def test_subject_tracking(self):
query = core.Query("input|c1|0-759|-|CAG25751.1|putative", 0)
sub1 = core.Subject("a1", "a", 1, 2, "+", "c", 0.5, 1, 0.5, 1e-8,
"loc")
query.add_subject(sub1)
containers = [query.cluster_name_to_subjects, query.subjects]
# check it was properly added to the various containers
for container in containers:
self.assertEqual(len(container), 1)
self.assertEqual(query.cluster_name_to_subjects["a"], [sub1])
assert list(query.subjects) == ["a1"]
sub2 = core.Subject("a2", "b", 1, 2, "+", "c", 0.5, 1, 0.5, 1e-8,
"loc")
query.add_subject(sub2)
for container in containers:
self.assertEqual(len(container), 2)
self.assertEqual(query.cluster_name_to_subjects["a"], [sub1])
self.assertEqual(query.cluster_name_to_subjects["b"], [sub2])
# check we don't override when cluster names overlap
sub3 = core.Subject("a3", "a", 1, 2, "+", "c", 0.5, 1, 0.5, 1e-8,
"loc")
query.add_subject(sub3)
self.assertEqual(len(query.subjects), 3)
# check the new subject was properly added to the old list
self.assertEqual(query.cluster_name_to_subjects["a"], [sub1, sub3])
self.assertEqual(query.cluster_name_to_subjects["b"], [sub2])
# check ordering preserved on subject names
self.assertEqual(list(query.subjects), ["a1", "a2", "a3"])
# check the getter has the same results as direct access
self.assertEqual(query.get_subjects_by_cluster("a"), [sub1, sub3])
# check that an empty iterable is returned if cluster not known
self.assertEqual(query.get_subjects_by_cluster("new_name"), [])
def setUp(self):
self.query_lines = ["input|c1|0-759|-|CAG25751.1|putative",
"input|c1|0-759|-|CAG25751.2|putative",
"input|c1|0-759|-|CAG25751.3|putative"]
self.queries = OrderedDict()
for line in self.query_lines:
self.queries[line] = core.Query(line, 0)
assert not self.queries[line].subjects
def test_init(self):
query_line = "input|c1|0-759|-|CAG25751.1|putative"
query = core.Query(query_line, 0)
self.assertEqual(query.entry, query_line)
self.assertEqual(query.cluster_number, 1)
self.assertEqual(query.id, "CAG25751.1")
self.assertEqual(query.index, 0)
for container in [query.cluster_name_to_subjects, query.subjects]:
self.assertEqual(len(container), 0)