def test_extendHelix(self):
"""StructureNode extendHelix should extend the helix as far as possible
"""
#single paired node is root[4]
op_str = ViennaStructure('....(......)...')
op = op_str.toTree()
#can't extend if base pairs not allowed
op[4].extendHelix(Rna('AAAAAAAAAAAAAAA'))
self.assertEqual(str(op), op_str)
#should extend a pair 5'
op[4].extendHelix(Rna('AAACCAAAAAAGGAA'))
self.assertEqual(str(op), '...((......))..')
#should extend multiple pairs 5'
op = op_str.toTree()
op[4].extendHelix(Rna('CCCCCUUUUUUGGGG'))
self.assertEqual(str(op), '.((((......))))')
#should extend a pair 3', but must leave > 2-base loop
op = op_str.toTree()
op[4].extendHelix(Rna('AAAACCCCGGGGAAA'))
self.assertEqual(str(op), '....((....))...')
op[4][0].insert(1, StructureNode(Data=Stem(Start=1, End=1, Length=1)))
op.renumber()
self.assertEqual(str(op), '....((.()...))...')
op[4][0].extendHelix(Rna('AAAACCCUACGGGGAAA'))
self.assertEqual(str(op), '....(((()..)))...')
#should extend a pair in both directions if possible
op = op_str.toTree()
op[4].extendHelix(Rna('AAACCCAAAAGGGAA'))
self.assertEqual(str(op), '...(((....)))..')
def test_extendHelix(self):
"""StructureNode extendHelix should extend the helix as far as possible
"""
#single paired node is root[4]
op_str = ViennaStructure('....(......)...')
op = op_str.toTree()
#can't extend if base pairs not allowed
op[4].extendHelix(Rna('AAAAAAAAAAAAAAA'))
self.assertEqual(str(op), op_str)
#should extend a pair 5'
op[4].extendHelix(Rna('AAACCAAAAAAGGAA'))
self.assertEqual(str(op), '...((......))..')
#should extend multiple pairs 5'
op = op_str.toTree()
op[4].extendHelix(Rna('CCCCCUUUUUUGGGG'))
self.assertEqual(str(op), '.((((......))))')
#should extend a pair 3', but must leave > 2-base loop
op = op_str.toTree()
op[4].extendHelix(Rna('AAAACCCCGGGGAAA'))
self.assertEqual(str(op), '....((....))...')
op[4][0].insert(1, StructureNode(Data=Stem(Start=1,End=1,Length=1)))
op.renumber()
self.assertEqual(str(op), '....((.()...))...')
op[4][0].extendHelix(Rna( 'AAAACCCUACGGGGAAA'))
self.assertEqual(str(op), '....(((()..)))...')
#should extend a pair in both directions if possible
op = op_str.toTree()
op[4].extendHelix(Rna('AAACCCAAAAGGGAA'))
self.assertEqual(str(op), '...(((....)))..')
def test_fitSeq(self):
"""StructureNode fitSeq should adjust structure to match sequence"""
#this is just a minimal test, since we know that both breakBadPairs()
#and extendHelices() work fine with more extensive tests.
s = ViennaStructure('..(((.....)))......(((.....)))...')
r = Rna('UCCCCACUGAGGGGUUUGGGGGGUUUUCGCCCU')
t = s.toTree()
t.fitSeq(r)
self.assertEqual(str(t), '.((((.....))))...(((.((...)).))).')
def test_fitSeq(self):
"""StructureNode fitSeq should adjust structure to match sequence"""
#this is just a minimal test, since we know that both breakBadPairs()
#and extendHelices() work fine with more extensive tests.
s = ViennaStructure('..(((.....)))......(((.....)))...')
r = Rna( 'UCCCCACUGAGGGGUUUGGGGGGUUUUCGCCCU')
t = s.toTree()
t.fitSeq(r)
self.assertEqual(str(t), '.((((.....))))...(((.((...)).))).')
def test_breakBadPairs(self):
"""StructureNode breakBadPairs should eliminate mispaired bases."""
oh_str = ViennaStructure(self.OneHelixStr)
#no change if all pairs valid
oh = oh_str.toTree()
oh.breakBadPairs(Rna('CCCCCGGGGG'))
self.assertEqual(str(oh), str(oh_str))
#break everything if all pairs invalid
oh.breakBadPairs(Rna('CCCCCAAAAA'))
self.assertEqual(str(oh), '..........')
#break a single pair
oh = oh_str.toTree()
oh.breakBadPairs(Rna('GCCCCGGGGG'))
self.assertEqual(str(oh), '.(((()))).')
