class OuterLoopTest(unittest.TestCase):
def setUp(self):
self.structure = "...((..((..))....)).."
self.parser = Parser(self.structure)
self.loops = self.parser.indices()
self.flanking = self.parser.indices(flanking=True)
def test_hairpins(self):
ans = [tuple([[9, 10]])]
self.assertEqual(self.loops['hairpin'], ans)
def test_flanking_hairpins(self):
ans = [tuple([[8, 9, 10, 11]])]
self.assertEqual(self.flanking['hairpin'], ans)
def test_external(self):
ans = [([0, 1, 2], [19, 20])]
self.assertEqual(self.loops['external'], ans)
def test_flanking_external(self):
ans = [([0, 1, 2, 3], [18, 19, 20])]
self.assertEqual(self.flanking['external'], ans)
def test_internal(self):
ans = [([5, 6], [13, 14, 15, 16])]
self.assertEqual(self.loops['internal'], ans)
def test_flanking_internal(self):
ans = [([4, 5, 6, 7], [12, 13, 14, 15, 16, 17])]
self.assertEqual(self.flanking['internal'], ans)
class OuterLoopTest(unittest.TestCase):
def setUp(self):
self.structure = "...((..((..))....)).."
self.parser = Parser(self.structure)
self.loops = self.parser.indices()
self.flanking = self.parser.indices(flanking=True)
def test_hairpins(self):
ans = [tuple([[9, 10]])]
self.assertEqual(self.loops['hairpin'], ans)
def test_flanking_hairpins(self):
ans = [tuple([[8, 9, 10, 11]])]
self.assertEqual(self.flanking['hairpin'], ans)
def test_external(self):
ans = [([0, 1, 2], [19, 20])]
self.assertEqual(self.loops['external'], ans)
def test_flanking_external(self):
ans = [([0, 1, 2, 3], [18, 19, 20])]
self.assertEqual(self.flanking['external'], ans)
def test_internal(self):
ans = [([5, 6], [13, 14, 15, 16])]
self.assertEqual(self.loops['internal'], ans)
def test_flanking_internal(self):
ans = [([4, 5, 6, 7], [12, 13, 14, 15, 16, 17])]
self.assertEqual(self.flanking['internal'], ans)
class NestedParserTest(unittest.TestCase):
def setUp(self):
self.structure = "...((..(((....)))...((((...))))...))..."
self.parser = Parser(self.structure)
self.loops = self.parser.indices()
seq = "aaaccaacccuuuugggtttccccuuuggggtttggttt"
self.sequences = self.parser.loops(seq)
def test_hairpins(self):
ans = [tuple([[24, 25, 26]]), tuple([[10, 11, 12, 13]])]
self.assertEqual(self.loops['hairpin'], ans)
def test_external_loop(self):
ans = [([0, 1, 2], [36, 37, 38])]
self.assertEqual(self.loops['external'], ans)
def test_internal_loops(self):
self.assertFalse('internal' in self.loops)
# def test_junction_loops(self):
# ans = [([5, 6], [17, 18, 19], [31, 32, 33])]
# self.parser._tree.print_tree()
# self.assertEqual(self.loops['junction'], ans)
def test_extract_hairpins(self):
ans = ['uuu', 'uuuu']
self.assertEqual(self.sequences['hairpin'], ans)
class NestedParserTest(unittest.TestCase):
def setUp(self):
self.structure = "...((..(((....)))...((((...))))...))..."
self.parser = Parser(self.structure)
self.loops = self.parser.indices()
seq = "aaaccaacccuuuugggtttccccuuuggggtttggttt"
self.sequences = self.parser.loops(seq)
def test_hairpins(self):
ans = [tuple([[24, 25, 26]]), tuple([[10, 11, 12, 13]])]
self.assertEqual(self.loops['hairpin'], ans)
def test_external_loop(self):
ans = [([0, 1, 2], [36, 37, 38])]
self.assertEqual(self.loops['external'], ans)
def test_internal_loops(self):
self.assertFalse('internal' in self.loops)
# def test_junction_loops(self):
# ans = [([5, 6], [17, 18, 19], [31, 32, 33])]
# self.parser._tree.print_tree()
# self.assertEqual(self.loops['junction'], ans)
def test_extract_hairpins(self):
ans = ['uuu', 'uuuu']
self.assertEqual(self.sequences['hairpin'], ans)
class Ty1Test(unittest.TestCase):
def setUp(self):
self.structure = '(((((((.....((((((((...))))).)))......(((((((.........(((((.((.........(((((.(((((............(((.(((...((((....((..(((((....))))))).))))......((..(((...)))..)).))).)))........)))))))))).)).)))))..)))))))..)))).................(((.....))).((((....))))...((((((((.........(.(((((...((((..(((.........)))..))))....))))))))))))))........................((((((((....((((((..............))))))..............(((.(((((.((.......)).))))).)))....(((..(((((.((.((((........))))))((......))...........((((((((............))))))))......)))))..)))....(((((............))))).)))))..))).(((((......(((((((..........)))))))...)))))...................))).......'
