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

property blocks#

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

A codon block can be:

a quartet, if all 4 XYn codons have the same amino acid.
a doublet, if XYt and XYc or XYa and XYg have the same aa.
a singlet, otherwise.

Returns a list of the quartets, doublets, and singlets in the order UUU -> GGG.

Note that a doublet cannot span the purine/pyrimidine boundary, and a quartet cannot span the boundary between two codon blocks whose first two bases differ.

changes(other)#

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

X is the string representation of the amino acid in self, Y is the string representation of the amino acid in other. Always returns a 2-character string.

get_alphabet(include_stop=False)#

get_stop_indices(dna, start=0)#: 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

Parameters:

seq: a Sequence or string of amino acids

to_table()#: returns aa to codon mapping as a cogent3 Table

translate(dna, start=0)#

Translates DNA to protein with current GeneticCode.

Parameters:

dna: str: a string of nucleotides
start: int: position to begin translation (used to implement frames)

Returns:

String containing amino acid sequence. Translates the entire sequence.
It is the caller’s responsibility to find open reading frames.