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Seq.py

# Copyright 2000-2002 Brad Chapman.
# Copyright 2004-2005 by M de Hoon.
# Copyright 2007-2009 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.
"""Provides objects to represent biological sequences with alphabets.

See also U{http://biopython.org/wiki/Seq} and the chapter in our tutorial:
 - U{http://biopython.org/DIST/docs/tutorial/Tutorial.html}
 - U{http://biopython.org/DIST/docs/tutorial/Tutorial.pdf}
"""
__docformat__ ="epytext en" #Don't just use plain text in epydoc API pages!

import string #for maketrans only
import array
import sys

import Alphabet
from Alphabet import IUPAC
from Data.IUPACData import ambiguous_dna_complement, ambiguous_rna_complement
from Bio.Data import CodonTable

def _maketrans(complement_mapping) :
    """Makes a python string translation table (PRIVATE).

    Arguments:
     - complement_mapping - a dictionary such as ambiguous_dna_complement
       and ambiguous_rna_complement from Data.IUPACData.

    Returns a translation table (a string of length 256) for use with the
    python string's translate method to use in a (reverse) complement.
    
    Compatible with lower case and upper case sequences.

    For internal use only.
    """
    before = ''.join(complement_mapping.keys())
    after  = ''.join(complement_mapping.values())
    before = before + before.lower()
    after  = after + after.lower()
    return string.maketrans(before, after)

_dna_complement_table = _maketrans(ambiguous_dna_complement)
_rna_complement_table = _maketrans(ambiguous_rna_complement)

00048 class Seq(object):
    """A read-only sequence object (essentially a string with an alphabet).

    Like normal python strings, our basic sequence object is immutable.
    This prevents you from doing my_seq[5] = "A" for example, but does allow
    Seq objects to be used as dictionary keys.

    The Seq object provides a number of string like methods (such as count,
    find, split and strip), which are alphabet aware where appropriate.

    The Seq object also provides some biological methods, such as complement,
    reverse_complement, transcribe, back_transcribe and translate (which are
    not applicable to sequences with a protein alphabet).
    """
00062     def __init__(self, data, alphabet = Alphabet.generic_alphabet):
        """Create a Seq object.

        Arguments:
         - seq      - Sequence, required (string)
         - alphabet - Optional argument, an Alphabet object from Bio.Alphabet
        
        You will typically use Bio.SeqIO to read in sequences from files as
        SeqRecord objects, whose sequence will be exposed as a Seq object via
        the seq property.

        However, will often want to create your own Seq objects directly:

        >>> from Bio.Seq import Seq
        >>> from Bio.Alphabet import IUPAC
        >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
        ...              IUPAC.protein)
        >>> my_seq
        Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
        >>> print my_seq
        MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
        """
        # Enforce string storage
        assert (type(data) == type("") or # must use a string
                type(data) == type(u""))  # but can be a unicode string
        self._data = data
        self.alphabet = alphabet  # Seq API requirement
 
    # A data property is/was a Seq API requirement
    def _set_data(self, value) :
        #TODO - In the next release, actually raise an exception?
        #The Seq object is like a python string, it should be read only!
        import warnings
        warnings.warn("Writing to the Seq object's .data propery is deprecated.",
                      DeprecationWarning)
        self._data = value
    data = property(fget= lambda self : str(self),
                    fset=_set_data,
                    doc="Sequence as a string (DEPRECATED)")

00102     def __repr__(self):
        """Returns a (truncated) representation of the sequence for debugging."""
        if len(self) > 60 :
            #Shows the last three letters as it is often useful to see if there
            #is a stop codon at the end of a sequence.
            #Note total length is 54+3+3=60
            return "%s('%s...%s', %s)" % (self.__class__.__name__,
                                   str(self)[:54], str(self)[-3:],
                                   repr(self.alphabet))
        else :
            return "%s(%s, %s)" % (self.__class__.__name__,
                                  repr(self.data),
                                   repr(self.alphabet))
00115     def __str__(self):
        """Returns the full sequence as a python string.

