# Copyright 2000-2001 by Andrew Dalke.
# Revisions copyright 2008 by Peter Cock.
# All rights reserved.
# 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.
 
"""Standard nucleotide and protein alphabets defined by IUPAC."""
 
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
 
assert IUPACData.extended_protein_letters == IUPACData.extended_protein_letters.upper()
 
 
class ExtendedIUPACProtein(Alphabet.ProteinAlphabet):
    """Extended uppercase IUPAC protein single letter alphabet including X etc.
 
    In addition to the standard 20 single letter protein codes, this includes:
 
    B = "Asx";  Aspartic acid (R) or Asparagine (N)
    X = "Xxx";  Unknown or 'other' amino acid
    Z = "Glx";  Glutamic acid (E) or Glutamine (Q)
    J = "Xle";  Leucine (L) or Isoleucine (I), used in mass-spec (NMR)
    U = "Sec";  Selenocysteine
    O = "Pyl";  Pyrrolysine
 
    This alphabet is not intended to be used with X for Selenocysteine
    (an ad-hoc standard prior to the IUPAC adoption of U instead).
    """
    letters = IUPACData.extended_protein_letters
 
extended_protein = ExtendedIUPACProtein()
 
assert IUPACData.protein_letters == IUPACData.protein_letters.upper()
 
 
class IUPACProtein(ExtendedIUPACProtein):
    """Uppercase IUPAC protein single letter alphabet of the 20 standard amino acids."""
    letters = IUPACData.protein_letters
 
protein = IUPACProtein()
 
##################### DNA
 
 
# The next two are the IUPAC definitions, from:
#   http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html
class IUPACAmbiguousDNA(Alphabet.DNAAlphabet):
    """Uppercase IUPAC ambiguous DNA."""
    letters = IUPACData.ambiguous_dna_letters
 
ambiguous_dna = IUPACAmbiguousDNA()
 
 
class IUPACUnambiguousDNA(IUPACAmbiguousDNA):
    """Uppercase IUPAC unambiguous DNA (letters GATC only)."""
    letters = IUPACData.unambiguous_dna_letters
 
unambiguous_dna = IUPACUnambiguousDNA()
 
 
# Also from the URL, but not part of the standard
class ExtendedIUPACDNA(Alphabet.DNAAlphabet):
    """Extended IUPAC DNA alphabet.
 
    In addition to the standard letter codes GATC, this includes:
 
    B = 5-bromouridine
    D = 5,6-dihydrouridine
    S = thiouridine
    W = wyosine
    """
    letters = IUPACData.extended_dna_letters
 
extended_dna = ExtendedIUPACDNA()
 
##################### RNA
 
 
class IUPACAmbiguousRNA(Alphabet.RNAAlphabet):
    """Uppercase IUPAC ambiguous RNA."""
    letters = IUPACData.ambiguous_rna_letters
 
ambiguous_rna = IUPACAmbiguousRNA()
 
 
class IUPACUnambiguousRNA(IUPACAmbiguousRNA):
    """Uppercase IUPAC unambiguous RNA (letters GAUC only)."""
    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