# This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """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 4.0 """ from __future__ import print_function from Bio import Alphabet from Bio.Alphabet import IUPAC from Bio.Data import IUPACData unambiguous_dna_by_name = {} unambiguous_dna_by_id = {} unambiguous_rna_by_name = {} unambiguous_rna_by_id = {} generic_by_name = {} # unambiguous DNA or RNA generic_by_id = {} # unambiguous DNA or RNA ambiguous_dna_by_name = {} ambiguous_dna_by_id = {} ambiguous_rna_by_name = {} ambiguous_rna_by_id = {} ambiguous_generic_by_name = {} # ambiguous DNA or RNA ambiguous_generic_by_id = {} # ambiguous DNA or RNA # standard IUPAC unambiguous codons standard_dna_table = None standard_rna_table = None # In the future, the back_table could return a statistically # appropriate distribution of codons, so do not cache the results of # back_table lookups! class TranslationError(Exception): pass class CodonTable(object): """A codon-table, or genetic code.""" nucleotide_alphabet = Alphabet.generic_nucleotide protein_alphabet = Alphabet.generic_protein forward_table = {} # only includes codons which actually code back_table = {} # for back translations start_codons = [] stop_codons = [] # Not always called from derived classes! def __init__(self, nucleotide_alphabet=nucleotide_alphabet, protein_alphabet=protein_alphabet, forward_table=forward_table, back_table=back_table, start_codons=start_codons, stop_codons=stop_codons): self.nucleotide_alphabet = nucleotide_alphabet self.protein_alphabet = protein_alphabet self.forward_table = forward_table self.back_table = back_table self.start_codons = start_codons self.stop_codons = stop_codons def __str__(self): """Returns a simple text representation of the codon table. e.g. >>> import Bio.Data.CodonTable >>> print(Bio.Data.CodonTable.standard_dna_table) >>> print(Bio.Data.CodonTable.generic_by_id[1]) """ if self.id: answer = "Table %i" % self.id else: answer = "Table ID unknown" if self.names: answer += " " + ", ".join([x for x in self.names if x]) # Use the main four letters (and the conventional ordering) # even for ambiguous tables letters = self.nucleotide_alphabet.letters if isinstance(self.nucleotide_alphabet, Alphabet.DNAAlphabet) \ or (letters is not None and "T" in letters): letters = "TCAG" else: # Should be either RNA or generic nucleotides, # e.g. Bio.Data.CodonTable.generic_by_id[1] letters = "UCAG" # Build the table... answer += "\n\n |" + "|".join(" %s " % c2 for c2 in letters) + "|" answer += "\n--+" + "+".join("---------" for c2 in letters) + "+--" for c1 in letters: for c3 in letters: line = c1 + " |" for c2 in letters: codon = c1 + c2 + c3 line += " %s" % codon if codon in self.stop_codons: line += " Stop|" else: try: amino = self.forward_table[codon] except KeyError: amino = "?" except TranslationError: amino = "?" if codon in self.start_codons: line += " %s(s)|" % amino else: line += " %s |" % amino line += " " + c3 answer += "\n" + line answer += "\n--+" + "+".join("---------" for c2 in letters) + "+--" return answer def make_back_table(table, default_stop_codon): """Back a back-table (naive single codon mapping). ONLY RETURNS A SINGLE CODON, chosen from the possible alternatives based on their sort order. """ # Do the sort so changes in the hash implementation won't affect # the result when one amino acid is coded by more than one codon. back_table = {} for key in sorted(table): back_table[table[key]] = key back_table[None] = default_stop_codon return back_table class NCBICodonTable(CodonTable): nucleotide_alphabet = Alphabet.generic_nucleotide protein_alphabet = IUPAC.protein def __init__(self, id, names, table, start_codons, stop_codons): self.id = id self.names = names self.forward_table = table self.back_table = make_back_table(table, stop_codons[0]) self.start_codons = start_codons self.stop_codons = stop_codons class NCBICodonTableDNA(NCBICodonTable): nucleotide_alphabet = IUPAC.unambiguous_dna class NCBICodonTableRNA(NCBICodonTable): nucleotide_alphabet = IUPAC.unambiguous_rna # ######## Deal with ambiguous forward translations class AmbiguousCodonTable(CodonTable): def __init__(self, codon_table, ambiguous_nucleotide_alphabet, ambiguous_nucleotide_values, ambiguous_protein_alphabet, ambiguous_protein_values): CodonTable.