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python-biopython  1.60
Classes | Namespaces | Functions | Variables
CodonTable.py File Reference

Go to the source code of this file.

Classes

class  Bio.Data.CodonTable.TranslationError
class  Bio.Data.CodonTable.CodonTable
class  Bio.Data.CodonTable.NCBICodonTable
class  Bio.Data.CodonTable.NCBICodonTableDNA
class  Bio.Data.CodonTable.NCBICodonTableRNA
class  Bio.Data.CodonTable.AmbiguousCodonTable
class  Bio.Data.CodonTable.AmbiguousForwardTable

Namespaces

namespace  Bio.Data.CodonTable

Functions

def Bio.Data.CodonTable.make_back_table
def Bio.Data.CodonTable.list_possible_proteins
def Bio.Data.CodonTable.list_ambiguous_codons
def Bio.Data.CodonTable.register_ncbi_table

Variables

dictionary Bio.Data.CodonTable.unambiguous_dna_by_name = {}
dictionary Bio.Data.CodonTable.unambiguous_dna_by_id = {}
dictionary Bio.Data.CodonTable.unambiguous_rna_by_name = {}
dictionary Bio.Data.CodonTable.unambiguous_rna_by_id = {}
dictionary Bio.Data.CodonTable.generic_by_name = {}
dictionary Bio.Data.CodonTable.generic_by_id = {}
dictionary Bio.Data.CodonTable.ambiguous_dna_by_name = {}
dictionary Bio.Data.CodonTable.ambiguous_dna_by_id = {}
dictionary Bio.Data.CodonTable.ambiguous_rna_by_name = {}
dictionary Bio.Data.CodonTable.ambiguous_rna_by_id = {}
dictionary Bio.Data.CodonTable.ambiguous_generic_by_name = {}
dictionary Bio.Data.CodonTable.ambiguous_generic_by_id = {}
 Bio.Data.CodonTable.standard_dna_table = None
 Bio.Data.CodonTable.standard_rna_table = None
string Bio.Data.CodonTable.alt_name = 'SGC0'
 These tables created from the data file ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt using the following: import re for line in open("gc.prt").readlines(): if line[:2] == " {": names = [] id = None aa = None start = None bases = [] elif line[:6] == " name": names.append(re.search('"([^"]*)"', line).group(1)) elif line[:8] == " name": names.append(re.search('"(.
dictionary Bio.Data.CodonTable.table
list Bio.Data.CodonTable.stop_codons = [ 'TAA', 'TAG', 'TGA', ]
list Bio.Data.CodonTable.start_codons = [ 'TTG', 'CTG', 'ATG', ]

Class Documentation

class Bio::Data::CodonTable::TranslationError

Definition at line 38 of file CodonTable.py.