def test_ungapped_to_gapped_general(self):
"""ungapped_to_gapped: should return object of right type
"""
s = RnaSequence(self.gapped)
p = self.simple
#in case of RnaSequence
obs_seq, obs_pairs = ungapped_to_gapped(s, p)
assert obs_seq is s
self.assertEqualItems(obs_pairs, self.simple_g)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
#in case of str input
s = self.gapped
obs_seq, obs_pairs = ungapped_to_gapped(s, p)
assert obs_seq is s
self.assertEqualItems(obs_pairs, self.simple_g)
assert not isinstance(obs_seq, RnaSequence)
assert isinstance(obs_seq, str)
assert isinstance(obs_pairs, Pairs)
def test_ungapped_to_gapped_simple(self):
"""ungapped_to_gapped: should work on basic case"""
s = self.gapped
p = self.simple
obs_seq, obs_pairs = ungapped_to_gapped(s, p)
assert obs_seq is s
self.assertEqualItems(obs_pairs, self.simple_g)
assert not isinstance(obs_seq, RnaSequence)
assert isinstance(obs_seq, str)
assert isinstance(obs_pairs, Pairs)
def test_ungapped_to_gapped_duplicates(self):
"""ungapped_to_gapped: should work when pairs are duplicated"""
s = self.gapped
p = self.duplicates
obs_seq, obs_pairs = ungapped_to_gapped(s, p)
assert obs_seq is s
self.assertEqualItems(obs_pairs, self.duplicates_g)
assert not isinstance(obs_seq, RnaSequence)
assert isinstance(obs_seq, str)
assert isinstance(obs_pairs, Pairs)
def test_ungapped_to_gapped_out_of_order(self):
"""ungapped_to_gapped: should work when pairs out of order
"""
s = RnaSequence(self.gapped)
p = self.out_order
obs_seq, obs_pairs = ungapped_to_gapped(s, p)
assert obs_seq is s
self.assertEqualItems(obs_pairs, self.out_order_g)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
def test_ungapped_to_gapped_general(self):
"""ungapped_to_gapped: should return object of right type
"""
s = RnaSequence(self.gapped)
p = self.simple
#in case of RnaSequence
obs_seq, obs_pairs = ungapped_to_gapped(s,p)
assert obs_seq is s
self.assertEqualItems(obs_pairs, self.simple_g)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
#in case of str input
s = self.gapped
obs_seq, obs_pairs = ungapped_to_gapped(s,p)
assert obs_seq is s
self.assertEqualItems(obs_pairs, self.simple_g)
assert not isinstance(obs_seq, RnaSequence)
assert isinstance(obs_seq, str)
assert isinstance(obs_pairs, Pairs)
def test_ungapped_to_gapped_duplicates(self):
"""ungapped_to_gapped: should work when pairs are duplicated"""
s = self.gapped
p = self.duplicates
obs_seq, obs_pairs = ungapped_to_gapped(s,p)
assert obs_seq is s
self.assertEqualItems(obs_pairs, self.duplicates_g)
assert not isinstance(obs_seq, RnaSequence)
assert isinstance(obs_seq, str)
assert isinstance(obs_pairs, Pairs)
def test_ungapped_to_gapped_simple(self):
"""ungapped_to_gapped: should work on basic case"""
s = self.gapped
p = self.simple
obs_seq, obs_pairs = ungapped_to_gapped(s,p)
assert obs_seq is s
self.assertEqualItems(obs_pairs, self.simple_g)
assert not isinstance(obs_seq, RnaSequence)
assert isinstance(obs_seq, str)
assert isinstance(obs_pairs, Pairs)
def test_ungapped_to_gapped_out_of_order(self):
"""ungapped_to_gapped: should work when pairs out of order
"""
s = RnaSequence(self.gapped)
p = self.out_order
obs_seq, obs_pairs = ungapped_to_gapped(s,p)
assert obs_seq is s
self.assertEqualItems(obs_pairs, self.out_order_g)
assert isinstance(obs_seq, RnaSequence)
assert isinstance(obs_pairs, Pairs)
