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)