def test_get_base_pairs(self):
"""Calculates one canonical and two noncanonicals correctly."""
m = ModernaStructure('file', RNA_HAIRPIN, 'D')
result = m.get_base_pairs()
result = map(str, result['31'])
self.assertTrue('31 +/+ 39' in result)
self.assertTrue('31 HS 32' in result)
self.assertTrue('31 SS 30' in result)
def test_wc_pairs_hairpin(self):
"""Exactly two W-C pairs in a hairpin are recognized."""
m = ModernaStructure('file', RNA_HAIRPIN, 'D')
result = m.get_base_pairs()
# calc number of +/+ pairs
count = 0
for val in result.values():
for bpair in val:
if bpair.type == '+/+':
count += 1
self.assertEqual(count, 4)
def test_wc_pairs_1ehz(self):
"""All W-C pairs in a tRNA are recognized."""
m = ModernaStructure('file', RNA_1EHZ, 'A')
result = m.get_base_pairs()
# calc number of +/+ pairs
gc_count, au_count = 0, 0
for key in result:
val = result[key]
for bpair in val:
if bpair.type == '+/+':
gc_count += 1
elif bpair.type == '-/-':
au_count += 1
#print gc_count, au_count
self.assertEqual(au_count, 14)
self.assertEqual(gc_count, 26)
"""# canonical from 1ehz according to rnaview
def test_get_base_pairs_generator(self):
"""aaa"""
m = ModernaStructure('file', RNA_HAIRPIN, 'D')
result = map(str, list(m.get_base_pairs('generator')))
self.assertTrue('30 +/+ 40' in result)
self.assertTrue(len(result) >= 4)
def test_structure_unpaired(self):
"""Single-stranded structure has no pairs."""
m = ModernaStructure('file', EXAMPLE_CHAR, 'C')
result = m.get_base_pairs()
self.assertEqual(result['37'], [])
