cogent3.core.genetic_code.GeneticCode#

class GeneticCode(code_sequence, ID=None, name=None, start_codon_sequence=None)#

Holds codon to amino acid mapping, and vice versa.

Use the get_code() function to get one of the included code instances. These are created as follows.

>>> code_sequence = 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG'
>>> gc = GeneticCode(code_sequence)
>>> sgc['UUU'] == 'F'
>>> sgc['TTT'] == 'F'
>>> sgc['F'] == ['TTT', 'TTC']          #in arbitrary order
>>> sgc['*'] == ['TAA', 'TAG', 'TGA']   #in arbitrary order

code_sequence : 64 character string containing NCBI genetic code translation

GeneticCode is immutable once created.

Attributes
blocks

Returns list of lists of codon blocks in the genetic code.

Methods

changes(other)

Returns dict of {codon:'XY'} for codons that differ.

get_stop_indices(dna[, start])

returns indexes for stop codons in the specified frame

is_start(codon)

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

is_stop(codon)

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

sixframes(dna)

Returns six-frame translation as dict containing {frame:translation}

to_regex(seq)

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(dna[, start])

Translates DNA to protein with current GeneticCode.

get_alphabet