__init__(self, ambiguous_nucleotide_alphabet, ambiguous_protein_alphabet, AmbiguousForwardTable(codon_table.forward_table, ambiguous_nucleotide_values, ambiguous_protein_values), codon_table.back_table, # These two are WRONG! I need to get the # list of ambiguous codons which code for # the stop codons XXX list_ambiguous_codons(codon_table.start_codons, ambiguous_nucleotide_values), list_ambiguous_codons(codon_table.stop_codons, ambiguous_nucleotide_values) ) self._codon_table = codon_table # Be sneaky and forward attribute lookups to the original table. # This lets us get the names, if the original table is an NCBI # table. def __getattr__(self, name): return getattr(self._codon_table, name) def list_possible_proteins(codon, forward_table, ambiguous_nucleotide_values): c1, c2, c3 = codon x1 = ambiguous_nucleotide_values[c1] x2 = ambiguous_nucleotide_values[c2] x3 = ambiguous_nucleotide_values[c3] possible = {} stops = [] for y1 in x1: for y2 in x2: for y3 in x3: try: possible[forward_table[y1 + y2 + y3]] = 1 except KeyError: # If tripping over a stop codon stops.append(y1 + y2 + y3) if stops: if possible: raise TranslationError("ambiguous codon %r codes for both" " proteins and stop codons" % codon) # This is a true stop codon - tell the caller about it raise KeyError(codon) return list(possible) def list_ambiguous_codons(codons, ambiguous_nucleotide_values): """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. """ # Note ambiguous_nucleotide_values['R'] = 'AG' (etc) # This will generate things like 'TRR' from ['TAG', 'TGA'], which # we don't want to include: c1_list = sorted(letter for (letter, meanings) in ambiguous_nucleotide_values.items() if set(codon[0] for codon in codons).issuperset(set(meanings))) c2_list = sorted(letter for (letter, meanings) in ambiguous_nucleotide_values.items() if set(codon[1] for codon in codons).issuperset(set(meanings))) c3_list = sorted(letter for (letter, meanings) in ambiguous_nucleotide_values.items() if set(codon[2] for codon in codons).issuperset(set(meanings))) # candidates is a list (not a set) to preserve the iteration order candidates = [] for c1 in c1_list: for c2 in c2_list: for c3 in c3_list: codon = c1 + c2 + c3 if codon not in candidates and codon not in codons: candidates.append(codon) answer = codons[:] # copy # print "Have %i new candidates" % len(candidates) for ambig_codon in candidates: wanted = True # e.g. 'TRR' -> 'TAA', 'TAG', 'TGA', 'TGG' for codon in [c1 + c2 + c3 for c1 in ambiguous_nucleotide_values[ambig_codon[0]] for c2 in ambiguous_nucleotide_values[ambig_codon[1]] for c3 in ambiguous_nucleotide_values[ambig_codon[2]]]: if codon not in codons: # This ambiguous codon can code for a non-stop, exclude it! wanted = False # print "Rejecting %s" % ambig_codon continue if wanted: answer.append(ambig_codon) return answer assert list_ambiguous_codons(['TGA', 'TAA'], IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TRA'] assert list_ambiguous_codons(['TAG', 'TGA'], IUPACData.ambiguous_dna_values) == ['TAG', 'TGA'] assert list_ambiguous_codons(['TAG', 'TAA'], IUPACData.ambiguous_dna_values) == ['TAG', 'TAA', 'TAR'] assert list_ambiguous_codons(['UAG', 'UAA'], IUPACData.ambiguous_rna_values) == ['UAG', 'UAA', 'UAR'] assert list_ambiguous_codons(['TGA', 'TAA', 'TAG'], IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TAG', 'TAR', 'TRA'] # Forward translation is "onto", that is, any given codon always maps # to the same protein, or it doesn't map at all. Thus, I can build # off of an existing table to produce the ambiguous mappings. # # This handles the general case. Perhaps it's overkill? # >>> t = CodonTable.ambiguous_dna_by_id[1] # >>> t.forward_table["AAT"] # 'N' # >>> t.forward_table["GAT"] # 'D' # >>> t.forward_table["RAT"] # 'B' # >>> t.forward_table["YTA"] # 'L' class AmbiguousForwardTable(object): def __init__(self, forward_table, ambiguous_nucleotide, ambiguous_protein): self.forward_table = forward_table self.ambiguous_nucleotide = ambiguous_nucleotide self.ambiguous_protein = ambiguous_protein inverted = {} for name, val in ambiguous_protein.items(): for c in val: x = inverted.get(c, {}) x[name] = 1 inverted[c] = x for name, val in inverted.items(): inverted[name] = list(val) self._inverted = inverted self._cache = {} def get(self, codon, failobj=None): try: return self.