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
#'Bacterial and Plant Plastid' (which used to be just 'Bacterial')
names = [x.strip() for x in name.replace(" and ","; ").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.iteritems():
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.iteritems())
_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
IUPACData.extended_protein_values)
ambiguous_rna_by_id = {}
for key, val in unambiguous_rna_by_id.items():
ambiguous_rna_by_id[key] = AmbiguousCodonTable(val,
IUPAC.ambiguous_rna,
IUPACData.ambiguous_rna_values,
IUPAC.extended_protein,
IUPACData.extended_protein_values)
#The following isn't very elegant, but seems to work nicely.
_merged_values = dict(IUPACData.ambiguous_rna_values.iteritems())
_merged_values["T"] = "U"
for key, val in generic_by_name.items():
ambiguous_generic_by_name[key] = AmbiguousCodonTable(val,
Alphabet.NucleotideAlphabet(),
_merged_values,
IUPAC.extended_protein,
IUPACData.extended_protein_values)
for key, val in generic_by_id.items():
ambiguous_generic_by_id[key] = AmbiguousCodonTable(val,
Alphabet.NucleotideAlphabet(),
_merged_values,
IUPAC.extended_protein,
IUPACData.extended_protein_values)
del _merged_values
del key, val
#Basic sanity test,
for n in ambiguous_generic_by_id.keys() :