self.parser = Parser(self.structure)
self.loops = self.parser.indices()
def test_hairpins(self):
ans = [
tuple([[20, 21, 22]]),
tuple([[121, 122, 123, 124]]),
tuple([[150, 151, 152]]),
tuple([[230, 231, 232, 233, 234]]),
tuple([[243, 244, 245, 246]]),
tuple([[290, 291, 292, 293, 294, 295, 296, 297, 298]]),
tuple([[
368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379,
380, 381
]]),
tuple([[414, 415, 416, 417, 418, 419, 420]]),
tuple([[455, 456, 457, 458, 459, 460, 461, 462]]),
tuple([[471, 472, 473, 474, 475, 476]]),
tuple(
[[498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508,
509]]),
tuple(
[[543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553,
554]]),
tuple([[590, 591, 592, 593, 594, 595, 596, 597, 598, 599]])
]
ans.reverse()
self.assertEqual(self.loops['hairpin'], ans)
class EmptyLeftSideTest(unittest.TestCase):
def setUp(self):
self.structure = "((((..))....))"
self.parser = Parser(self.structure)
self.loops = self.parser.indices(flanking=True)
def test_internal_loops(self):
val = self.loops['internal']
ans = [tuple([[1, 2], [7, 8, 9, 10, 11, 12]])]
self.assertEqual(val, ans)
class EmptyLeftSideTest(unittest.TestCase):
def setUp(self):
self.structure = "((((..))....))"
self.parser = Parser(self.structure)
self.loops = self.parser.indices(flanking=True)
def test_internal_loops(self):
val = self.loops['internal']
ans = [tuple([[1, 2], [7, 8, 9, 10, 11, 12]])]
self.assertEqual(val, ans)
class RfamDialectTest(unittest.TestCase):
def setUp(self):
self.structure = '.AAA....<<<<aaa....>>>>'
self.parser = Parser(self.structure, dialect='rfam')
self.loops = self.parser.indices()
def test_finds_hairpins(self):
self.assertTrue('hairpin' in self.loops)
def test_finds_no_internal(self):
self.assertFalse('internal' in self.loops)
class RfamDialectTest(unittest.TestCase):
def setUp(self):
self.structure = '.AAA....<<<<aaa....>>>>'
self.parser = Parser(self.structure, dialect='rfam')
self.loops = self.parser.indices()
def test_finds_hairpins(self):
self.assertTrue('hairpin' in self.loops)
def test_finds_no_internal(self):
self.assertFalse('internal' in self.loops)
class SimpleParserTest(unittest.TestCase):
def setUp(self):
self.structure = "((..((..))....))..((...))"
self.parser = Parser(self.structure)
self.loops = self.parser.indices()
self.flanking = self.parser.indices(flanking=True)
def test_hairpins(self):
ans = [tuple([[6, 7]]), tuple([[20, 21, 22]])]
self.assertEqual(self.loops['hairpin'], ans)
def test_flanking_hairpins(self):
ans = [tuple([[5, 6, 7, 8]]), tuple([[19, 20, 21, 22, 23]])]
self.assertEqual(self.flanking['hairpin'], ans)
def test_internal(self):
ans = [([2, 3], [10, 11, 12, 13])]
print(self.parser._tree.print_tree())
self.assertEqual(self.loops['internal'], ans)
def test_flanking_internal(self):
ans = [([1, 2, 3, 4], [9, 10, 11, 12, 13, 14])]
self.assertEqual(self.flanking['internal'], ans)
class SimpleParserTest(unittest.TestCase):
def setUp(self):
self.structure = "((..((..))....))..((...))"
self.parser = Parser(self.structure)
self.loops = self.parser.indices()
self.flanking = self.parser.indices(flanking=True)
def test_hairpins(self):
ans = [tuple([[6, 7]]), tuple([[20, 21, 22]])]
self.assertEqual(self.loops['hairpin'], ans)
def test_flanking_hairpins(self):
ans = [tuple([[5, 6, 7, 8]]), tuple([[19, 20, 21, 22, 23]])]
self.assertEqual(self.flanking['hairpin'], ans)
def test_internal(self):
ans = [([2, 3], [10, 11, 12, 13])]
print(self.parser._tree.print_tree())
self.assertEqual(self.loops['internal'], ans)
def test_flanking_internal(self):
ans = [([1, 2, 3, 4], [9, 10, 11, 12, 13, 14])]
self.assertEqual(self.flanking['internal'], ans)
class Ty1Test(unittest.TestCase):
def setUp(self):
self.structure = '(((((((.....((((((((...))))).)))......(((((((.........(((((.((.........(((((.(((((............(((.(((...((((....((..(((((....))))))).))))......((..(((...)))..)).))).)))........)))))))))).)).)))))..)))))))..)))).................(((.....))).((((....))))...((((((((.........(.(((((...((((..(((.........)))..))))....))))))))))))))........................((((((((....((((((..............))))))..............(((.(((((.((.......)).))))).)))....(((..(((((.((.((((........))))))((......))...........((((((((............))))))))......)))))..)))....(((((............))))).)))))..))).(((((......(((((((..........)))))))...)))))...................))).......'
self.parser = Parser(self.structure)
self.loops = self.parser.indices()
def test_hairpins(self):
ans = [tuple([[20,21,22]]),
tuple([[121,122,123,124]]),
tuple([[150,151,152]]),
tuple([[230,231,232,233,234]]),
tuple([[243,244,245,246]]),
tuple([[290,291,292,293,294,295,296,297,298]]),
tuple([[368,369,370,371,372,373,374,375,376,377,378,379,380,381]]),
tuple([[414,415,416,417,418,419,420]]),
tuple([[455,456,457,458,459,460,461,462]]),
tuple([[471,472,473,474,475,476]]),
tuple([[498,499,500,501,502,503,504,505,506,507,508,509]]),
tuple([[543,544,545,546,547,548,549,550,551,552,553,554]]),
tuple([[590,591,592,593,594,595,596,597,598,599]])]
ans.reverse()
self.assertEqual(self.loops['hairpin'], ans)