__getitem__(codon) except KeyError: return failobj def __getitem__(self, codon): try: x = self._cache[codon] except KeyError: pass else: if x is TranslationError: raise TranslationError(codon) # no unique translation if x is KeyError: raise KeyError(codon) # it's a stop codon return x try: x = self.forward_table[codon] self._cache[codon] = x return x except KeyError: pass # XXX Need to make part of this into a method which returns # a list of all possible encodings for a codon! try: possible = list_possible_proteins(codon, self.forward_table, self.ambiguous_nucleotide) except KeyError: self._cache[codon] = KeyError raise KeyError(codon) # stop codon except TranslationError: self._cache[codon] = TranslationError raise TranslationError(codon) # does not code assert len(possible) > 0, "unambiguous codons must code" # Hah! Only one possible protein, so use it if len(possible) == 1: self._cache[codon] = possible[0] return possible[0] # See if there's an ambiguous protein encoding for the multiples. # Find residues which exist in every coding set. ambiguous_possible = {} for amino in possible: for term in self._inverted[amino]: ambiguous_possible[term] = ambiguous_possible.get(term, 0) + 1 n = len(possible) possible = [] for amino, val in ambiguous_possible.items(): if val == n: possible.append(amino) # No amino acid encoding for the results if len(possible) == 0: self._cache[codon] = TranslationError raise TranslationError(codon) # no valid translation # All of these are valid, so choose one # To be unique, sort by smallet ambiguity then alphabetically # Can get this if "X" encodes for everything. # def _sort(x, y, table = self.ambiguous_protein): # a = cmp(len(table[x]), len(table[y])) # if a == 0: # return cmp(x, y) # return a # Sort by key is 2.x and 3.x compatible possible.sort(key=lambda x: (len(self.ambiguous_protein[x]), x)) x = possible[0] self._cache[codon] = x return x def 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).""" # In most cases names are divided by "; ", however there is also # Table 11 'Bacterial, Archaeal and Plant Plastid Code', previously # 'Bacterial and Plant Plastid' which used to be just 'Bacterial' names = [x.strip() for x in name.replace(" and ", "; ").replace(", ", "; ").split("; ")] dna = NCBICodonTableDNA(id, names + [alt_name], table, start_codons, stop_codons) ambig_dna = AmbiguousCodonTable(dna, IUPAC.ambiguous_dna, IUPACData.ambiguous_dna_values, IUPAC.extended_protein, IUPACData.extended_protein_values) # replace all T's with U's for the RNA tables rna_table = {} generic_table = {} for codon, val in table.items(): generic_table[codon] = val codon = codon.replace("T", "U") generic_table[codon] = val rna_table[codon] = val rna_start_codons = [] generic_start_codons = [] for codon in start_codons: generic_start_codons.append(codon) codon = codon.replace("T", "U") generic_start_codons.append(codon) rna_start_codons.append(codon) rna_stop_codons = [] generic_stop_codons = [] for codon in stop_codons: generic_stop_codons.append(codon) codon = codon.replace("T", "U") generic_stop_codons.append(codon) rna_stop_codons.append(codon) generic = NCBICodonTable(id, names + [alt_name], generic_table, generic_start_codons, generic_stop_codons) # The following isn't very elegant, but seems to work nicely. _merged_values = dict(IUPACData.ambiguous_rna_values.items()) _merged_values["T"] = "U" ambig_generic = AmbiguousCodonTable(generic, Alphabet.NucleotideAlphabet(), _merged_values, IUPAC.extended_protein, IUPACData.extended_protein_values) rna = NCBICodonTableRNA(id, names + [alt_name], rna_table, rna_start_codons, rna_stop_codons) ambig_rna = AmbiguousCodonTable(rna, IUPAC.ambiguous_rna, IUPACData.ambiguous_rna_values, IUPAC.extended_protein, IUPACData.extended_protein_values) if id == 1: global standard_dna_table, standard_rna_table standard_dna_table = dna standard_rna_table = rna