def __init__(self,
alphabet=DNA,
neutral_alphabet='N',
neutral_value=0.25,
dtype=None,
alphabet_axis=1,
dummy_axis=None):
# make sure the alphabet axis and the dummy axis are valid:
if dummy_axis is not None:
if alphabet_axis == dummy_axis:
raise ValueError("dummy_axis can't be the same as dummy_axis")
if not (dummy_axis >= 0 and dummy_axis <= 2):
raise ValueError("dummy_axis can be either 0,1 or 2")
assert alphabet_axis >= 0 and (alphabet_axis < 2 or
(alphabet_axis <= 2
and dummy_axis is not None))
self.alphabet_axis = alphabet_axis
self.dummy_axis = dummy_axis
self.alphabet = parse_alphabet(alphabet)
self.dtype = parse_dtype(dtype)
self.neutral_alphabet = neutral_alphabet
self.neutral_value = neutral_value
# set the transform parameters correctly
if dummy_axis is not None and dummy_axis < 2:
# dummy axis is added somewhere in the middle, so the alphabet axis is at the end now
existing_alphabet_axis = 2
else:
# alphabet axis stayed the same
existing_alphabet_axis = 1
# check if no swapping needed
if existing_alphabet_axis == self.alphabet_axis:
self.alphabet_axis = None
# how to transform the input
self.transform = Compose([
OneHot(self.alphabet,
neutral_alphabet=self.neutral_alphabet,
neutral_value=self.neutral_value,
dtype=self.dtype), # one-hot-encode
DummyAxis(self.dummy_axis), # optionally inject the dummy axis
SwapAxes(existing_alphabet_axis,
self.alphabet_axis), # put the alphabet axis elsewhere
])
def test_parse_alphabet():
assert parse_alphabet(['A', 'C']) == ['A', 'C']
assert parse_alphabet('AC') == ['A', 'C']