def test_assemble_seq(self): """should correctly fill in a sequence with N's""" expect = DNA.makeSequence("NAAAAANNCCCCCNNGGGNNN") frags = ["AAAAA","CCCCC","GGG"] positions = [(11, 16), (18, 23), (25, 28)] self.assertEqual(_assemble_seq(frags, 10, 31, positions), expect) positions = [(1, 6), (8, 13), (15, 18)] self.assertEqual(_assemble_seq(frags, 0, 21, positions), expect) # should work with: # start matches first frag start expect = DNA.makeSequence("AAAAANNCCCCCNNGGGNNN") positions = [(0, 5), (7, 12), (14, 17)] self.assertEqual(_assemble_seq(frags, 0, 20, positions), expect) # end matches last frag_end expect = DNA.makeSequence("NAAAAANNCCCCCNNGGG") positions = [(11, 16), (18, 23), (25, 28)] self.assertEqual(_assemble_seq(frags, 10, 28, positions), expect) # both start and end matched expect = DNA.makeSequence("AAAAANNCCCCCNNGGG") positions = [(10, 15), (17, 22), (24, 27)] self.assertEqual(_assemble_seq(frags, 10, 27, positions), expect) # one frag expect = DNA.makeSequence(''.join(frags)) positions = [(10, 23)] self.assertEqual(_assemble_seq([''.join(frags)],10,23,positions), expect)
def test_assemble_seq(self): """should correctly fill in a sequence with N's""" expect = DNA.makeSequence("NAAAAANNCCCCCNNGGGNNN") frags = ["AAAAA", "CCCCC", "GGG"] positions = [(11, 16), (18, 23), (25, 28)] self.assertEqual(_assemble_seq(frags, 10, 31, positions), expect) positions = [(1, 6), (8, 13), (15, 18)] self.assertEqual(_assemble_seq(frags, 0, 21, positions), expect) # should work with: # start matches first frag start expect = DNA.makeSequence("AAAAANNCCCCCNNGGGNNN") positions = [(0, 5), (7, 12), (14, 17)] self.assertEqual(_assemble_seq(frags, 0, 20, positions), expect) # end matches last frag_end expect = DNA.makeSequence("NAAAAANNCCCCCNNGGG") positions = [(11, 16), (18, 23), (25, 28)] self.assertEqual(_assemble_seq(frags, 10, 28, positions), expect) # both start and end matched expect = DNA.makeSequence("AAAAANNCCCCCNNGGG") positions = [(10, 15), (17, 22), (24, 27)] self.assertEqual(_assemble_seq(frags, 10, 27, positions), expect) # one frag expect = DNA.makeSequence(''.join(frags)) positions = [(10, 23)] self.assertEqual(_assemble_seq([''.join(frags)], 10, 23, positions), expect)