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

Classes
AmbiguousCodonTable  
AmbiguousForwardTable  
CodonTable  
NCBICodonTable  
NCBICodonTableDNA  
NCBICodonTableRNA  

Exceptions
TranslationError  

Function Summary
  list_ambiguous_codons(codons)
  list_possible_proteins(codon, forward_table, ambiguous_nucleotide_values)
  make_back_table(table, default_stop_codon)
  register_ncbi_table(name, alt_name, id, table, start_codons, stop_codons)

Variable Summary
dict ambiguous_dna_by_id = {1: <Bio.Data.CodonTable.Ambiguous...
dict ambiguous_dna_by_name = {'Ascidian Mitochondrial': <Bio....
dict ambiguous_rna_by_id = {1: <Bio.Data.CodonTable.Ambiguous...
dict ambiguous_rna_by_name = {'Ascidian Mitochondrial': <Bio....
NCBICodonTableDNA standard_dna_table = <Bio.Data.CodonTable.NCBICodonTable...
NCBICodonTableRNA standard_rna_table = <Bio.Data.CodonTable.NCBICodonTable...
dict unambiguous_dna_by_id = {1: <Bio.Data.CodonTable.NCBICod...
dict unambiguous_dna_by_name = {'Ascidian Mitochondrial': <Bi...
dict unambiguous_rna_by_id = {1: <Bio.Data.CodonTable.NCBICod...
dict unambiguous_rna_by_name = {'Ascidian Mitochondrial': <Bi...

Variable Details

ambiguous_dna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaace49d8\
8>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaace4e3f\
8>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaace4ea2\
8>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaace5e09\
8>,
...                                                                    

ambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0x2aaaace46bd8>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0x2aaaace3d3f8>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2\
aaaace49128>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0x2aaaace42368>,
...                                                                    

ambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaace7690\
8>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaace76f3\
8>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaace9c5a\
8>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaace9cbd\
8>,
...                                                                    

ambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0x2aaaace6b758>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0x2aaaace60f38>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2\
aaaace6dc68>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0x2aaaace65ea8>,
...                                                                    

standard_dna_table

Type:
NCBICodonTableDNA
Value:
<Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aaaace63fc8>     

standard_rna_table

Type:
NCBICodonTableRNA
Value:
<Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aaaadabc878>     

unambiguous_dna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aaaace63fc8>\
,
 2: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aaaadabc8c0>\
,
 3: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aaaadabc950>\
,
 4: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aaaadabca28>\
,
...                                                                    

unambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableDNA i\
nstance at 0x2aaaadabce18>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableDNA inst\
ance at 0x2aaaadabcea8>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aa\
aadabcd40>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableDNA in\
stance at 0x2aaaace3d290>,
...                                                                    

unambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aaaadabc878>\
,
 2: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aaaadabc908>\
,
 3: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aaaadabc998>\
,
 4: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aaaadabca70>\
,
...                                                                    

unambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableRNA i\
nstance at 0x2aaaadabce60>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableRNA inst\
ance at 0x2aaaadabcef0>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aa\
aadabcd88>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableRNA in\
stance at 0x2aaaace3d3b0>,
...                                                                    

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