def test_insert_all_fragments_retain_template(self):
"""The template sequence should not change."""
m2 = RnaModel(template=self.t,
alignment=self.a,
model_chain_name='A',
data_type='file',
data=MINI_TEMPLATE)
m2.insert_all_fragments()
self.assertEqual(self.t.get_sequence(), self.seq_before)
def test_gaps_in_target(self):
"""Moderna should model gaps in the target, too."""
a = read_alignment(ALIGN_TARGET_GAP)
m = RnaModel(self.t, a)
m.apply_alignment()
m.insert_all_fragments()
self.assertEqual(
m.get_sequence().seq_with_modifications.replace('_', ''),
'..CUGACCU#P')
def test_create_model_with_gaps(self):
"""Should create the model automatically."""
a = read_alignment(ALIGN_1B23_1QF6)
t = Template(RNA_1B23, 'file', 'R')
m = RnaModel(t, a)
m.apply_alignment()
m.insert_all_fragments()
self.assertEqual(
m.get_sequence().seq_with_modifications.replace('_', ''),
'GCCGAUAUAGCUCAGDDGGDAGAGCAGCGCAUUCGUEAUGCGAAG7UCGUAGGTPCGACUCCUAUUAUCGGCACCA'
)
def test_doublegap_model(self):
"""Should create a model filling two gaps"""
a = read_alignment('''> target
GGGAUAGUUCCAGABU#A
> template
GGGA-AG--CCAGABU#A
''')
t = Template(DOUBLEGAP, 'file', 'A')
m = RnaModel(t, a)
m.apply_alignment()
m.insert_all_fragments()
m.fix_backbone()
self.assertEqual(m.get_sequence(), Sequence('GGGAUAGUUCCAGABU#A'))
def test_oppositegap_model(self):
"""Should create a model with close gaps in the other respective sequence"""
a = read_alignment('''> target
GGGAGAGCRUUAG-BU#A
> template
GGGAGAGCR--AGABU#A
''')
t = Template(OPPOSITEGAP, 'file', 'A')
m = RnaModel(t, a)
m.apply_alignment()
m.insert_all_fragments()
self.assertEqual(
m.get_sequence().seq_with_modifications.replace('_', ''),
'GGGAGAGCRUUAGBU#A')