        Note that Biopython 1.44 and earlier would give a truncated
        version of repr(my_seq) for str(my_seq).  If you are writing code
        which need to be backwards compatible with old Biopython, you
        should continue to use my_seq.tostring() rather than str(my_seq).
        """
        return self._data

    # TODO - Alphabet aware __eq__ etc would be nice, but has implications for
    # __hash__ and therefore use as dictionary keys. See also:
    # http://mail.python.org/pipermail/python-dev/2002-December/031455.html

    def __len__(self): return len(self._data)       # Seq API requirement

    def __getitem__(self, index) :                 # Seq API requirement
        #Note since Python 2.0, __getslice__ is deprecated
        #and __getitem__ is used instead.
        #See http://docs.python.org/ref/sequence-methods.html
        if isinstance(index, int) :
            #Return a single letter as a string
            return self._data[index]
        else :
            #Return the (sub)sequence as another Seq object
            return Seq(self._data[index], self.alphabet)

00142     def __add__(self, other):
        """Add another sequence or string to this sequence."""
        if hasattr(other, "alphabet") :
            #other should be a Seq or a MutableSeq
            if not Alphabet._check_type_compatible([self.alphabet,
                                                    other.alphabet]) :
                raise TypeError("Incompatable alphabets %s and %s" \
                                % (repr(self.alphabet), repr(other.alphabet)))
            #They should be the same sequence type (or one of them is generic)
            a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
            return self.__class__(str(self) + str(other), a)
        elif isinstance(other, basestring) :
            #other is a plain string - use the current alphabet
            return self.__class__(str(self) + other, self.alphabet)
        else :
            raise TypeError

    def __radd__(self, other):
        if hasattr(other, "alphabet") :
            #other should be a Seq or a MutableSeq
            if not Alphabet._check_type_compatible([self.alphabet,
                                                    other.alphabet]) :
                raise TypeError("Incompatable alphabets %s and %s" \
                                % (repr(self.alphabet), repr(other.alphabet)))
            #They should be the same sequence type (or one of them is generic)
            a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
            return self.__class__(str(other) + str(self), a)
        elif isinstance(other, basestring) :
            #other is a plain string - use the current alphabet
            return self.__class__(other + str(self), self.alphabet)
        else :
            raise TypeError

00175     def tostring(self):                            # Seq API requirement
        """Returns the full sequence as a python string.

        Although not formally deprecated, you are now encouraged to use
        str(my_seq) instead of my_seq.tostring()."""
        return str(self)
    
00182     def tomutable(self):   # Needed?  Or use a function?
        """Returns the full sequence as a MutableSeq object.

        >>> from Bio.Seq import Seq
        >>> from Bio.Alphabet import IUPAC
        >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAAL",
        ...              IUPAC.protein)
        >>> my_seq
        Seq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
        >>> my_seq.tomutable()
        MutableSeq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())

        Note that the alphabet is preserved.
        """
        return MutableSeq(str(self), self.alphabet)

00198     def _get_seq_str_and_check_alphabet(self, other_sequence) :
        """string/Seq/MutableSeq to string, checking alphabet (PRIVATE).

        For a string argument, returns the string.

        For a Seq or MutableSeq, it checks the alphabet is compatible
        (raising an exception if it isn't), and then returns a string.
        """
        try :
            other_alpha = other_sequence.alphabet
        except AttributeError :
            #Assume other_sequence is a string
            return other_sequence

        #Other should be a Seq or a MutableSeq
        if not Alphabet._check_type_compatible([self.alphabet, other_alpha]) :
            raise TypeError("Incompatable alphabets %s and %s" \
                            % (repr(self.alphabet), repr(other_alpha)))
        #Return as a string
        return str(other_sequence)
    
00219     def count(self, sub, start=0, end=sys.maxint):
        """Non-overlapping count method, like that of a python string.

        This behaves like the python string method of the same name,
        which does a non-overlapping count!

        Returns an integer, the number of occurrences of substring
        argument sub in the (sub)sequence given by [start:end].
        Optional arguments start and end are interpreted as in slice
        notation.
    
        Arguments:
         - sub - a string or another Seq object to look for
         - start - optional integer, slice start
         - end - optional integer, slice end

        e.g.

        >>> from Bio.Seq import Seq
        >>> my_seq = Seq("AAAATGA")
        >>> print my_seq.count("A")
        5
        >>> print my_seq.count("ATG")
        1
        >>> print my_seq.count(Seq("AT"))
        1
        >>> print my_seq.count("AT", 2, -1)
        1

        HOWEVER, please note because python strings and Seq objects (and
        MutableSeq objects) do a non-overlapping search, this may not give
        the answer you expect:

        >>> "AAAA".count("AA")
        2
        >>> print Seq("AAAA").count("AA")
        2

        A non-overlapping search would give the answer as three!
        """
        #If it has one, check the alphabet:
        sub_str = self._get_seq_str_and_check_alphabet(sub)
        return str(self).count(sub_str, start, end)

00263     def __contains__(self, char) :
        """Implements the 'in' keyword, like a python string.

        e.g.

