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')
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')
def __init__(self, chars, degens, gap=IUPAC_gap, missing=IUPAC_missing, MolType=None, constructor=None):
"""Returns new AlphabetGroup."""
if constructor is None:
if max(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.DegenGapped = constructor(chars + gap + degens + missing, gap, MolType=MolType)
self._items = [self.Base, self.Degen, self.Gapped, self.DegenGapped]
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 __init__(self, chars, degens, gap=IUPAC_gap, missing=IUPAC_missing, \
MolType=None, constructor=None):
"""Returns new AlphabetGroup."""
if constructor is None:
if max(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.DegenGapped = constructor(chars+gap+degens+missing, gap, \
MolType=MolType)
self._items = [self.Base, self.Degen, self.Gapped, self.DegenGapped]
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)