unambiguous_dna_by_id[id] = dna unambiguous_rna_by_id[id] = rna generic_by_id[id] = generic ambiguous_dna_by_id[id] = ambig_dna ambiguous_rna_by_id[id] = ambig_rna ambiguous_generic_by_id[id] = ambig_generic if alt_name is not None: names.append(alt_name) for name in names: unambiguous_dna_by_name[name] = dna unambiguous_rna_by_name[name] = rna generic_by_name[name] = generic ambiguous_dna_by_name[name] = ambig_dna ambiguous_rna_by_name[name] = ambig_rna ambiguous_generic_by_name[name] = ambig_generic ########################################################################## # Start of auto-generated output from Scripts/update_ncbi_codon_table.py # ########################################################################## register_ncbi_table(name='Standard', alt_name='SGC0', id=1, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG', 'TGA'], start_codons=['TTG', 'CTG', 'ATG']) register_ncbi_table(name='Vertebrate Mitochondrial', alt_name='SGC1', id=2, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'M', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG', 'AGA', 'AGG'], start_codons=['ATT', 'ATC', 'ATA', 'ATG', 'GTG']) register_ncbi_table(name='Yeast Mitochondrial', alt_name='SGC2', id=3, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'T', 'CTC': 'T', 'CTA': 'T', 'CTG': 'T', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'M', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG'], start_codons=['ATA', 'ATG']) register_ncbi_table(name='Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma', alt_name='SGC3', id=4, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG'], start_codons=['TTA', 'TTG', 'CTG', 'ATT', 'ATC', 'ATA', 'ATG', 'GTG']) register_ncbi_table(name='Invertebrate Mitochondrial', alt_name='SGC4', id=5, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'M', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'S', 'AGG': 'S', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG'], start_codons=['TTG', 'ATT', 'ATC', 'ATA', 'ATG', 'GTG']) register_ncbi_table(name='Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear', alt_name='SGC5', id=6, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Q', 'TAG': 'Q', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TGA'], start_codons=['ATG']) register_ncbi_table(name='Echinoderm Mitochondrial; Flatworm Mitochondrial', alt_name='SGC8', id=9, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'N', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'S', 'AGG': 'S', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG'], start_codons=['ATG', 'GTG']) register_ncbi_table(name='Euplotid Nuclear', alt_name='SGC9', id=10, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG'], start_codons=['ATG']) register_ncbi_table(name='Bacterial, Archaeal and Plant Plastid', alt_name=None, id=11, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG', 'TGA'], start_codons=['TTG', 'CTG', 'ATT', 'ATC', 'ATA', 'ATG', 'GTG']) register_ncbi_table(name='Alternative Yeast Nuclear', alt_name=None, id=12, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'S', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG', 'TGA'], start_codons=['CTG', 'ATG']) register_ncbi_table(name='Ascidian Mitochondrial', alt_name=None, id=13, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'M', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'G', 'AGG': 'G', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG'], start_codons=['TTG', 'ATA', 'ATG', 'GTG']) register_ncbi_table(name='Alternative Flatworm Mitochondrial', alt_name=None, id=14, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'N', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'S', 'AGG': 'S', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAG'], start_codons=['ATG']) register_ncbi_table(name='Blepharisma Macronuclear', alt_name=None, id=15, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAG': 'Q', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TGA'], start_codons=['ATG']) register_ncbi_table(name='Chlorophycean Mitochondrial', alt_name=None, id=16, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAG': 'L', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TGA'], start_codons=['ATG']) register_ncbi_table(name='Trematode