def test_parse_nodes(self):
self.assertEqual(parse_nodes(self.data),
[('Rosalind_0498', 'AAATAAA'),
('Rosalind_2391', 'AAATTTT'),
('Rosalind_2323', 'TTTTCCC'),
('Rosalind_0442', 'AAATCCC'),
('Rosalind_5013', 'GGGTGGG')])
def test_directional_multiple(self):
labeled = parse_nodes(self.data)
comparer = compare_multiple(labeled)
current, overlaps = next(comparer)
path = overlaps.pop(0)
self.assertEqual(directional(current, path),
('Rosalind_0498', 'Rosalind_2391'))
def test_pick_best_matches(self): #note that the current scoring includes identity matches that might be irrelevant
labeled = parse_nodes(self.data)
sample = list(compare_multiple(labeled))[0]
current = sample[0]
overlaps = sample[1]
scored_pairs = make_score_dict(current, overlaps)
best_pair = pick_best_matches(scored_pairs)
self.assertEqual(best_pair, (('Rosalind_0498', 'AAATAAA'), ('Rosalind_0442', 'AAATCCC')))
def test_make_score_dict(self):
labeled = parse_nodes(self.data)
sample = list(compare_multiple(labeled))[0]
current = sample[0]
overlaps = sample[1]
scored_pairs = make_score_dict(current, overlaps)
self.assertNotIn((current, current), scored_pairs.keys())
self.assertEqual(len(scored_pairs), 2)
self.assertEqual(sorted(scored_pairs.values()), [1, 2])
def test_make_score_dict(self):
labeled = parse_nodes(self.data)
sample = list(compare_multiple(labeled))[0]
current = sample[0]
overlaps = sample[1]
scored_pairs = make_score_dict(current, overlaps)
self.assertNotIn((current, current), scored_pairs.keys())
self.assertEqual(len(scored_pairs), 2)
self.assertEqual(sorted(scored_pairs.values()), [1, 2])
def test_get_o3_matches_short_seq(self):
self.longMessage = True #for debugging without truncation
labeled = parse_nodes(self.data)
#print(labeled)
actual = compare_all_pairs_both_ways(labeled)
expected = [('Rosalind_2391', 'Rosalind_2323'),
('Rosalind_0498', 'Rosalind_2391'),
('Rosalind_0498', 'Rosalind_0442')]
self.assertEqual(set(expected), set(actual), msg='{0},{1}'.format(expected, actual))
def test_compare_multiple(self):
self.longMessage = True #for debugging without truncation
labeled = parse_nodes(self.data)
actual = compare_multiple(labeled)
expected = [('Rosalind_0498', 'Rosalind_2391'),
('Rosalind_2391', 'Rosalind_2323'),
('Rosalind_0498', 'Rosalind_0442')]
self.assertEqual(set(expected),
set(actual),
msg='{0},{1}'.format(expected, actual))
def test_compare_base_count_sums(self):
"""
simplest way only works for simplest examples.
"""
labeled = parse_nodes(self.data)
sample = list(compare_multiple(labeled))[0]
current = sample[0]
overlaps = sample[1]
self.assertEqual(compare_base_counts(current, overlaps[0]), 1)
self.assertEqual(compare_base_counts(current, overlaps[1]), 2)
self.assertEqual(compare_base_counts(overlaps[0], overlaps[1]), 0)
def test_directional_best_pair(self):
labeled = parse_nodes(self.data)
sample = list(compare_multiple(labeled))[0]
current = sample[0]
overlaps = sample[1]
scored_pairs = make_score_dict(current, overlaps)
self.assertNotIn((current, current), scored_pairs.keys())
best_pair = pick_best_matches(scored_pairs)
self.assertNotIn((current, current), list(best_pair))
tup = directional(list(best_pair)[0], list(best_pair)[1])
self.assertEqual(tup, ('Rosalind_0498', 'Rosalind_0442'))
def test_compare_base_count_sums(self):
"""
simplest way only works for simplest examples.
"""
labeled = parse_nodes(self.data)
sample = list(compare_multiple(labeled))[0]
current = sample[0]
overlaps = sample[1]
self.assertEqual(compare_base_counts(current, overlaps[0]), 1)
self.assertEqual(compare_base_counts(current, overlaps[1]), 2)
self.assertEqual(compare_base_counts(overlaps[0], overlaps[1]), 0)
def test_directional_best_pair(self):
labeled = parse_nodes(self.data)
sample = list(compare_multiple(labeled))[0]
current = sample[0]
overlaps = sample[1]
scored_pairs = make_score_dict(current, overlaps)
self.assertNotIn((current, current), scored_pairs.keys())
best_pair = pick_best_matches(scored_pairs)
self.assertNotIn((current, current), list(best_pair))
tup = directional(list(best_pair)[0], list(best_pair)[1])
self.assertEqual(tup, ('Rosalind_0498', 'Rosalind_0442'))
def test_pick_best_matches(
self
): #note that the current scoring includes identity matches that might be irrelevant
labeled = parse_nodes(self.data)
sample = list(compare_multiple(labeled))[0]
current = sample[0]
overlaps = sample[1]
scored_pairs = make_score_dict(current, overlaps)
best_pair = pick_best_matches(scored_pairs)
self.assertEqual(best_pair, (('Rosalind_0498', 'AAATAAA'),
('Rosalind_0442', 'AAATCCC')))
def test_compare_multiple(self):
self.longMessage = True #for debugging without truncation
labeled = parse_nodes(self.data)
actual = compare_multiple(labeled)
expected = [('Rosalind_0498', 'Rosalind_2391'), ('Rosalind_2391', 'Rosalind_2323'), ('Rosalind_0498', 'Rosalind_0442')]
self.assertEqual(set(expected), set(actual), msg='{0},{1}'.format(expected, actual))
def test_parse_nodes(self):
self.assertEqual(parse_nodes(self.data), [('Rosalind_0498', 'AAATAAA'),
('Rosalind_2391', 'AAATTTT'),
('Rosalind_2323', 'TTTTCCC'),
('Rosalind_0442', 'AAATCCC'),
('Rosalind_5013', 'GGGTGGG')])
def test_directional_multiple(self):
labeled = parse_nodes(self.data)
comparer = compare_multiple(labeled)
current, overlaps = next(comparer)
path = overlaps.pop(0)
self.assertEqual(directional(current, path), ('Rosalind_0498', 'Rosalind_2391'))