#break two pairs
oh = oh_str.toTree()
oh.breakBadPairs(Rna('GCCCCCGGGG'))
self.assertEqual(str(oh), '.(((..))).')
#break internal pairs
oh = oh_str.toTree()
oh.breakBadPairs(Rna('GCCGCGGGGG'))
self.assertEqual(str(oh), '.((.().)).')
#repeat with multiple independent helices
th_str = ViennaStructure('((.)).((.))')
th = th_str.toTree()
th.breakBadPairs(Rna('CCUGGCUUCGG'))
self.assertEqual(str(th), th_str)
th.breakBadPairs(Rna('CGUAGCAGUUU'))
self.assertEqual(str(th), '(...).((.))')
th = th_str.toTree()
th.breakBadPairs(Rna('UUUUUUUUUUU'))
self.assertEqual(str(th), '...........')
def test_breakBadPairs(self):
"""StructureNode breakBadPairs should eliminate mispaired bases."""
oh_str = ViennaStructure(self.OneHelixStr)
#no change if all pairs valid
oh = oh_str.toTree()
oh.breakBadPairs(Rna('CCCCCGGGGG'))
self.assertEqual(str(oh), str(oh_str))
#break everything if all pairs invalid
oh.breakBadPairs(Rna('CCCCCAAAAA'))
self.assertEqual(str(oh), '..........')
#break a single pair
oh = oh_str.toTree()
oh.breakBadPairs(Rna('GCCCCGGGGG'))
self.assertEqual(str(oh), '.(((()))).')
#break two pairs
oh = oh_str.toTree()
oh.breakBadPairs(Rna('GCCCCCGGGG'))
self.assertEqual(str(oh), '.(((..))).')
#break internal pairs
oh = oh_str.toTree()
oh.breakBadPairs(Rna('GCCGCGGGGG'))
self.assertEqual(str(oh), '.((.().)).')
#repeat with multiple independent helices
th_str = ViennaStructure('((.)).((.))')
th = th_str.toTree()
th.breakBadPairs(Rna('CCUGGCUUCGG'))
self.assertEqual(str(th), th_str)
th.breakBadPairs(Rna('CGUAGCAGUUU'))
self.assertEqual(str(th), '(...).((.))')
th = th_str.toTree()
th.breakBadPairs(Rna('UUUUUUUUUUU'))
self.assertEqual(str(th), '...........')
def test_extendHelices(self):
"""StructureNode extendHelices should extend all helices"""
e = ViennaStructure('........')
t = e.toTree()
t.extendHelices(Rna('CCCCCCCCCC'))
self.assertEqual(str(t), e)
#no pairs if sequence can't form them
s = ViennaStructure('(.....(...)..)...((.....))...')
r = Rna('AAAAAAAAAAAAAAAAAAAAAAAAAAAAA')
t = s.toTree()
t.extendHelices(r)
self.assertEqual(str(t), s)
#should be able to extend a single helix
s = ViennaStructure('(.....(...)..)...((.....))...')
r = Rna('CAAAAACAAAGAAGCCCCCCCAGGGGGGG')
t = s.toTree()
t.extendHelices(r)
self.assertEqual(str(t), '(.....(...)..)((((((...))))))')
#should be able to extend multiple helices
s = ViennaStructure('(.....(...)..)...((.....))...')
r = Rna('AAAAACCCAGGGUUCCCCCAUAAAGGGAA')
t = s.toTree()
t.extendHelices(r)
self.assertEqual(str(t), '((...((...))))..(((.....)))..')
def test_extendHelices(self):
"""StructureNode extendHelices should extend all helices"""
e = ViennaStructure('........')
t = e.toTree()
t.extendHelices(Rna('CCCCCCCCCC'))
self.assertEqual(str(t), e)
#no pairs if sequence can't form them
s = ViennaStructure('(.....(...)..)...((.....))...')
r = Rna('AAAAAAAAAAAAAAAAAAAAAAAAAAAAA')
t = s.toTree()
t.extendHelices(r)
self.assertEqual(str(t), s)
#should be able to extend a single helix
s = ViennaStructure('(.....(...)..)...((.....))...')
r = Rna('CAAAAACAAAGAAGCCCCCCCAGGGGGGG')
t = s.toTree()
t.extendHelices(r)
self.assertEqual(str(t), '(.....(...)..)((((((...))))))')
#should be able to extend multiple helices
s = ViennaStructure('(.....(...)..)...((.....))...')
r = Rna('AAAAACCCAGGGUUCCCCCAUAAAGGGAA')
t = s.toTree()
t.extendHelices(r)
self.assertEqual(str(t), '((...((...))))..(((.....)))..')
