core.genetic_code.GeneticCode

core.genetic_code.GeneticCode(
    ID,
    name,
    ncbi_code_sequence,
    ncbi_start_codon_map,
    moltype=c3_moltype.DNA,
)

Holds codon to amino acid mapping, and vice versa.

Notes

We add additional states to the genetic code to represent gapped codons and missing data.

Methods

Name	Description
get_alphabet	returns a codon alphabet
is_start	Returns True if codon is a start codon, False otherwise.
is_stop	Returns True if codon is a stop codon, False otherwise.
sixframes	Returns the six reading frames of the genetic code.
to_regex	returns a regex pattern with an amino acid expanded to its codon set
to_table	returns aa to codon mapping as a cogent3 Table
translate	Translates DNA to protein.

get_alphabet

core.genetic_code.GeneticCode.get_alphabet(
    include_gap=False,
    include_missing=False,
    include_stop=False,
)

returns a codon alphabet

Parameters

Name	Type	Description	Default
include_gap	bool	alphabet includes the gap motif	False
include_missing	bool	alphabet includes the missing state as 3 * IUPAC_missing	False
include_stop	bool	if True, this is just a kmer alphabet	False

Notes

If include_stop, the returned alphabet includes all codons, and is thus a KmerAlphabet. Otherwise its a SenseCodonAlphabet.

is_start

core.genetic_code.GeneticCode.is_start(codon)

Returns True if codon is a start codon, False otherwise.

is_stop

core.genetic_code.GeneticCode.is_stop(codon)

Returns True if codon is a stop codon, False otherwise.

sixframes

core.genetic_code.GeneticCode.sixframes(seq)

Returns the six reading frames of the genetic code.

Returns

Name	Type	Description
	A dictionary with keys (strand, start) where strand is "+"/"-"

to_regex

core.genetic_code.GeneticCode.to_regex(seq)

returns a regex pattern with an amino acid expanded to its codon set

Parameters

Name	Type	Description	Default
seq	str | PySeq[str] | Sequence	a Sequence or string of amino acids	required

to_table

core.genetic_code.GeneticCode.to_table()

returns aa to codon mapping as a cogent3 Table

translate

core.genetic_code.GeneticCode.translate(
    dna,
    start=0,
    rc=False,
    incomplete_ok=True,
)

Translates DNA to protein.

Parameters

Name	Type	Description	Default
dna	str | npt.NDArray[numpy.integer]	a string of nucleotides	required
start	int	position to begin translation (used to implement frames)	0
rc	bool	if True, returns the translation of the reverse complement sequence	False
incomplete_ok	bool	if True, translates codons that are a mix of gaps and bases as a gap. If False, raises an AlphabetError on those incomplete cases.	True

Notes

Sequences are truncated to be a multiple of 3. Codons containing ambiguous nucleotides are translated as ‘X’, codons containing a gap character are translated as ‘-’ unless incomplete_ok is False. Codons with a mix of ambiguous nucleotides are translated as ‘X’.

Returns

Name	Type	Description
	The amino acid sequence as a string.