def test_make_trans(self):
"""make_trans should return trans table mapping chars to default"""
a = make_trans()
self.assertEqual('abc123'.translate(a), 'abc123')
a = make_trans('a', 'x')
self.assertEqual('abc123'.translate(a), 'xbc123')
a = make_trans('ac', 'xa')
self.assertEqual('abc123'.translate(a), 'xba123')
a = make_trans('ac', 'xa', '.')
self.assertEqual('abc123'.translate(a), 'x.a...')
self.assertRaises(ValueError, make_trans, 'ac', 'xa', 'av')
"""
mismatches = 0
if pairs is None:
try:
pairs = sequence.Alphabet.Pairs
except AttributeError:
pairs = sequence.Pairs
for up, down in self.directed():
curr = (sequence[up], sequence[down])
if curr not in pairs:
mismatches += 1
return mismatches
wuss_to_vienna_table = make_trans('<([{>)]} ', '(((()))) ', '.')
def wuss_to_vienna(data):
"""Converts WUSS format string to Vienna format.
Any pseudoknots or unrecognized chars will convert to unpaired bases.
Spaces will be preserved.
"""
return ViennaStructure(data.translate(wuss_to_vienna_table))
class StructureString(str):
"""Base class for ViennaStructure and WussStructure. Immutable.
StructureString holds a structure and a energy. By default energy is
set to None.
