (0.7, 0.75)),
('m', (0.3, 0.33))], [(0, 'None'), (1, 'None'),
(2, 0), (3, 1), (4, 2)]))
alignment_cost = sum((abs(alignment[0][i][1][0] - alignment[0][i][1][1]))
for i in range(len(alignment[0])))
assert (alignment_cost == mat[len(mat) - 1][len(mat[0]) - 1])