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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....
dict generic_by_id = {1: <Bio.Data.CodonTable.NCBICodonTable ...
dict generic_by_name = {'Ascidian Mitochondrial': <Bio.Data.C...
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 0x2aaaab7b5f8\
0>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaab7b65f\
0>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaab7b6c2\
0>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaab7b729\
0>,
...

ambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0x2aaaab7b1dd0>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0x2aaaaabac5f0>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2\
aaaab7b5320>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0x2aaaaabb8560>,
...

ambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaab7cab0\
0>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaab7c917\
0>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaab7c97a\
0>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2aaaab7c9dd\
0>,
...

ambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0x2aaaab7c4950>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0x2aaaab7bb170>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x2\
aaaab7c6e60>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0x2aaaab7cf0e0>,
...

generic_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTable instance at 0x2aaaabbfbdd0>,
 2: <Bio.Data.CodonTable.NCBICodonTable instance at 0x2aaaabbfbea8>,
 3: <Bio.Data.CodonTable.NCBICodonTable instance at 0x2aaaabbfbf80>,
 4: <Bio.Data.CodonTable.NCBICodonTable instance at 0x2aaaaaba70e0>,
 5: <Bio.Data.CodonTable.NCBICodonTable instance at 0x2aaaaaba7200>,
 6: <Bio.Data.CodonTable.NCBICodonTable instance at 0x2aaaaaba72d8>,
 9: <Bio.Data.CodonTable.NCBICodonTable instance at 0x2aaaaaba73b0>,
 10: <Bio.Data.CodonTable.NCBICodonTable instance at 0x2aaaaaba7488>,
...

generic_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTable inst\
ance at 0x2aaaaaba7ab8>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTable instanc\
e at 0x2aaaaaba7e18>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTable instance at 0x2aaaaa\
ba7710>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTable insta\
nce at 0x2aaaaabac518>,
...

standard_dna_table

Type:
NCBICodonTableDNA
Value:
<Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aaaaab9d4d0>

standard_rna_table

Type:
NCBICodonTableRNA
Value:
<Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aaaabbfbe18>

unambiguous_dna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aaaaab9d4d0>\
,
 2: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aaaabbfbe60>\
,
 3: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aaaabbfbf38>\
,
 4: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aaaaaba7098>\
,
...

unambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableDNA i\
nstance at 0x2aaaaaba7908>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableDNA inst\
ance at 0x2aaaaaba7c68>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x2aa\
aaaba7560>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableDNA in\
stance at 0x2aaaaabac368>,
...

unambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aaaabbfbe18>\
,
 2: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aaaabbfbef0>\
,
 3: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aaaabbfbfc8>\
,
 4: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aaaaaba7128>\
,
...

unambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableRNA i\
nstance at 0x2aaaaaba7b48>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableRNA inst\
ance at 0x2aaaaaba7ea8>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x2aa\
aaaba77a0>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableRNA in\
stance at 0x2aaaaabac5a8>,
...

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