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

Last updated for Version 3.9

Classes [hide private]
  TranslationError
  CodonTable
  NCBICodonTable
  NCBICodonTableDNA
  NCBICodonTableRNA
  AmbiguousCodonTable
  AmbiguousForwardTable
Functions [hide private]
 
make_back_table(table, default_stop_codon) source code
 
list_possible_proteins(codon, forward_table, ambiguous_nucleotide_values) source code
 
list_ambiguous_codons(codons, ambiguous_nucleotide_values)
Extends a codon list to include all possible ambigous codons.
source code
 
register_ncbi_table(name, alt_name, id, table, start_codons, stop_codons)
Turns codon table data into objects, and stores them in the dictionaries (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]

list_ambiguous_codons(codons, ambiguous_nucleotide_values)

source code 
Extends 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'.
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.


Variables Details [hide private]

ambiguous_generic_by_name

Value:
{}