Bio.Data.CodonTable module

Codon tables based on those from the NCBI.

These tables are based on parsing the NCBI file ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt using Scripts/update_ncbi_codon_table.py

Last updated at Version 4.4 (May 2019)

exception Bio.Data.CodonTable.TranslationError

Bases: Exception

Container for translation specific exceptions.

class Bio.Data.CodonTable.CodonTable(nucleotide_alphabet=NucleotideAlphabet(), protein_alphabet=ProteinAlphabet(), forward_table={}, back_table={}, start_codons=[], stop_codons=[])

Bases: object

A codon-table, or genetic code.

__init__(self, nucleotide_alphabet=NucleotideAlphabet(), protein_alphabet=ProteinAlphabet(), forward_table={}, back_table={}, start_codons=[], stop_codons=[])

Initialize the class.

nucleotide_alphabet = NucleotideAlphabet()

protein_alphabet = ProteinAlphabet()

forward_table = {}

back_table = {}

start_codons = []

stop_codons = []

__str__(self)

Return a simple text representation of the codon table.

e.g.:

>>> import Bio.Data.CodonTable
>>> print(Bio.Data.CodonTable.standard_dna_table)
Table 1 Standard, SGC0

  |  T      |  C      |  A      |  G      |
--+---------+---------+---------+---------+--
T | TTT F   | TCT S   | TAT Y   | TGT C   | T
T | TTC F   | TCC S   | TAC Y   | TGC C   | C
...
G | GTA V   | GCA A   | GAA E   | GGA G   | A
G | GTG V   | GCG A   | GAG E   | GGG G   | G
--+---------+---------+---------+---------+--
>>> print(Bio.Data.CodonTable.generic_by_id[1])
Table 1 Standard, SGC0

  |  U      |  C      |  A      |  G      |
--+---------+---------+---------+---------+--
U | UUU F   | UCU S   | UAU Y   | UGU C   | U
U | UUC F   | UCC S   | UAC Y   | UGC C   | C
...
G | GUA V   | GCA A   | GAA E   | GGA G   | A
G | GUG V   | GCG A   | GAG E   | GGG G   | G
--+---------+---------+---------+---------+--

Bio.Data.CodonTable.make_back_table(table, default_stop_codon)

Back a back-table (naive single codon mapping).

ONLY RETURNS A SINGLE CODON, chosen from the possible alternatives based on their sort order.

class Bio.Data.CodonTable.NCBICodonTable(id, names, table, start_codons, stop_codons)

Bases: Bio.Data.CodonTable.CodonTable

Codon table for generic nucleotide sequences.

nucleotide_alphabet = NucleotideAlphabet()

protein_alphabet = IUPACProtein()

__init__(self, id, names, table, start_codons, stop_codons)

Initialize the class.

__repr__(self)

Represent the NCBI codon table class as a string for debugging.

class Bio.Data.CodonTable.NCBICodonTableDNA(id, names, table, start_codons, stop_codons)

Bases: Bio.Data.CodonTable.NCBICodonTable

Codon table for unambiguous DNA sequences.

nucleotide_alphabet = IUPACUnambiguousDNA()

class Bio.Data.CodonTable.NCBICodonTableRNA(id, names, table, start_codons, stop_codons)

Bases: Bio.Data.CodonTable.NCBICodonTable

Codon table for unambiguous RNA sequences.

nucleotide_alphabet = IUPACUnambiguousRNA()

class Bio.Data.CodonTable.AmbiguousCodonTable(codon_table, ambiguous_nucleotide_alphabet, ambiguous_nucleotide_values, ambiguous_protein_alphabet, ambiguous_protein_values)

Bases: Bio.Data.CodonTable.CodonTable

Base codon table for ambiguous sequences.

__init__(self, codon_table, ambiguous_nucleotide_alphabet, ambiguous_nucleotide_values, ambiguous_protein_alphabet, ambiguous_protein_values)

Initialize the class.

__getattr__(self, name)

Forward attribute lookups to the original table.

Bio.Data.CodonTable.list_possible_proteins(codon, forward_table, ambiguous_nucleotide_values)

Return all possible encoded amino acids for ambiguous codon.

Bio.Data.CodonTable.list_ambiguous_codons(codons, ambiguous_nucleotide_values)

Extend a codon list to include all possible ambigous codons.

e.g.:

['TAG', 'TAA'] -> ['TAG', 'TAA', 'TAR']
['UAG', 'UGA'] -> ['UAG', 'UGA', 'URA']

Note that [‘TAG’, ‘TGA’] -> [‘TAG’, ‘TGA’], this does not add ‘TRR’ (which could also mean ‘TAA’ or ‘TGG’). Thus only two more codons are added in the following:

e.g.:

['TGA', 'TAA', 'TAG'] -> ['TGA', 'TAA', 'TAG', 'TRA', 'TAR']

Returns a new (longer) list of codon strings.

class Bio.Data.CodonTable.AmbiguousForwardTable(forward_table, ambiguous_nucleotide, ambiguous_protein)

Bases: object

Forward table for translation of ambiguous nucleotide sequences.

__init__(self, forward_table, ambiguous_nucleotide, ambiguous_protein)

Initialize the class.

__contains__(self, codon)

Check if codon works as key for ambiguous forward_table.

Only returns ‘True’ if forward_table[codon] returns a value.

get(self, codon, failobj=None)

Implement get for dictionary-like behaviour.

__getitem__(self, codon)

Implement dictionary-like behaviour for AmbiguousForwardTable.

forward_table[codon] will either return an amino acid letter, or throws a KeyError (if codon does not encode an amino acid) or a TranslationError (if codon does encode for an amino acid, but either is also a stop codon or does encode several amino acids, for which no unique letter is available in the given alphabet.

Bio.Data.CodonTable.register_ncbi_table(name, alt_name, id, table, start_codons, stop_codons)

Turn codon table data into objects (PRIVATE).

The data is stored in the dictionaries.