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
|
.. jupyter-execute::
:hide-code:
import set_working_directory
Protein sequences
-----------------
.. authors, Gavin Huttley, Kristian Rother, Patrick Yannul
Creating a ProteinSequence with a name
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
from cogent3 import make_seq
p = make_seq("THISISAPRQTEIN", "myProtein", moltype="protein")
type(p)
.. jupyter-execute::
p
Converting a DNA sequence string to protein sequence string
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
from cogent3 import get_code
standard_code = get_code(1)
standard_code.translate("TTTGCAAAC")
Conversion to a ``ProteinSequence`` from a ``DnaSequence`` is shown in :ref:`translation`.
Converting a nucleic acid sequence object to protein
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
from cogent3 import make_seq
nuc = make_seq("TTTGCAAAC", moltype="dna")
pep = nuc.get_translation()
pep
Loading protein sequences from a Phylip file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
from cogent3 import load_aligned_seqs
seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein")
|
