def test_genes(FakeITree, gene_intervals):
tree = itree.ITree(nodes=gene_intervals)
mock_tree = FakeITree(nodes=gene_intervals)
for search in gene_intervals:
if len(mock_tree.search(search)) != len(tree.search(search)):
tree.search(search)
assert len(mock_tree.search(search)) == len(tree.search(search))
def test_ptree(self):
intervals = [
(8, 11), (10, 12), (9, 13)
]
mytree = itree.ITree()
mytree.construct(intervals)
mytree.dump()
def test_small(self):
intervals = [
(0, 8),
(1, 3),
(5, 7),
]
mytree = itree.ITree()
mytree.construct(intervals)
mytree.dump()
def test_search(FakeITree, itree_random_intervals, itree_random_queries, seed):
random.seed(random.randint(0, sys.maxsize))
tree = itree.ITree(nodes=itree_random_intervals)
mock_tree = FakeITree(nodes=itree_random_intervals)
for search in itree_random_queries:
if len(mock_tree.search(search)) != len(tree.search(search)):
tree.search(search)
print(f"seed == {seed}")
assert len(mock_tree.search(search)) == len(tree.search(search))
def test_random_remove(itree_random_intervals):
t = itree.ITree()
for node in itree_random_intervals:
t.insert(node)
for node in itree_random_intervals[::5]:
old_size = len(t)
t.remove(node)
new_size = len(t)
assert new_size == old_size-1
def test_node_really_removed(itree_complex_sample):
t = itree.ITree()
nodes = list(sorted(list(set(itree_complex_sample))))
for node in nodes:
t.insert(node)
for node in nodes[::5]:
t.remove(node)
for r in t.search(node):
assert f"({r.start},{r.end})" != f"({node.start},{node.end})"
def test_remove_nothing(FakeITree, FakeNode, itree_simple_sample):
tree = itree.ITree(nodes=itree_simple_sample)
nonpresent_node = FakeNode(100000,200000)
assert nonpresent_node not in itree_simple_sample, \
f"{nonpresent_node} is in the sample; revise the test"
expected = FakeITree(itree_simple_sample)
tree.remove(nonpresent_node)
test_node = itree_simple_sample[0]
assert len(tree) == len(expected)
assert tree.search(test_node) == expected.search(test_node)
def test_remove_all_nodes(itree_random_intervals):
t = itree.ITree()
nodes = list(sorted(list(set(itree_random_intervals))))
for node in nodes:
t.insert(node)
for node in nodes:
old_size = len(t)
t.remove(node)
new_size = len(t)
assert new_size == old_size-1
assert len(t) == 0
def test_big(self):
intervals = [
(1, 4),
(6, 8),
(15, 19),
(2, 6),
(10, 12),
(17, 22),
(5, 6),
(8, 11),
(14, 18),
(22, 25),
(1, 3),
(9, 13),
(17, 20),
(21, 24),
(1, 12)
]
mytree = itree.ITree()
mytree.construct(intervals)
mytree.dump()
icontrol = {(15, 19), (14, 18)}
itest = {x for x in mytree.find_intervals_for_point(16)}
self.assertEqual(icontrol, itest)
icontrol = {
(9, 13),
(8, 11),
(6, 8),
(1, 12),
(10, 12),
}
itest = set([x for x in mytree.find_intervals_for_interval((7, 11))])
self.assertEqual(icontrol, itest)
icontrol = {
(9, 13),
(8, 11),
(1, 12),
(10, 12),
}
itest = set([x for x in mytree.find_intervals_for_interval((8, 11))])
self.assertEqual(icontrol, itest)
def constructor(self, intervals) -> Callable[[], itree.ITree]:
self._object = itree.ITree(intervals)
return lambda: itree.ITree(intervals)
def test_insert(itree_simple_sample):
t = itree.ITree()
for node in itree_simple_sample:
t.insert(node)
def test_random_insert(FakeNode, itree_random_intervals):
t = itree.ITree()
for node in itree_random_intervals:
t.insert(node)
def test_complex_insert(itree_complex_sample):
t = itree.ITree()
for node in itree_complex_sample:
t.insert(node)
def test_search_empty_tree(FakeITree, FakeNode):
tree = itree.ITree()
test_node = FakeNode(3,15)
assert tree.search(test_node) == []
def test_node_str(itree_simple_sample):
tree = itree.ITree(nodes=itree_simple_sample)
expected = f"ITree(root=({tree.root.start},{tree.root.end}))"
assert str(tree) == expected
def test_tree_pstring(itree_simple_sample):
tree = itree.ITree(nodes=itree_simple_sample)
assert tree.pstring() == simple_tree_pstring
