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Alphabets
---------
.. authors Gavin Huttley
``Alphabet`` and ``MolType``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
``MolType`` instances have an ``Alphabet``.
.. jupyter-execute::
from cogent3 import DNA, PROTEIN
print(DNA.alphabet)
print(PROTEIN.alphabet)
``Alphabet`` instances have a ``MolType``.
.. jupyter-execute::
PROTEIN.alphabet.moltype == PROTEIN
Creating tuple alphabets
^^^^^^^^^^^^^^^^^^^^^^^^
You can create a tuple alphabet of, for example, dinucleotides or trinucleotides.
.. jupyter-execute::
dinuc_alphabet = DNA.alphabet.get_word_alphabet(2)
print(dinuc_alphabet)
trinuc_alphabet = DNA.alphabet.get_word_alphabet(3)
print(trinuc_alphabet)
Convert a sequence into integers
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
seq = "TAGT"
indices = DNA.alphabet.to_indices(seq)
indices
Convert integers to a sequence
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
seq = DNA.alphabet.from_indices([0, 2, 3, 0])
seq
or
.. jupyter-execute::
seq = DNA.alphabet.from_ordinals_to_seq([0, 2, 3, 0])
seq
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