def add_intervals(graph, exonsDb):
iv_tree = IntervalTree()
for node in graph.nodes():
exon = exonsDb[node]
iv_tree.add_interval(exon)
return iv_tree
class TestFindRI(unittest.TestCase):
def setUp(self):
self.exonsDB = {}
self.ex1 = Exon('chrX', 1000, 2000, 'ex1.1', '+')
self.ex2 = Exon('chrX', 3000, 4000, 'ex1.1', '+')
self.ex3 = Exon('chrX', 5000, 6000, 'ex1.1', '+')
self.ex4 = Exon('chrX', 7000, 8000, 'ex1.1', '+')
self.exonsDB[str(self.ex1)] = self.ex1
self.exonsDB[str(self.ex2)] = self.ex2
self.exonsDB[str(self.ex3)] = self.ex3
self.exonsDB[str(self.ex4)] = self.ex4
self.tree = IntervalTree()
self.tree.add_interval(self.ex1)
self.tree.add_interval(self.ex2)
self.tree.add_interval(self.ex3)
self.tree.add_interval(self.ex4)
self.graph = nx.DiGraph()
def test_no_retained_introns(self):
self.path1 = [str(self.ex1), str(self.ex2), str(self.ex3)]
self.path2 = [str(self.ex1), str(self.ex3), str(self.ex4)]
self.graph.add_path(self.path1)
self.graph.add_path(self.path2)
self.events = list(find_RI(self.graph, self.tree, self.exonsDB))
self.assertEqual(len(self.events), 0)
def test_one_retained_introns(self):
self.ex5 = Exon('chrX', 3000, 6000, 'ex1.1', '+')
self.exonsDB[str(self.ex5)] = self.ex5
self.tree.add_interval(self.ex5)
self.path1 = [str(self.ex1), str(self.ex2),
str(self.ex3), str(self.ex4)]
self.path2 = [str(self.ex1), str(self.ex5), str(self.ex4)]
self.graph.add_path(self.path1)
self.graph.add_path(self.path2)
self.events = list(find_RI(self.graph, self.tree, self.exonsDB))
self.assertEqual(len(self.events), 1)
def test_two_retained_introns(self):
self.ex5 = Exon('chrX', 1000, 4000, 'ex1.1', '+')
self.exonsDB[str(self.ex5)] = self.ex5
self.tree.add_interval(self.ex5)
self.ex6 = Exon('chrX', 5000, 8000, 'ex1.1', '+')
self.exonsDB[str(self.ex6)] = self.ex6
self.tree.add_interval(self.ex6)
self.path1 = [str(self.ex1), str(self.ex2),
str(self.ex3), str(self.ex4)]
self.path2 = [str(self.ex5), str(self.ex6)]
self.graph.add_path(self.path1)
self.graph.add_path(self.path2)
self.events = list(find_RI(self.graph, self.tree, self.exonsDB))
self.assertEqual(len(self.events), 2)
def remove_overlaps(events, exonsDB):
tree = IntervalTree()
all_nodes = set()
for path in events:
for node in path:
all_nodes.add(node)
exon = exonsDB[node]
tree.add_interval(exon)
overlapped_exons = set()
for node in all_nodes:
exon = exonsDB[node]
for overlap in tree.find(exon.start, exon.end):
if (overlap.start != exon.start or
overlap.end != exon.end):
overlapped_exons.add(node)
new_events = []
for path in events:
if len(set(path).intersection(overlapped_exons)) == 0:
new_events.append(path)
return new_events
