1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
|
Alphabets
---------
.. authors Gavin Huttley
``Alphabet`` and ``MolType``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
``MolType`` instances have an ``Alphabet``.
.. doctest::
>>> from cogent import DNA, PROTEIN
>>> print DNA.Alphabet
('T', 'C', 'A', 'G')
>>> print PROTEIN.Alphabet
('A', 'C', 'D', 'E', ...
``Alphabet`` instances have a ``MolType``.
.. doctest::
>>> PROTEIN.Alphabet.MolType == PROTEIN
True
Creating tuple alphabets
^^^^^^^^^^^^^^^^^^^^^^^^
You can create a tuple alphabet of, for example, dinucleotides or trinucleotides.
.. doctest::
>>> dinuc_alphabet = DNA.Alphabet.getWordAlphabet(2)
>>> print dinuc_alphabet
('TT', 'CT', 'AT', 'GT', ...
>>> trinuc_alphabet = DNA.Alphabet.getWordAlphabet(3)
>>> print trinuc_alphabet
('TTT', 'CTT', 'ATT', ...
Convert a sequence into integers
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doctest::
>>> seq = 'TAGT'
>>> indices = DNA.Alphabet.toIndices(seq)
>>> indices
[0, 2, 3, 0]
Convert integers to a sequence
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. doctest::
>>> seq = DNA.Alphabet.fromIndices([0,2,3,0])
>>> seq
['T', 'A', 'G', 'T']
or
.. doctest::
>>> seq = DNA.Alphabet.fromOrdinalsToSequence([0,2,3,0])
>>> seq
DnaSequence(TAGT)
|
