Available genetic codes¶

from cogent3 import available_codes

available_codes()

Specify a genetic code using either 'Name' or Code ID (as an integer or string)
Code ID	Name
1	Standard
2	Vertebrate Mitochondrial
3	Yeast Mitochondrial
4	Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
5	Invertebrate Mitochondrial
6	Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
9	Echinoderm Mitochondrial; Flatworm Mitochondrial
10	Euplotid Nuclear
11	Bacterial, Archaeal and Plant Plastid
12	Alternative Yeast Nuclear
13	Ascidian Mitochondrial
14	Alternative Flatworm Mitochondrial
15	Blepharisma Macronuclear
16	Chlorophycean Mitochondrial
21	Trematode Mitochondrial
22	Scenedesmus obliquus Mitochondrial
23	Thraustochytrium Mitochondrial
24	Rhabdopleuridae Mitochondrial
25	Candidate Division SR1 and Gracilibacteria
26	Pachysolen tannophilus Nuclear
27	Karyorelict Nuclear
28	Condylostoma Nuclear
29	Mesodinium Nuclear
30	Peritrich Nuclear
31	Blastocrithidia Nuclear
32	Balanophoraceae Plastid
33	Cephalodiscidae Mitochondrial

27 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:

from cogent3 import load_aligned_seqs

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

5 x 21 dna alignment

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

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

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.

from cogent3 import get_code

gc = get_code(4)
gc