def test_modify_insertions(self):
x = assembly.MutableSequence('chr', 5, 8, 'ATCG')
x.modify(6, 'insert')
self.assertEqual(x.emit(), ('chr', 'AinsertCG'))
x.modify(8, 'tail')
self.assertEqual(x.emit(), ('chr', 'AinsertCtail'))
x.modify(5, 'headA')
self.assertEqual(x.emit(), ('chr', 'headAinsertCtail'))
def test_modify_deletions_remember(self):
x = assembly.MutableSequence('chr', 5, 8, 'ATCG')
x.replace(6, 7, 'T')
self.assertEqual(x.emit(), ('chr', 'ATG'))
x.modify(7, 'x')
self.assertEqual(x.emit(), ('chr', 'ATxG'))
x.replay_deletions()
self.assertEqual(x.emit(), ('chr', 'ATG'))
def test_good_coords(self):
x = assembly.MutableSequence('chr', 1, 5)
x = assembly.MutableSequence('chr', 5, 5)
x = assembly.MutableSequence('chr', 100, 2000)
x = assembly.MutableSequence('chr name with spaces 5 @#$ --', 1, 5)
x = assembly.MutableSequence('chr', 5, 5, 'A')
x = assembly.MutableSequence('chr', 5, 6, 'AT')
def test_modify_deletions(self):
x = assembly.MutableSequence('chr', 5, 8, 'ATCG')
self.assertRaises(Exception, x.replace, 6, 9, 'AT')
x.replace(6, 7, 'CT')
self.assertEqual(x.emit(), ('chr', 'ACTG'))
x.replace(6, 7, '')
self.assertEqual(x.emit(), ('chr', 'AG'))
x.modify(7, 'x')
self.assertEqual(x.emit(), ('chr', 'AxG'))
x.modify(6, 'y')
self.assertEqual(x.emit(), ('chr', 'AyxG'))
x.replace(7, 7, '123')
self.assertEqual(x.emit(), ('chr', 'Ay123G'))
x.modify(7, 'z')
self.assertEqual(x.emit(), ('chr', 'AyzG'))
def test_modify_one(self):
x = assembly.MutableSequence('chr', 5, 8, 'ATCG')
self.assertRaises(Exception, x.modify, 4, 'G')
self.assertRaises(Exception, x.modify, 9, 'G')
self.assertEqual(x.emit(), ('chr', 'ATCG'))
x.modify(5, 'G')
self.assertEqual(x.emit(), ('chr', 'GTCG'))
x.modify(6, 'G')
self.assertEqual(x.emit(), ('chr', 'GGCG'))
x.modify(7, 'G')
self.assertEqual(x.emit(), ('chr', 'GGGG'))
x.modify(8, 'G')
self.assertEqual(x.emit(), ('chr', 'GGGG'))
x.modify(6, 'j')
self.assertEqual(x.emit(), ('chr', 'GjGG'))
x.modify(8, 'Y')
self.assertEqual(x.emit(), ('chr', 'GjGY'))
def test_modify_deletions_simple(self):
x = assembly.MutableSequence('chr', 5, 8, 'ATCG')
x.replace(6, 7, 'T')
self.assertEqual(x.emit(), ('chr', 'ATG'))
def test_modify_blank(self):
x = assembly.MutableSequence('chr', 5, 8)
self.assertEqual(x.emit(), ('chr', 'NNNN'))
x.modify(6, 'G')
self.assertEqual(x.emit(), ('chr', 'NGNN'))