def test_gapped_to_ungapped_simple(self):
"""gapped_to_ungapped: should work for simple case"""
s = RnaSequence(self.gapped)
p = self.simple_g
obs_seq, obs_pairs = gapped_to_ungapped(s, p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.simple)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_simple(self):
"""gapped_to_ungapped: should work for simple case"""
s = RnaSequence(self.gapped)
p = self.simple_g
obs_seq, obs_pairs = gapped_to_ungapped(s,p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.simple)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_no_gaps(self):
"""gapped_to_ungapped: should return same pairs when no gaps
"""
s = RnaSequence(self.ungapped)
p = Pairs(self.simple)
obs_seq, obs_pairs = gapped_to_ungapped(s, p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.simple)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_pseudo(self):
"""gapped_to_ungapped: shouldn't care about pseudoknots
"""
s = RnaSequence(self.gapped)
p = Pairs(self.pseudo_g)
obs_seq, obs_pairs = gapped_to_ungapped(s, p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.pseudo)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_duplicates(self):
"""gapped_to_ungapped: should work when pairs contains duplicates
"""
s = RnaSequence(self.gapped)
p = Pairs(self.duplicates_g)
obs_seq, obs_pairs = gapped_to_ungapped(s, p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.duplicates)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_out_of_order(self):
"""gapped_to_ungapped: should work when pairs are out of order
"""
s = RnaSequence(self.gapped)
p = Pairs(self.out_order_g)
obs_seq, obs_pairs = gapped_to_ungapped(s, p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.out_order)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_no_gaps(self):
"""gapped_to_ungapped: should return same pairs when no gaps
"""
s = RnaSequence(self.ungapped)
p = Pairs(self.simple)
obs_seq, obs_pairs = gapped_to_ungapped(s,p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.simple)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_pseudo(self):
"""gapped_to_ungapped: shouldn't care about pseudoknots
"""
s = RnaSequence(self.gapped)
p = Pairs(self.pseudo_g)
obs_seq, obs_pairs = gapped_to_ungapped(s,p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.pseudo)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_duplicates(self):
"""gapped_to_ungapped: should work when pairs contains duplicates
"""
s = RnaSequence(self.gapped)
p = Pairs(self.duplicates_g)
obs_seq, obs_pairs = gapped_to_ungapped(s,p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.duplicates)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_out_of_order(self):
"""gapped_to_ungapped: should work when pairs are out of order
"""
s = RnaSequence(self.gapped)
p = Pairs(self.out_order_g)
obs_seq, obs_pairs = gapped_to_ungapped(s,p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.out_order)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_general(self):
"""gapped_to_ungapped: should return object of right type
"""
s = RnaSequence(self.gapped)
p = self.simple_g
#in case of RnaSequence
obs_seq, obs_pairs = gapped_to_ungapped(s, p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.simple)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
#in case of str input
s = self.gapped
obs_seq, obs_pairs = gapped_to_ungapped(s, p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.simple)
assert not isinstance(obs_seq, RnaSequence)
assert isinstance(obs_seq, str)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_general(self):
"""gapped_to_ungapped: should return object of right type
"""
s = RnaSequence(self.gapped)
p = self.simple_g
#in case of RnaSequence
obs_seq, obs_pairs = gapped_to_ungapped(s,p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.simple)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
#in case of str input
s = self.gapped
obs_seq, obs_pairs = gapped_to_ungapped(s,p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.simple)
assert not isinstance(obs_seq, RnaSequence)
assert isinstance(obs_seq, str)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_general_seq(self):
"""gapped_to_ungapped: when input is Sequence obj, treat as string
"""
s = Sequence(self.gapped)
p = self.simple_g
obs_seq, obs_pairs = gapped_to_ungapped(s, p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.simple)
#assert not isinstance(obs_seq, Sequence)
#assert isinstance(obs_seq, str)
assert isinstance(obs_seq, Sequence)
assert isinstance(obs_pairs, Pairs)
def test_gapped_to_ungapped_general_seq(self):
"""gapped_to_ungapped: when input is Sequence obj, treat as string
"""
s = Sequence(self.gapped)
p = self.simple_g
obs_seq, obs_pairs = gapped_to_ungapped(s,p)
self.assertEqual(obs_seq, self.ungapped)
self.assertEqualItems(obs_pairs, self.simple)
#assert not isinstance(obs_seq, Sequence)
#assert isinstance(obs_seq, str)
assert isinstance(obs_seq, Sequence)
assert isinstance(obs_pairs, Pairs)
