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# Set up the IUPAC alphabet properties
from Bio.PropertyManager import default_manager
from Bio import Alphabet
from Bio.Alphabet import IUPAC
from Bio.Data import IUPACData
from Bio import Transcribe, Translate
set_prop = default_manager.class_property
# weight tables
set_prop[IUPAC.IUPACUnambiguousDNA]["weight_table"] = \
IUPACData.unambiguous_dna_weights
set_prop[IUPAC.IUPACAmbiguousDNA]["weight_table"] = \
IUPACData.avg_ambiguous_dna_weights
set_prop[IUPAC.IUPACUnambiguousRNA]["weight_table"] = \
IUPACData.unambiguous_rna_weights
set_prop[IUPAC.IUPACAmbiguousRNA]["weight_table"] = \
IUPACData.avg_ambiguous_rna_weights
set_prop[IUPAC.IUPACProtein]["weight_table"] = \
IUPACData.protein_weights
set_prop[IUPAC.ExtendedIUPACProtein]["weight_table"] = \
IUPACData.avg_extended_protein_weights
set_prop[IUPAC.IUPACUnambiguousDNA]["weight_range_table"] = \
IUPACData.unambiguous_dna_weight_ranges
set_prop[IUPAC.IUPACAmbiguousDNA]["weight_range_table"] = \
IUPACData.ambiguous_dna_weight_ranges
set_prop[IUPAC.IUPACUnambiguousRNA]["weight_range_table"] = \
IUPACData.unambiguous_rna_weight_ranges
set_prop[IUPAC.IUPACAmbiguousRNA]["weight_range_table"] = \
IUPACData.ambiguous_rna_weight_ranges
set_prop[IUPAC.IUPACProtein]["weight_range_table"] = \
IUPACData.protein_weight_ranges
set_prop[IUPAC.ExtendedIUPACProtein]["weight_range_table"] = \
IUPACData.extended_protein_weight_ranges
# transcriber objects
set_prop[Alphabet.DNAAlphabet]["transcriber"] = \
Transcribe.generic_transcriber
set_prop[IUPAC.IUPACAmbiguousDNA]["transcriber"] = \
Transcribe.ambiguous_transcriber
set_prop[IUPAC.IUPACUnambiguousDNA]["transcriber"] = \
Transcribe.unambiguous_transcriber
set_prop[Alphabet.RNAAlphabet]["transcriber"] = \
Transcribe.generic_transcriber
set_prop[IUPAC.IUPACAmbiguousRNA]["transcriber"] = \
Transcribe.ambiguous_transcriber
set_prop[IUPAC.IUPACUnambiguousRNA]["transcriber"] = \
Transcribe.unambiguous_transcriber
# translator objects
for name, obj in Translate.unambiguous_dna_by_name.items():
property = "translator.name." + name
set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
set_prop[obj.table.protein_alphabet.__class__][property] = obj
for name, obj in Translate.unambiguous_rna_by_name.items():
property = "translator.name." + name
set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
property = "rna_translator.name." + name
set_prop[obj.table.protein_alphabet.__class__][property] = obj
for id, obj in Translate.unambiguous_dna_by_id.items():
property = "translator.id.%d" % id
set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
set_prop[obj.table.protein_alphabet.__class__][property] = obj
if id == 1:
set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
set_prop[obj.table.protein_alphabet.__class__]["translator"] = obj
for id, obj in Translate.unambiguous_rna_by_id.items():
property = "translator.id.%d" % id
set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
property = "rna_translator.id.%d" % id
set_prop[obj.table.protein_alphabet.__class__][property] = obj
if id == 1:
set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
set_prop[obj.table.protein_alphabet.__class__]["rna_translator"] = obj
# ambiguous translator objects
for name, obj in Translate.ambiguous_dna_by_name.items():
property = "translator.name." + name
set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
property = "ambiguous_translator.name." + name
set_prop[obj.table.protein_alphabet.__class__][property] = obj
for name, obj in Translate.ambiguous_rna_by_name.items():
property = "translator.name." + name
set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
property = "ambiguous_rna_translator.name." + name
set_prop[obj.table.protein_alphabet.__class__][property] = obj
for id, obj in Translate.ambiguous_dna_by_id.items():
property = "translator.id.%d" % id
set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
property = "ambiguous_translator.id.%d" % id
set_prop[obj.table.protein_alphabet.__class__][property] = obj
if id == 1:
set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
set_prop[obj.table.protein_alphabet.__class__]["ambiguous_translator"] = obj
for id, obj in Translate.ambiguous_rna_by_id.items():
property = "translator.id.%d" % id
set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
property = "ambiguous_rna_translator.id.%d" % id
set_prop[obj.table.protein_alphabet.__class__][property] = obj
if id == 1:
set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
set_prop[obj.table.protein_alphabet.__class__]["ambiguous_rna_translator"] = obj
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