def test_no_ASS(self):
self.graph = nx.DiGraph()
self.graph.add_path([str(self.ex1), str(self.ex2), str(self.ex3)])
self.graph.add_path([str(self.ex1), str(self.ex5), str(self.ex3)])
self.events = find_A5SS(self.graph, self.exonsDB)
self.assertEqual(len(self.events), 0)
def test_one_ASS(self):
'''
[]------->[=======]---->[]
[]------->[==]--------->[]
'''
self.graph = nx.DiGraph()
self.graph.add_path([str(self.ex1), str(self.ex2), str(self.ex3)])
self.graph.add_path([str(self.ex1), str(self.ex4), str(self.ex3)])
self.events = find_A5SS(self.graph, self.exonsDB)
self.assertEqual(len(self.events), 1)
self.assertEqual(len(self.events[0]), 2) # two isoforms
def test_two_events(self):
'''
[]------->[=======]---->[]
[]------->[==]--------->[]
[]---------->[=======]----------->[]
[]---------->[====]-------------->[]
'''
self.ex5 = Exon('chrX', 7000, 8000, 'ex1.1', '+')
self.ex6 = Exon('chrX', 9000, 10000, 'ex1.1', '+')
self.ex7 = Exon('chrX', 7000, 8500, 'ex1.1', '+')
self.exonsDB[str(self.ex5)] = self.ex5
self.exonsDB[str(self.ex6)] = self.ex6
self.exonsDB[str(self.ex7)] = self.ex7
self.graph = nx.DiGraph()
self.graph.add_path([str(self.ex1), str(self.ex2), str(self.ex3)])
self.graph.add_path([str(self.ex1), str(self.ex4), str(self.ex3)])
self.graph.add_path([str(self.ex3), str(self.ex5), str(self.ex6)])
self.graph.add_path([str(self.ex3), str(self.ex7), str(self.ex6)])
self.events = find_A5SS(self.graph, self.exonsDB)
self.assertEqual(len(self.events), 2) # two SS
self.assertEqual(len(self.events[0]), 2) # two isoforms
self.assertEqual(len(self.events[1]), 2) # two isoforms
