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.. jupyter-execute::
:hide-code:
import set_working_directory
***********************
Available genetic codes
***********************
.. jupyter-execute::
from cogent3 import available_codes
available_codes()
In cases where a ``cogent3`` object method has a ``gc`` argument, you can just use the number under "Code ID" column.
For example:
.. jupyter-execute::
from cogent3 import load_aligned_seqs
nt_seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna")
nt_seqs[:21]
We specify the genetic code, and that codons that are incomplete as they contain a gap, are converted to ``?``.
.. jupyter-execute::
aa_seqs = nt_seqs.get_translation(gc=1, incomplete_ok=True)
aa_seqs[:20]
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.
.. jupyter-execute::
from cogent3 import get_code
gc = get_code(4)
gc
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