Available genetic codes¶

[1]:

from cogent3 import available_codes

available_codes()

[1]:

Specify a genetic code using either 'Name' or Code ID (as an integer or string)
Code ID	Name
1	Standard Nuclear
2	Vertebrate Mitochondrial
3	Yeast Mitochondrial
4	Mold, Protozoan, and Coelenterate Mitochondrial, and Mycoplasma/Spiroplasma Nuclear
5	Invertebrate Mitochondrial
6	Ciliate, Dasycladacean and Hexamita Nuclear
9	Echinoderm and Flatworm Mitochondrial
10	Euplotid Nuclear
11	Bacterial Nuclear and Plant Plastid
12	Alternative Yeast Nuclear
13	Ascidian Mitochondrial
14	Alternative Flatworm Mitochondrial
15	Blepharisma Nuclear
16	Chlorophycean Mitochondrial
20	Trematode Mitochondrial
22	Scenedesmus obliquus Mitochondrial
23	Thraustochytrium Mitochondrial

17 rows x 2 columns

In cases where a cogent3 object method has a gc argument, you can just use the number under “Code ID” column.

For example:

[2]:

from cogent3 import load_aligned_seqs

nt_seqs = load_aligned_seqs("../data/brca1-bats.fasta", moltype="dna")
nt_seqs[:21]

[2]:

5 x 21 dna alignment

We specify the genetic code, and that codons that are incomplete as they contain a gap, are converted to ?.

[3]:

aa_seqs = nt_seqs.get_translation(gc=1, incomplete_ok=True)
aa_seqs[:20]

[3]:

5 x 20 protein alignment

Getting a genetic code with `get_code()`¶

This function can be used directly to get a genetic code. We will get the code with ID 4.

[4]:

from cogent3 import get_code

gc = get_code(4)
gc

[4]: