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__init__.py

# Copyright 2000-2002 by Andrew Dalke.
# Revisions copyright 2007-2010 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.

"""Alphabets used in Seq objects etc to declare sequence type and letters.

This is used by sequences which contain a finite number of similar words.
"""

00013 class Alphabet:
    size = None     # default to no fixed size for words
    letters = None  # default to no fixed alphabet
                    # In general, a list-like object. However,
                    # assuming letters are single characters, use a
                    # string. This is expected for use with Seq like
                    # objects.

    def __repr__(self):
        return self.__class__.__name__ + "()"

00024     def contains(self, other):
        """Does this alphabet 'contain' the other (OBSOLETE?).

        Returns a boolean.  This relies on the Alphabet subclassing
        hierarchy only, and does not check the letters property.
        This isn't ideal, and doesn't seem to work as intended
        with the AlphabetEncoder classes."""
        return isinstance(other, self.__class__)

00033     def _case_less(self):
        """Return an case-less variant of the current alphabet (PRIVATE)."""
        #TODO - remove this method by dealing with things in subclasses?
        if isinstance(self, ProteinAlphabet):
            return generic_protein
        elif isinstance(self, DNAAlphabet):
            return generic_dna
        elif isinstance(self, NucleotideAlphabet):
            return generic_rna
        elif isinstance(self, NucleotideAlphabet):
            return generic_nucleotide
        elif isinstance(self, SingleLetterAlphabet):
            return single_letter_alphabet
        else:
            return generic_alphabet

00049     def _upper(self):
        """Return an upper case variant of the current alphabet (PRIVATE)."""
        if not self.letters or self.letters==self.letters.upper():
            #Easy case, no letters or already upper case!
            return self
        else:
            #TODO - Raise NotImplementedError and handle via subclass?
            return self._case_less()

00058     def _lower(self):
        """Return a lower case variant of the current alphabet (PRIVATE)."""
        if not self.letters or self.letters==self.letters.lower():
            #Easy case, no letters or already lower case!
            return self
        else:
            #TODO - Raise NotImplementedError and handle via subclass?
            return self._case_less()

generic_alphabet = Alphabet()

00069 class SingleLetterAlphabet(Alphabet):
    size = 1
    letters = None   # string of all letters in the alphabet

single_letter_alphabet = SingleLetterAlphabet()

########### Protein

00077 class ProteinAlphabet(SingleLetterAlphabet):
    pass

generic_protein = ProteinAlphabet()

########### DNA
00083 class NucleotideAlphabet(SingleLetterAlphabet):
    pass

generic_nucleotide = NucleotideAlphabet()

00088 class DNAAlphabet(NucleotideAlphabet):
    pass

generic_dna = DNAAlphabet()


########### RNA

00096 class RNAAlphabet(NucleotideAlphabet):
    pass

generic_rna = RNAAlphabet()



########### Other per-sequence encodings

00105 class SecondaryStructure(SingleLetterAlphabet):
    letters = "HSTC"

00108 class ThreeLetterProtein(Alphabet):
    size = 3
    letters = [
        "Ala", "Asx", "Cys", "Asp", "Glu", "Phe", "Gly", "His", "Ile",
        "Lys", "Leu", "Met", "Asn", "Pro", "Gln", "Arg", "Ser", "Thr",
        "Sec", "Val", "Trp", "Xaa", "Tyr", "Glx",
        ]
        
###### Non per-sequence modifications

# (These are Decorator classes)

00120 class AlphabetEncoder:
    def __init__(self, alphabet, new_letters):
        self.alphabet = alphabet
        self.new_letters = new_letters
        if alphabet.letters is not None:
            self.letters = alphabet.letters + new_letters
        else:
            self.letters = None
    def __getattr__(self, key):
        if key[:2] == "__" and key[-2:] == "__":
            raise AttributeError(key)
        return getattr(self.alphabet, key)

    def __repr__(self):
        return "%s(%r, %r)" % (self.__class__.__name__, self.alphabet,
                               self.new_letters)

00137     def contains(self, other):
        """Does this alphabet 'contain' the other (OBSOLETE?).

        This is isn't implemented for the base AlphabetEncoder,
        which will always return 0 (False)."""
        return 0

00144     def _upper(self):
        """Return an upper case variant of the current alphabet (PRIVATE)."""
        return AlphabetEncoder(self.alphabet._upper(), self.new_letters.upper())

00148     def _lower(self):
        """Return a lower case variant of the current alphabet (PRIVATE)."""
        return AlphabetEncoder(self.alphabet._lower(), self.new_letters.lower())

    
00153 class Gapped(AlphabetEncoder):
    def __init__(self, alphabet, gap_char = "-"):
        AlphabetEncoder.__init__(self, alphabet, gap_char)
        self.gap_char = gap_char

00158     def contains(self, other):
        """Does this alphabet 'contain' the other (OBSOLETE?).

        Returns a boolean.  This relies on the Alphabet subclassing
        hierarchy, and attempts to check the gap character.  This fails
        if the other alphabet does not have a gap character!
        """
        return other.gap_char == self.gap_char and \
               self.alphabet.contains(other.alphabet)

00168     def _upper(self):
        """Return an upper case variant of the current alphabet (PRIVATE)."""
        return Gapped(self.alphabet._upper(), self.gap_char.upper())

00172     def _lower(self):
        """Return a lower case variant of the current alphabet (PRIVATE)."""
        return Gapped(self.alphabet._lower(), self.gap_char.lower())

            
00177 class HasStopCodon(AlphabetEncoder):
    def __init__(self, alphabet, stop_symbol = "*"):
        AlphabetEncoder.__init__(self, alphabet, stop_symbol)
        self.stop_symbol = stop_symbol
        
    def __cmp__(self, other):
        x = cmp(self.alphabet, other.alphabet)
        if x == 0:
            return cmp(self.stop_symbol, other.stop_symbol)
        return x

00188     def contains(self, other):
        """Does this alphabet 'contain' the other (OBSOLETE?).

        Returns a boolean.  This relies on the Alphabet subclassing
        hierarchy, and attempts to check the stop symbol.  This fails
        if the other alphabet does not have a stop symbol!
        """
        return other.stop_symbol == self.stop_symbol and \
               self.alphabet.contains(other.alphabet)

00198     def _upper(self):
        """Return an upper case variant of the current alphabet (PRIVATE)."""
        return HasStopCodon(self.alphabet._upper(), self.stop_symbol.upper())

00202     def _lower(self):
        """Return a lower case variant of the current alphabet (PRIVATE)."""
        return HasStopCodon(self.alphabet._lower(), self.stop_symbol.lower())


def _get_base_alphabet(alphabet):
    """Returns the non-gapped non-stop-codon Alphabet object (PRIVATE)."""
    a = alphabet
    while isinstance(a, AlphabetEncoder):
        a = a.alphabet
    assert isinstance(a, Alphabet), \
           "Invalid alphabet found, %s" % repr(a)
    return a

def _ungap(alphabet):
    """Returns the alphabet without any gap encoder (PRIVATE)."""
    #TODO - Handle via method of the objects?
    if not hasattr(alphabet, "gap_char"):
        return alphabet
    elif isinstance(alphabet, Gapped):
        return alphabet.alphabet
    elif isinstance(alphabet, HasStopCodon):
        return HasStopCodon(_ungap(alphabet.alphabet), stop_symbol=alphabet.stop_symbol)
    elif isinstance(alphabet, AlphabetEncoder):
        return AlphabetEncoder(_ungap(alphabet.alphabet), letters=alphabet.letters)
    else:
        raise NotImplementedError
    
def _consensus_base_alphabet(alphabets):
    """Returns a common but often generic base alphabet object (PRIVATE).

    This throws away any AlphabetEncoder information, e.g. Gapped alphabets.

    Note that DNA+RNA -> Nucleotide, and Nucleotide+Protein-> generic single
    letter.  These DO NOT raise an exception!"""
    common = None
    for alpha in alphabets:
        a = _get_base_alphabet(alpha)
        if common is None:
            common = a
        elif common == a:
            pass
        elif isinstance(a, common.__class__):
            pass
        elif isinstance(common, a.__class__):
            common = a
        elif isinstance(a, NucleotideAlphabet) \
        and isinstance(common, NucleotideAlphabet):
            #e.g. Give a mix of RNA and DNA alphabets
            common = generic_nucleotide
        elif isinstance(a, SingleLetterAlphabet) \
        and isinstance(common, SingleLetterAlphabet):
            #This is a pretty big mis-match!
            common = single_letter_alphabet
        else:
            #We have a major mis-match... take the easy way out!
            return generic_alphabet
    if common is None:
        #Given NO alphabets!
        return generic_alphabet
    return common

def _consensus_alphabet(alphabets):
    """Returns a common but often generic alphabet object (PRIVATE).

    >>> from Bio.Alphabet import IUPAC
    >>> _consensus_alphabet([IUPAC.extended_protein, IUPAC.protein])
    ExtendedIUPACProtein()
    >>> _consensus_alphabet([generic_protein, IUPAC.protein])
    ProteinAlphabet()

    Note that DNA+RNA -> Nucleotide, and Nucleotide+Protein-> generic single
    letter.  These DO NOT raise an exception!

    >>> _consensus_alphabet([generic_dna, generic_nucleotide])
    NucleotideAlphabet()
    >>> _consensus_alphabet([generic_dna, generic_rna])
    NucleotideAlphabet()
    >>> _consensus_alphabet([generic_dna, generic_protein])
    SingleLetterAlphabet()
    >>> _consensus_alphabet([single_letter_alphabet, generic_protein])
    SingleLetterAlphabet()
    
    This is aware of Gapped and HasStopCodon and new letters added by
    other AlphabetEncoders.  This WILL raise an exception if more than
    one gap character or stop symbol is present.

    >>> from Bio.Alphabet import IUPAC
    >>> _consensus_alphabet([Gapped(IUPAC.extended_protein), HasStopCodon(IUPAC.protein)])
    HasStopCodon(Gapped(ExtendedIUPACProtein(), '-'), '*')
    >>> _consensus_alphabet([Gapped(IUPAC.protein, "-"), Gapped(IUPAC.protein, "=")])
    Traceback (most recent call last):
        ...
    ValueError: More than one gap character present
    >>> _consensus_alphabet([HasStopCodon(IUPAC.protein, "*"), HasStopCodon(IUPAC.protein, "+")])
    Traceback (most recent call last):
        ...
    ValueError: More than one stop symbol present
    """
    base = _consensus_base_alphabet(alphabets)
    gap = None
    stop = None
    new_letters = ""
    for alpha in alphabets:
        #Gaps...
        if not hasattr(alpha, "gap_char"):
            pass
        elif gap is None:
            gap = alpha.gap_char
        elif gap == alpha.gap_char:
            pass
        else:
            raise ValueError("More than one gap character present")
        #Stops...
        if not hasattr(alpha, "stop_symbol"):
            pass
        elif stop is None:
            stop = alpha.stop_symbol
        elif stop == alpha.stop_symbol:
            pass
        else:
            raise ValueError("More than one stop symbol present")
        #New letters...
        if hasattr(alpha, "new_letters"):
            for letter in alpha.new_letters:
                if letter not in new_letters \
                and letter != gap and letter != stop:
                    new_letters += letter

    alpha = base
    if new_letters:
        alpha = AlphabetEncoder(alpha, new_letters)
    if gap:
        alpha = Gapped(alpha, gap_char=gap)
    if stop:
        alpha = HasStopCodon(alpha, stop_symbol=stop)
    return alpha

def _check_type_compatible(alphabets):
    """Returns True except for DNA+RNA or Nucleotide+Protein (PRIVATE).

    >>> _check_type_compatible([generic_dna, generic_nucleotide])
    True
    >>> _check_type_compatible([generic_dna, generic_rna])
    False
    >>> _check_type_compatible([generic_dna, generic_protein])
    False
    >>> _check_type_compatible([single_letter_alphabet, generic_protein])
    True

    This relies on the Alphabet subclassing hierarchy.  It does not
    check things like gap characters or stop symbols."""
    dna, rna, nucl, protein = False, False, False, False
    for alpha in alphabets:
        a = _get_base_alphabet(alpha)
        if isinstance(a, DNAAlphabet):
            dna = True
            nucl = True
            if rna or protein : return False
        elif isinstance(a, RNAAlphabet):
            rna = True
            nucl = True
            if dna or protein : return False
        elif isinstance(a, NucleotideAlphabet):
            nucl = True
            if protein : return False
        elif isinstance(a, ProteinAlphabet):
            protein = True
            if nucl : return False
    return True

def _verify_alphabet(sequence):
    """Check all letters in sequence are in the alphabet (PRIVATE).

    >>> from Bio.Seq import Seq
    >>> from Bio.Alphabet import IUPAC
    >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
    ...              IUPAC.protein)
    >>> _verify_alphabet(my_seq)
    True

    This example has an X, which is not in the IUPAC protein alphabet
    (you should be using the IUPAC extended protein alphabet):

    >>> bad_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVFX",
    ...                IUPAC.protein)
    >>> _verify_alphabet(bad_seq)
    False

    This replaces Bio.utils.verify_alphabet() since we are deprecating
    that. Potentially this could be added to the Alphabet object, and
    I would like it to be an option when creating a Seq object... but
    that might slow things down.
    """
    letters = sequence.alphabet.letters
    if not letters:
        raise ValueError("Alphabet does not define letters.")
    for letter in sequence:
        if letter not in letters:
            return False
    return True


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