        >>> from Bio.Seq import Seq
        >>> from Bio.Alphabet import generic_dna, generic_rna, generic_protein
        >>> my_dna = Seq("ATATGAAATTTGAAAA", generic_dna)
        >>> "AAA" in my_dna
        True
        >>> Seq("AAA") in my_dna
        True
        >>> Seq("AAA", generic_dna) in my_dna
        True

        Like other Seq methods, this will raise a type error if another Seq
        (or Seq like) object with an incompatible alphabet is used:

        >>> Seq("AAA", generic_rna) in my_dna
        Traceback (most recent call last):
           ...
        TypeError: Incompatable alphabets DNAAlphabet() and RNAAlphabet()
        >>> Seq("AAA", generic_protein) in my_dna
        Traceback (most recent call last):
           ...
        TypeError: Incompatable alphabets DNAAlphabet() and ProteinAlphabet()
        """
        #If it has one, check the alphabet:
        sub_str = self._get_seq_str_and_check_alphabet(char)
        return sub_str in str(self)

00294     def find(self, sub, start=0, end=sys.maxint):
        """Find method, like that of a python string.

        This behaves like the python string method of the same name.

        Returns an integer, the index of the first occurrence of substring
        argument sub in the (sub)sequence given by [start:end].

        Arguments:
         - sub - a string or another Seq object to look for
         - start - optional integer, slice start
         - end - optional integer, slice end

        Returns -1 if the subsequence is NOT found.
        
        e.g. Locating the first typical start codon, AUG, in an RNA sequence:

        >>> from Bio.Seq import Seq
        >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
        >>> my_rna.find("AUG")
        3
        """
        #If it has one, check the alphabet:
        sub_str = self._get_seq_str_and_check_alphabet(sub)
        return str(self).find(sub_str, start, end)

00320     def rfind(self, sub, start=0, end=sys.maxint):
        """Find from right method, like that of a python string.

        This behaves like the python string method of the same name.

        Returns an integer, the index of the last (right most) occurrence of
        substring argument sub in the (sub)sequence given by [start:end].

        Arguments:
         - sub - a string or another Seq object to look for
         - start - optional integer, slice start
         - end - optional integer, slice end

        Returns -1 if the subsequence is NOT found.

        e.g. Locating the last typical start codon, AUG, in an RNA sequence:

        >>> from Bio.Seq import Seq
        >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
        >>> my_rna.rfind("AUG")
        15
        """
        #If it has one, check the alphabet:
        sub_str = self._get_seq_str_and_check_alphabet(sub)
        return str(self).rfind(sub_str, start, end)

00346     def startswith(self, prefix, start=0, end=sys.maxint) :
        """Does the Seq start with the given prefix?  Returns True/False.

        This behaves like the python string method of the same name.

        Return True if the sequence starts with the specified prefix
        (a string or another Seq object), False otherwise.
        With optional start, test sequence beginning at that position.
        With optional end, stop comparing sequence at that position.
        prefix can also be a tuple of strings to try.  e.g.
        
        >>> from Bio.Seq import Seq
        >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
        >>> my_rna.startswith("GUC")
        True
        >>> my_rna.startswith("AUG")
        False
        >>> my_rna.startswith("AUG", 3)
        True
        >>> my_rna.startswith(("UCC","UCA","UCG"),1)
        True
        """
        #If it has one, check the alphabet:
        if isinstance(prefix, tuple) :
            #TODO - Once we drop support for Python 2.4, instead of this
            #loop offload to the string method (requires Python 2.5+).
            #Check all the alphabets first...
            prefix_strings = [self._get_seq_str_and_check_alphabet(p) \
                              for p in prefix]
            for prefix_str in prefix_strings :
                if str(self).startswith(prefix_str, start, end) :
                    return True
            return False
        else :
            prefix_str = self._get_seq_str_and_check_alphabet(prefix)
            return str(self).startswith(prefix_str, start, end)

00383     def endswith(self, suffix, start=0, end=sys.maxint) :
        """Does the Seq end with the given suffix?  Returns True/False.

        This behaves like the python string method of the same name.

        Return True if the sequence ends with the specified suffix
        (a string or another Seq object), False otherwise.
        With optional start, test sequence beginning at that position.
        With optional end, stop comparing sequence at that position.
        suffix can also be a tuple of strings to try.  e.g.

        >>> from Bio.Seq import Seq
        >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
        >>> my_rna.endswith("UUG")
        True
        >>> my_rna.endswith("AUG")
        False
        >>> my_rna.endswith("AUG", 0, 18)
        True
        >>> my_rna.endswith(("UCC","UCA","UUG"))
        True
        """        
        #If it has one, check the alphabet:
        if isinstance(suffix, tuple) :
            #TODO - Once we drop support for Python 2.4, instead of this
            #loop offload to the string method (requires Python 2.5+).
            #Check all the alphabets first...
            suffix_strings = [self._get_seq_str_and_check_alphabet(p) \
                              for p in suffix]
            for suffix_str in suffix_strings :
                if str(self).endswith(suffix_str, start, end) :
                    return True
            return False
        else :
            suffix_str = self._get_seq_str_and_check_alphabet(suffix)
            return str(self).endswith(suffix_str, start, end)


00421     def split(self, sep=None, maxsplit=-1) :
        """Split method, like that of a python string.

        This behaves like the python string method of the same name.

        Return a list of the 'words' in the string (as Seq objects),
        using sep as the delimiter string.  If maxsplit is given, at
        most maxsplit splits are done.  If maxsplit is ommited, all
        splits are made.

        Following the python string method, sep will by default be any
        white space (tabs, spaces, newlines) but this is unlikely to
        apply to biological sequences.
        
        e.g.

        >>> from Bio.Seq import Seq
        >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
        >>> my_aa = my_rna.translate()
        >>> my_aa
        Seq('VMAIVMGR*KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))
        >>> my_aa.split("*")
        [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))]
        >>> my_aa.split("*",1)
        [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))]

        See also the rsplit method:

        >>> my_aa.rsplit("*",1)
        [Seq('VMAIVMGR*KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))]
        """
        #If it has one, check the alphabet:
        sep_str = self._get_seq_str_and_check_alphabet(sep)
        #TODO - If the sep is the defined stop symbol, or gap char,
        #should we adjust the alphabet?
        return [Seq(part, self.alphabet) \
                for part in str(self).split(sep_str, maxsplit)]

00459     def rsplit(self, sep=None, maxsplit=-1) :
        """Right split method, like that of a python string.

        This behaves like the python string method of the same name.

        Return a list of the 'words' in the string (as Seq objects),
        using sep as the delimiter string.  If maxsplit is given, at
        most maxsplit splits are done COUNTING FROM THE RIGHT.
        If maxsplit is ommited, all splits are made.

        Following the python string method, sep will by default be any
        white space (tabs, spaces, newlines) but this is unlikely to
        apply to biological sequences.
        
        e.g. print my_seq.rsplit("*",1)

        See also the split method.
        """
        #If it has one, check the alphabet:
        sep_str = self._get_seq_str_and_check_alphabet(sep)
        return [Seq(part, self.alphabet) \
                for part in str(self).rsplit(sep_str, maxsplit)]

00482     def strip(self, chars=None) :
        """Returns a new Seq object with leading and trailing ends stripped.

        This behaves like the python string method of the same name.

        Optional argument chars defines which characters to remove.  If
        ommitted or None (default) then as for the python string method,
        this defaults to removing any white space.
        
        e.g. print my_seq.strip("-")

        See also the lstrip and rstrip methods.
        """
        #If it has one, check the alphabet:
        strip_str = self._get_seq_str_and_check_alphabet(chars)
        return Seq(str(self).strip(strip_str), self.alphabet)

00499     def lstrip(self, chars=None) :
        """Returns a new Seq object with leading (left) end stripped.

        This behaves like the python string method of the same name.

        Optional argument chars defines which characters to remove.  If
        ommitted or None (default) then as for the python string method,
        this defaults to removing any white space.
        
        e.g. print my_seq.lstrip("-")

        See also the strip and rstrip methods.
        """
        #If it has one, check the alphabet:
        strip_str = self._get_seq_str_and_check_alphabet(chars)
        return Seq(str(self).lstrip(strip_str), self.alphabet)

00516     def rstrip(self, chars=None) :
        """Returns a new Seq object with trailing (right) end stripped.

        This behaves like the python string method of the same name.

        Optional argument chars defines which characters to remove.  If
        ommitted or None (default) then as for the python string method,
        this defaults to removing any white space.
        
        e.g. Removing a nucleotide sequence's polyadenylation (poly-A tail):

        >>> from Bio.Alphabet import IUPAC
        >>> from Bio.Seq import Seq
        >>> my_seq = Seq("CGGTACGCTTATGTCACGTAGAAAAAA", IUPAC.unambiguous_dna)
        >>> my_seq
        Seq('CGGTACGCTTATGTCACGTAGAAAAAA', IUPACUnambiguousDNA())
        >>> my_seq.rstrip("A")
        Seq('CGGTACGCTTATGTCACGTAG', IUPACUnambiguousDNA())

        See also the strip and lstrip methods.
        """
        #If it has one, check the alphabet:
        strip_str = self._get_seq_str_and_check_alphabet(chars)
        return Seq(str(self).rstrip(strip_str), self.alphabet)

00541     def complement(self):
        """Returns the complement sequence. New Seq object.

        >>> from Bio.Seq import Seq
        >>> from Bio.Alphabet import IUPAC
        >>> my_dna = Seq("CCCCCGATAG", IUPAC.unambiguous_dna)
        >>> my_dna
        Seq('CCCCCGATAG', IUPACUnambiguousDNA())
        >>> my_dna.complement()
        Seq('GGGGGCTATC', IUPACUnambiguousDNA())

        You can of course used mixed case sequences,

        >>> from Bio.Seq import Seq
        >>> from Bio.Alphabet import generic_dna
        >>> my_dna = Seq("CCCCCgatA-GD", generic_dna)
        >>> my_dna
        Seq('CCCCCgatA-GD', DNAAlphabet())
        >>> my_dna.complement()
        Seq('GGGGGctaT-CH', DNAAlphabet())

        Note in the above example, ambiguous character D denotes
        G, A or T so its complement is H (for C, T or A).
        
        Trying to complement a protein sequence raises an exception.

        >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
        >>> my_protein.complement()
        Traceback (most recent call last):
           ...
        ValueError: Proteins do not have complements!
        """
        base = Alphabet._get_base_alphabet(self.alphabet)
        if isinstance(base, Alphabet.ProteinAlphabet) :
            raise ValueError("Proteins do not have complements!")
        if isinstance(base, Alphabet.DNAAlphabet) :
            ttable = _dna_complement_table
        elif isinstance(base, Alphabet.RNAAlphabet) :
            ttable = _rna_complement_table
        elif ('U' in self._data or 'u' in self._data) \
        and ('T' in self._data or 't' in self._data):
            #TODO - Handle this cleanly?
            raise ValueError("Mixed RNA/DNA found")
        elif 'U' in self._data or 'u' in self._data:
            ttable = _rna_complement_table
        else:
            ttable = _dna_complement_table
        #Much faster on really long sequences than the previous loop based one.
        #thx to Michael Palmer, University of Waterloo
        return Seq(str(self).translate(ttable), self.alphabet)

00592     def reverse_complement(self):
        """Returns the reverse complement sequence. New Seq object.

        >>> from Bio.Seq import Seq
        >>> from Bio.Alphabet import IUPAC
        >>> my_dna = Seq("CCCCCGATAGNR", IUPAC.ambiguous_dna)
        >>> my_dna
        Seq('CCCCCGATAGNR', IUPACAmbiguousDNA())
        >>> my_dna.reverse_complement()
        Seq('YNCTATCGGGGG', IUPACAmbiguousDNA())

        Note in the above example, since R = G or A, its complement
        is Y (which denotes  C or T).

        You can of course used mixed case sequences,

        >>> from Bio.Seq import Seq
        >>> from Bio.Alphabet import generic_dna
        >>> my_dna = Seq("CCCCCgatA-G", generic_dna)
        >>> my_dna
        Seq('CCCCCgatA-G', DNAAlphabet())
        >>> my_dna.reverse_complement()
        Seq('C-TatcGGGGG', DNAAlphabet())

        Trying to complement a protein sequence raises an exception:

        >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
        >>> my_protein.reverse_complement()
        Traceback (most recent call last):
           ...
        ValueError: Proteins do not have complements!
        """
        #Use -1 stride/step to reverse the complement
        return self.complement()[::-1]

00627     def transcribe(self):
        """Returns the RNA sequence from a DNA sequence. New Seq object.