Mitochondrial', alt_name=None, id=21, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'M', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'N', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'S', 'AGG': 'S', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG'], start_codons=['ATG', 'GTG']) register_ncbi_table(name='Scenedesmus obliquus Mitochondrial', alt_name=None, id=22, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAG': 'L', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TCA', 'TAA', 'TGA'], start_codons=['ATG']) register_ncbi_table(name='Thraustochytrium Mitochondrial', alt_name=None, id=23, table={ 'TTT': 'F', 'TTC': 'F', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TTA', 'TAA', 'TAG', 'TGA'], start_codons=['ATT', 'ATG', 'GTG']) register_ncbi_table(name='Pterobranchia Mitochondrial', alt_name=None, id=24, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'S', 'AGG': 'K', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG'], start_codons=['TTG', 'CTG', 'ATG', 'GTG']) register_ncbi_table(name='Candidate Division SR1 and Gracilibacteria', alt_name=None, id=25, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'G', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG'], start_codons=['TTG', 'ATG', 'GTG']) ######################################################################## # End of auto-generated output from Scripts/update_ncbi_codon_table.py # ######################################################################## # This is currently missing in Version 4.0 of # ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt # and was entered by hand based on # http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG26 # # Code 26 is used so far only for the ascomycete fungus Pachysolen # tannophilus. The only difference to the standard code is the # translation of CUG as alanine (as opposed to leucine). As of # April 2016, there is no publication documenting this code. register_ncbi_table(name='Pachysolen tannophilus Nuclear Code', alt_name=None, id=26, table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'A', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }, stop_codons=['TAA', 'TAG', 'TGA'], start_codons=['TTG', 'CTG', 'ATG']) # Basic sanity test, for key, val in generic_by_name.items(): assert key in ambiguous_generic_by_name[key].names for key, val in generic_by_id.items(): assert ambiguous_generic_by_id[key].id == key del key, val for n in ambiguous_generic_by_id: assert ambiguous_rna_by_id[n].forward_table["GUU"] == "V" assert ambiguous_rna_by_id[n].forward_table["GUN"] == "V" if n != 23: # For table 23, UUN = F, L or stop. assert ambiguous_rna_by_id[n].forward_table["UUN"] == "X" # F or L # R = A or G, so URR = UAA or UGA / TRA = TAA or TGA = stop codons if "UAA" in unambiguous_rna_by_id[n].stop_codons \ and "UGA" in unambiguous_rna_by_id[n].stop_codons: try: print(ambiguous_dna_by_id[n].forward_table["TRA"]) assert False, "Should be a stop only" except KeyError: pass assert "URA" in ambiguous_generic_by_id[n].stop_codons assert "URA" in ambiguous_rna_by_id[n].stop_codons assert "TRA" in ambiguous_generic_by_id[n].stop_codons assert "TRA" in ambiguous_dna_by_id[n].stop_codons del n assert ambiguous_generic_by_id[1] == ambiguous_generic_by_name["Standard"] assert ambiguous_generic_by_id[4] == ambiguous_generic_by_name["SGC3"] assert ambiguous_generic_by_id[11] == ambiguous_generic_by_name["Bacterial"] assert ambiguous_generic_by_id[11] == ambiguous_generic_by_name["Archaeal"] assert ambiguous_generic_by_id[11] == ambiguous_generic_by_name["Plant Plastid"] assert ambiguous_generic_by_id[15] == ambiguous_generic_by_name['Blepharisma Macronuclear'] assert ambiguous_generic_by_id[24] == ambiguous_generic_by_name["Pterobranchia Mitochondrial"] assert generic_by_id[1] == generic_by_name["Standard"] assert generic_by_id[4] == generic_by_name["SGC3"] assert generic_by_id[11] == generic_by_name["Bacterial"] assert generic_by_id[11] == generic_by_name["Plant Plastid"] assert generic_by_id[15] == generic_by_name['Blepharisma Macronuclear'] assert generic_by_id[24] == generic_by_name["Pterobranchia Mitochondrial"]