def test_stats_table(self):
s1 = "QQEGIL"
s2 = "QQQERGII"
res = align(s1, s2, 10, 1, method='nw', stats=True,
table=True, matrix=parasail.pam10)
nptest.assert_array_equal(
res.matches_table, np.array(
[[1, 1, 1, 1, 1, 1, 1, 1],
[1, 2, 2, 2, 2, 2, 2, 2],
[1, 2, 2, 3, 2, 2, 2, 2],
[1, 2, 2, 2, 3, 3, 3, 3],
[1, 2, 2, 3, 2, 3, 4, 4],
[1, 2, 2, 3, 2, 3, 4, 4]]))
nptest.assert_array_equal(
res.similar_table, np.array(
[[1, 1, 1, 1, 1, 1, 1, 1],
[1, 2, 2, 2, 2, 2, 2, 2],
[1, 2, 2, 3, 2, 2, 2, 2],
[1, 2, 2, 2, 3, 3, 3, 3],
[1, 2, 2, 3, 2, 3, 4, 4],
[1, 2, 2, 3, 2, 3, 4, 4]]))
nptest.assert_array_equal(
res.length_table, np.array(
[[1, 1, 1, 4, 5, 6, 7, 8],
[1, 2, 2, 4, 5, 6, 7, 8],
[3, 3, 3, 3, 5, 6, 7, 8],
[4, 4, 4, 4, 4, 6, 7, 8],
[5, 5, 5, 5, 5, 7, 7, 8],
[6, 6, 6, 6, 8, 8, 8, 8]]))
def test_cigar(self):
s1 = "QQEGIL"
s2 = "QQQERGII"
res = align(
s1, s2, 10, 1, method='nw', matrix=parasail.pam10, trace=True
)
self.assertIsNotNone(res.cigar)
def test_assert_stats(self):
s1 = "QQEGIL"
s2 = "QQQERGII"
res = align(s1, s2, 10, 1, method='nw',
matrix=parasail.pam10, stats=True)
self.assertFalse(res.saturated)
self.assertEqual(res.score, 18)
self.assertEqual(res.end_query, 5)
self.assertEqual(res.end_query, 5)
self.assertEqual(res.matches, 4)
self.assertEqual(res.similar, 4)
self.assertEqual(res.length, 8)
def test_stats_rowcol(self):
s1 = "QQEGIL"
s2 = "QQQERGII"
res = align(s1, s2, 10, 1, method='nw', stats=True,
rowcol=True, matrix=parasail.pam10)
nptest.assert_array_equal(res.score_row, [-5, 5, 5, 4, -6, 2, 12, 18])
nptest.assert_array_equal(res.matches_row, [1, 2, 2, 3, 2, 3, 4, 4])
nptest.assert_array_equal(res.similar_row, [1, 2, 2, 3, 2, 3, 4, 4])
nptest.assert_array_equal(res.length_row, [6, 6, 6, 6, 8, 8, 8, 8])
nptest.assert_array_equal(res.score_col, [-7, 3, 3, 2, 12, 18])
nptest.assert_array_equal(res.matches_col, [1, 2, 2, 3, 4, 4])
nptest.assert_array_equal(res.similar_col, [1, 2, 2, 3, 4, 4])
nptest.assert_array_equal(res.length_col, [8, 8, 8, 8, 8, 8])
def test_table(self):
s1 = "QQEGIL"
s2 = "QQQERGII"
res = align(s1, s2, 10, 1,
matrix=parasail.pam10,
method='nw',
table=True)
nptest.assert_array_equal(
res.score_table, np.array(
[[9, -1, -2, -3, -4, -5, -6, -7],
[-1, 18, 8, 7, 6, 5, 4, 3],
[-2, 8, 17, 16, 6, 5, 4, 3],
[-3, 7, 7, 10, 3, 13, 3, 2],
[-4, 6, 6, 5, 2, 3, 22, 12],
[-5, 5, 5, 4, -6, 2, 12, 18]]))
def test_assert_nostats(self):
s1 = "QQEGIL"
s2 = "QQQERGII"
res = align(s1, s2, 10, 1, matrix=parasail.pam10, method='nw')
self.assertFalse(res.saturated)
self.assertEqual(res.score, 18)
self.assertEqual(res.end_query, 5)
self.assertEqual(res.end_query, 5)
with self.assertRaises(AttributeError):
res.matches
with self.assertRaises(AttributeError):
res.similar
with self.assertRaises(AttributeError):
res.length
def test_cigar(self):
s1 = "QQEGIL"
s2 = "QQQERGII"
res = align(s1,
s2,
10,
1,
matrix=parasail.pam10,
method='nw',
trace=True)
cigar = res.cigar
nptest.assert_array_equal(cigar.seq, [39, 24, 34, 39, 24])
self.assertEqual(cigar.len, 5)
self.assertEqual(cigar.beg_query, 0)
self.assertEqual(cigar.beg_ref, 0)
self.assertEqual(cigar.decode, '2=1X2D2=1X')