        >>> from Bio.Seq import Seq
        >>> from Bio.Alphabet import IUPAC
        >>> coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG",
        ...                  IUPAC.unambiguous_dna)
        >>> coding_dna
        Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA())
        >>> coding_dna.transcribe()
        Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA())

        Trying to transcribe a protein or RNA sequence raises an exception:

        >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
        >>> my_protein.transcribe()
        Traceback (most recent call last):
           ...
        ValueError: Proteins cannot be transcribed!
        """
        base = Alphabet._get_base_alphabet(self.alphabet)
        if isinstance(base, Alphabet.ProteinAlphabet) :
            raise ValueError("Proteins cannot be transcribed!")
        if isinstance(base, Alphabet.RNAAlphabet) :
            raise ValueError("RNA cannot be transcribed!")

        if self.alphabet==IUPAC.unambiguous_dna:
            alphabet = IUPAC.unambiguous_rna
        elif self.alphabet==IUPAC.ambiguous_dna:
            alphabet = IUPAC.ambiguous_rna
        else:
            alphabet = Alphabet.generic_rna
        return Seq(str(self).replace('T','U').replace('t','u'), alphabet)
    
00661     def back_transcribe(self):
        """Returns the DNA sequence from an RNA sequence. New Seq object.

        >>> from Bio.Seq import Seq
        >>> from Bio.Alphabet import IUPAC
        >>> messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG",
        ...                     IUPAC.unambiguous_rna)
        >>> messenger_rna
        Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA())
        >>> messenger_rna.back_transcribe()
        Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA())

        Trying to back-transcribe a protein or DNA sequence raises an
        exception:

        >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
        >>> my_protein.back_transcribe()
        Traceback (most recent call last):
           ...
        ValueError: Proteins cannot be back transcribed!
        """
        base = Alphabet._get_base_alphabet(self.alphabet)
        if isinstance(base, Alphabet.ProteinAlphabet) :
            raise ValueError("Proteins cannot be back transcribed!")
        if isinstance(base, Alphabet.DNAAlphabet) :
            raise ValueError("DNA cannot be back transcribed!")

        if self.alphabet==IUPAC.unambiguous_rna:
            alphabet = IUPAC.unambiguous_dna
        elif self.alphabet==IUPAC.ambiguous_rna:
            alphabet = IUPAC.ambiguous_dna
        else:
            alphabet = Alphabet.generic_dna
        return Seq(str(self).replace("U", "T").replace("u", "t"), alphabet)

00696     def translate(self, table="Standard", stop_symbol="*", to_stop=False,
                  cds=False):
        """Turns a nucleotide sequence into a protein sequence. New Seq object.

        This method will translate DNA or RNA sequences, and those with a
        nucleotide or generic alphabet.  Trying to translate a protein
        sequence raises an exception.

        Arguments:
         - table - Which codon table to use?  This can be either a name
                   (string) or an NCBI identifier (integer).  This defaults
                   to the "Standard" table.
         - stop_symbol - Single character string, what to use for terminators.
                         This defaults to the asterisk, "*".
         - to_stop - Boolean, defaults to False meaning do a full translation
                     continuing on past any stop codons (translated as the
                     specified stop_symbol).  If True, translation is
                     terminated at the first in frame stop codon (and the
                     stop_symbol is not appended to the returned protein
                     sequence).
         - cds - Boolean, indicates this is a complete CDS.  If True,
                 this checks the sequence starts with a valid alternative start
                 codon (which will be translated as methionine, M), that the
                 sequence length is a multiple of three, and that there is a
                 single in frame stop codon at the end (this will be excluded
                 from the protein sequence, regardless of the to_stop option).
                 If these tests fail, an exception is raised.
        
        e.g. Using the standard table:

        >>> coding_dna = Seq("GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")
        >>> coding_dna.translate()
        Seq('VAIVMGR*KGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
        >>> coding_dna.translate(stop_symbol="@")
        Seq('VAIVMGR@KGAR@', HasStopCodon(ExtendedIUPACProtein(), '@'))
        >>> coding_dna.translate(to_stop=True)
        Seq('VAIVMGR', ExtendedIUPACProtein())

        Now using NCBI table 2, where TGA is not a stop codon:

        >>> coding_dna.translate(table=2)
        Seq('VAIVMGRWKGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
        >>> coding_dna.translate(table=2, to_stop=True)
        Seq('VAIVMGRWKGAR', ExtendedIUPACProtein())

        In fact, GTG is an alternative start codon under NCBI table 2, meaning
        this sequence could be a complete CDS:

        >>> coding_dna.translate(table=2, cds=True)
        Seq('MAIVMGRWKGAR', ExtendedIUPACProtein())

        It isn't a valid CDS under NCBI table 1, due to both the start codon and
        also the in frame stop codons:
        
        >>> coding_dna.translate(table=1, cds=True)
        Traceback (most recent call last):
            ...
        TranslationError: First codon 'GTG' is not a start codon

        If the sequence has no in-frame stop codon, then the to_stop argument
        has no effect:

        >>> coding_dna2 = Seq("TTGGCCATTGTAATGGGCCGC")
        >>> coding_dna2.translate()
        Seq('LAIVMGR', ExtendedIUPACProtein())
        >>> coding_dna2.translate(to_stop=True)
        Seq('LAIVMGR', ExtendedIUPACProtein())

        NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid
        or a stop codon.  These are translated as "X".  Any invalid codon
        (e.g. "TA?" or "T-A") will throw a TranslationError.

