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