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
|
.. 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 PROTEIN
p = PROTEIN.make_seq("THISISAPRQTEIN", "myProtein")
type(p)
str(p)
Converting a DNA sequence string to protein sequence string
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
from cogent3.core.genetic_code import DEFAULT as standard_code
standard_code.translate("TTTGCAAAC")
Conversion to a ``ProteinSequence`` from a ``DnaSequence`` is shown in :ref:`translation`.
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")
|