        NOTE - Does NOT support gapped sequences.

        NOTE - This does NOT behave like the python string's translate
        method.  For that use str(my_seq).translate(...) instead.
        """
        try:
            table_id = int(table)
        except ValueError:
            table_id = None
        if isinstance(table, str) and len(table)==256 :
            raise ValueError("The Seq object translate method DOES NOT take " \
                             + "a 256 character string mapping table like " \
                             + "the python string object's translate method. " \
                             + "Use str(my_seq).translate(...) instead.")
        if isinstance(Alphabet._get_base_alphabet(self.alphabet),
                      Alphabet.ProteinAlphabet) :
            raise ValueError("Proteins cannot be translated!")
        if self.alphabet==IUPAC.unambiguous_dna:
            #Will use standard IUPAC protein alphabet, no need for X
            if table_id is None:
                codon_table = CodonTable.unambiguous_dna_by_name[table]
            else:
                codon_table = CodonTable.unambiguous_dna_by_id[table_id]
        #elif self.alphabet==IUPAC.ambiguous_dna:
        #    if table_id is None:
        #        codon_table = CodonTable.ambiguous_dna_by_name[table]
        #    else:
        #        codon_table = CodonTable.ambiguous_dna_by_id[table_id]
        elif self.alphabet==IUPAC.unambiguous_rna:
            #Will use standard IUPAC protein alphabet, no need for X
            if table_id is None:
                codon_table = CodonTable.unambiguous_rna_by_name[table]
            else:
                codon_table = CodonTable.unambiguous_rna_by_id[table_id]
        #elif self.alphabet==IUPAC.ambiguous_rna:
        #    if table_id is None:
        #        codon_table = CodonTable.ambiguous_rna_by_name[table]
        #    else:
        #        codon_table = CodonTable.ambiguous_rna_by_id[table_id]
        else:
            #This will use the extend IUPAC protein alphabet with X etc.
            #The same table can be used for RNA or DNA (we use this for
            #translating strings).
            if table_id is None:
                codon_table = CodonTable.ambiguous_generic_by_name[table]
            else:
                codon_table = CodonTable.ambiguous_generic_by_id[table_id]
        protein = _translate_str(str(self), codon_table, \
                                 stop_symbol, to_stop, cds)
        if stop_symbol in protein :
            alphabet = Alphabet.HasStopCodon(codon_table.protein_alphabet,
                                             stop_symbol = stop_symbol)
        else :
            alphabet = codon_table.protein_alphabet
        return Seq(protein, alphabet)

00824 class UnknownSeq(Seq):
    """A read-only sequence object of known length but unknown contents.

    If you have an unknown sequence, you can represent this with a normal
    Seq object, for example:

    >>> my_seq = Seq("N"*5)
    >>> my_seq
    Seq('NNNNN', Alphabet())
    >>> len(my_seq)
    5
    >>> print my_seq
    NNNNN

    However, this is rather wasteful of memory (especially for large
    sequences), which is where this class is most usefull:

    >>> unk_five = UnknownSeq(5)
    >>> unk_five
    UnknownSeq(5, alphabet = Alphabet(), character = '?')
    >>> len(unk_five)
    5
    >>> print(unk_five)
    ?????

    You can add unknown sequence together, provided their alphabets and
    characters are compatible, and get another memory saving UnknownSeq:

    >>> unk_four = UnknownSeq(4)
    >>> unk_four
    UnknownSeq(4, alphabet = Alphabet(), character = '?')
    >>> unk_four + unk_five
    UnknownSeq(9, alphabet = Alphabet(), character = '?')

