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# Define the IUPAC Alphabets you know and love
from Bio import Alphabet
from Bio.Data import IUPACData
##################### Protein
# From the IUPAC definition at:
# http://www.chem.qmw.ac.uk/iupac/AminoAcid/A2021.html#AA21
class IUPACProtein(Alphabet.ProteinAlphabet):
letters = IUPACData.protein_letters
protein = IUPACProtein()
# This could be considered the base class for the standard IUPAC
# protein, except that some encodings will use "X" to mean "unknown
# character", which causes a collision. If you use X for
# selenocysteines, then you'll need a new alphabet.
class ExtendedIUPACProtein(Alphabet.ProteinAlphabet):
letters = IUPACData.extended_protein_letters
# B = "Asx"; aspartic acid or asparagine
# X = "Sec"; selenocysteine Note: IUPAC is moving to use 'U' for this
# Z = "Glx"; glutamic acid or glutamine (or substances such as
# 4-carboxyglutamic acid and 5-oxoproline that yield glutamic
# acid on acid hydrolysis of peptides)
extended_protein = ExtendedIUPACProtein()
##################### DNA
# The next two are the IUPAC definitions, from:
# http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html
class IUPACAmbiguousDNA(Alphabet.DNAAlphabet):
letters = IUPACData.ambiguous_dna_letters
ambiguous_dna = IUPACAmbiguousDNA()
class IUPACUnambiguousDNA(IUPACAmbiguousDNA):
letters = IUPACData.unambiguous_dna_letters
unambiguous_dna = IUPACUnambiguousDNA()
# Also from the URL, but not part of the standard
class ExtendedIUPACDNA(Alphabet.DNAAlphabet):
letters = IUPACData.extended_dna_letters
# B == 5-bromouridine
# D == 5,6-dihydrouridine
# S == thiouridine
# W == wyosine
extended_dna = ExtendedIUPACDNA()
##################### RNA
class IUPACAmbiguousRNA(Alphabet.RNAAlphabet):
letters = IUPACData.ambiguous_rna_letters
ambiguous_rna = IUPACAmbiguousRNA()
class IUPACUnambiguousRNA(IUPACAmbiguousRNA):
letters = IUPACData.unambiguous_rna_letters
unambiguous_rna = IUPACUnambiguousRNA()
# are there extended forms?
#class ExtendedIUPACRNA(Alphabet.RNAAlphabet):
# letters = extended_rna_letters
# # B == 5-bromouridine
# # D == 5,6-dihydrouridine
# # S == thiouridine
# # W == wyosine
# We need to load the property resolution information, but we need to
# wait until after the systems have been loaded. (There's a nasty loop
# where, eg, translation objects need an alphabet, which need to be
# assocated with translators.)
from Bio.PropertyManager import default_manager
def _bootstrap(manager, klass, property):
assert manager is default_manager
del default_manager.class_resolver[IUPACProtein]
del default_manager.class_resolver[ExtendedIUPACProtein]
del default_manager.class_resolver[IUPACAmbiguousDNA]
del default_manager.class_resolver[IUPACUnambiguousDNA]
del default_manager.class_resolver[ExtendedIUPACDNA]
del default_manager.class_resolver[IUPACAmbiguousRNA]
del default_manager.class_resolver[IUPACUnambiguousRNA]
from Bio.Encodings import IUPACEncoding
return manager.resolve_class(klass, property)
default_manager.class_resolver[IUPACProtein] = _bootstrap
default_manager.class_resolver[ExtendedIUPACProtein] = _bootstrap
default_manager.class_resolver[IUPACAmbiguousDNA] = _bootstrap
default_manager.class_resolver[IUPACUnambiguousDNA] = _bootstrap
default_manager.class_resolver[ExtendedIUPACDNA] = _bootstrap
default_manager.class_resolver[IUPACAmbiguousRNA] = _bootstrap
default_manager.class_resolver[IUPACUnambiguousRNA] = _bootstrap
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