def test_one_skipped_exon(self): self.graph.add_path([str(self.ex1), str(self.ex2), str(self.ex3)]) self.graph.add_path([str(self.ex1), str(self.ex3)]) self.events = list(find_SE(self.graph)) self.assertEqual(len(self.events), 1) # one skipped exon self.assertEqual(len(self.events[0]) + 1, 2) # two isoforms
def test_no_skipped_exon(self): self.ex5 = Exon('chrX', 9000, 10000, 'ex1.1', '+') self.exonsDB[str(self.ex5)] = self.ex5 self.graph.add_path([str(self.ex1), str(self.ex2), str(self.ex3)]) self.graph.add_path([str(self.ex3), str(self.ex4), str(self.ex5)]) self.events = list(find_SE(self.graph)) self.assertEqual(len(self.events), 0)
def test_two_single_skipped_exon(self): self.ex5 = Exon('chrX', 9000, 10000, 'ex1.1', '+') self.exonsDB[str(self.ex5)] = self.ex5 self.graph.add_path([str(self.ex1), str(self.ex2), str(self.ex3)]) self.graph.add_path([str(self.ex1), str(self.ex3)]) self.graph.add_path([str(self.ex3), str(self.ex4), str(self.ex5)]) self.graph.add_path([str(self.ex3), str(self.ex5)]) self.events = list(find_SE(self.graph)) self.assertEqual(len(self.events), 2) # one skipped exon self.assertEqual(len(self.events[0]) + 1, 2) # two isoforms self.assertEqual(len(self.events[1]) + 1, 2) # two isoforms