def __init__(
self,
chars,
degens,
gap=IUPAC_gap,
missing=IUPAC_missing,
moltype=None,
constructor=None,
):
"""Returns new AlphabetGroup."""
if constructor is None:
if max(list(map(len, chars))) == 1:
constructor = CharAlphabet
chars = "".join(chars)
degens = "".join(degens)
else:
constructor = Alphabet # assume multi-char
self.base = constructor(chars, moltype=moltype)
self.degen = constructor(chars + degens, moltype=moltype)
self.gapped = constructor(chars + gap, gap, moltype=moltype)
self.degen_gapped = constructor(chars + gap + degens + missing,
gap,
moltype=moltype)
self._items = [self.base, self.degen, self.gapped, self.degen_gapped]
self._set_relationships()
# set complements if MolType was specified
if moltype is not None:
comps = moltype.complements
for i in self._items:
i._complement_array = _make_complement_array(i, comps)
def test_make_complement_array(self):
"""_make_complement_array should identify complements correctly"""
complement_array = _make_complement_array(RNA.alphabet, RNA.complements)
test = "UCAG"
test_array = [RNA.alphabet.index(i) for i in test]
complements = complement_array.take(test_array)
result = "".join([RNA.alphabet[i] for i in complements])
self.assertEqual(result, "AGUC")
