Package Bio :: Package Data :: Module CodonTable
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Module CodonTable

source code

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 4.2 (January 2018)

Classes [hide private]
  TranslationError
Container for translation specific exceptions.
  CodonTable
A codon-table, or genetic code.
  NCBICodonTable
Codon table for generic nucleotide sequences.
  NCBICodonTableDNA
Codon table for unambiguous DNA sequences.
  NCBICodonTableRNA
Codon table for unambiguous RNA sequences.
  AmbiguousCodonTable
Base codon table for ambiguous sequences.
  AmbiguousForwardTable
Forward table for translation of ambiguous nucleotide sequences.
Functions [hide private]
 
make_back_table(table, default_stop_codon)
Back a back-table (naive single codon mapping).
source code
 
list_possible_proteins(codon, forward_table, ambiguous_nucleotide_values)
Return all possible encoded amino acids for ambiguous codon.
source code
 
list_ambiguous_codons(codons, ambiguous_nucleotide_values)
Extend a codon list to include all possible ambigous codons.
source code
 
register_ncbi_table(name, alt_name, id, table, start_codons, stop_codons)
Turn codon table data into objects (PRIVATE).
source code
Variables [hide private]
  unambiguous_dna_by_name = {}
  unambiguous_dna_by_id = {}
  unambiguous_rna_by_name = {}
  unambiguous_rna_by_id = {}
  generic_by_name = {}
  generic_by_id = {}
  ambiguous_dna_by_name = {}
  ambiguous_dna_by_id = {}
  ambiguous_rna_by_name = {}
  ambiguous_rna_by_id = {}
  ambiguous_generic_by_name = {'Alternative Flatworm Mitochondri...
  ambiguous_generic_by_id = {}
  standard_dna_table = None
  standard_rna_table = None
  __package__ = 'Bio.Data'
Function Details [hide private]

make_back_table(table, default_stop_codon)

source code 

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

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

list_ambiguous_codons(codons, ambiguous_nucleotide_values)

source code 

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.

register_ncbi_table(name, alt_name, id, table, start_codons, stop_codons)

source code 

Turn codon table data into objects (PRIVATE).

The data is stored in the dictionaries.


Variables Details [hide private]

ambiguous_generic_by_name

Value:
{}