    If the alphabet or characters don't match up, the addition gives an
    ordinary Seq object:
    
    >>> unk_nnnn = UnknownSeq(4, character = "N")
    >>> unk_nnnn
    UnknownSeq(4, alphabet = Alphabet(), character = 'N')
    >>> unk_nnnn + unk_four
    Seq('NNNN????', Alphabet())

    Combining with a real Seq gives a new Seq object:

    >>> known_seq = Seq("ACGT")
    >>> unk_four + known_seq
    Seq('????ACGT', Alphabet())
    >>> known_seq + unk_four
    Seq('ACGT????', Alphabet())
    """
00875     def __init__(self, length, alphabet = Alphabet.generic_alphabet, character = None) :
        """Create a new UnknownSeq object.

        If character is ommited, it is determed from the alphabet, "N" for
        nucleotides, "X" for proteins, and "?" otherwise.
        """
        self._length = int(length)
        if self._length < 0 :
            #TODO - Block zero length UnknownSeq?  You can just use a Seq!
            raise ValueError("Length must not be negative.")
        self.alphabet = alphabet
        if character :
            if len(character) != 1 :
                raise ValueError("character argument should be a single letter string.")
            self._character = character
        else :
            base = Alphabet._get_base_alphabet(alphabet)
            #TODO? Check the case of the letters in the alphabet?
            #We may have to use "n" instead of "N" etc.
            if isinstance(base, Alphabet.NucleotideAlphabet) :
                self._character = "N"
            elif isinstance(base, Alphabet.ProteinAlphabet) :
                self._character = "X"
            else :
                self._character = "?"

00901     def __len__(self) :
        """Returns the stated length of the unknown sequence."""
        return self._length
    
00905     def __str__(self) :
        """Returns the unknown sequence as full string of the given length."""
        return self._character * self._length

00909     def __repr__(self):
        return "UnknownSeq(%i, alphabet = %s, character = %s)" \
               % (self._length, repr(self.alphabet), repr(self._character))

00913     def __add__(self, other) :
        if isinstance(other, UnknownSeq) \
        and other._character == self._character :
            #TODO - Check the alphabets match
            return UnknownSeq(len(self)+len(other),
                              self.alphabet, self._character)
        #Offload to the base class...
        return Seq(str(self), self.alphabet) + other

    def __radd__(self, other) :
        if isinstance(other, UnknownSeq) \
        and other._character == self._character :
            #TODO - Check the alphabets match
            return UnknownSeq(len(self)+len(other),
                              self.alphabet, self._character)
        #Offload to the base class...
        return other + Seq(str(self), self.alphabet)

    def __getitem__(self, index):
        if isinstance(index, int) :
            #TODO - Check the bounds without wasting memory
            return str(self)[index]
        else :
            #TODO - Work out the length without wasting memory
            return UnknownSeq(len(("#"*self._length)[index]),
                              self.alphabet, self._character)

00940     def count(self, sub, start=0, end=sys.maxint):
        """Non-overlapping count method, like that of a python string.

        This behaves like the python string (and Seq object) method of the
        same name, which does a non-overlapping count!

        Returns an integer, the number of occurrences of substring
        argument sub in the (sub)sequence given by [start:end].
        Optional arguments start and end are interpreted as in slice
        notation.
    
        Arguments:
         - sub - a string or another Seq object to look for
         - start - optional integer, slice start
         - end - optional integer, slice end

        >>> "NNNN".count("N")
        4
        >>> Seq("NNNN").count("N")
        4
        >>> UnknownSeq(4, character="N").count("N")
        4
        >>> UnknownSeq(4, character="N").count("A")
        0
        >>> UnknownSeq(4, character="N").count("AA")
        0

        HOWEVER, please note because that python strings and Seq objects (and
        MutableSeq objects) do a non-overlapping search, this may not give
        the answer you expect:

        >>> UnknownSeq(4, character="N").count("NN")
        2
        >>> UnknownSeq(4, character="N").count("NNN")
        1
        """
        sub_str = self._get_seq_str_and_check_alphabet(sub)
        if len(sub_str) == 1 :
            if str(sub_str) == self._character :
                if start==0 and end >= self._length :
                    return self._length
                else :
                    #This could be done more cleverly...
                    return str(self).count(sub_str, start, end)
            else :
                return 0
        else :
            if set(sub_str) == set(self._character) :
                if start==0 and end >= self._length :
                    return self._length // len(sub_str)
                else :
                    #This could be done more cleverly...
                    return str(self).count(sub_str, start, end)
            else :
                return 0

00996     def complement(self) :
        """The complement of an unknown nucleotide equals itself.

        >>> my_nuc = UnknownSeq(8)
        >>> my_nuc
        UnknownSeq(8, alphabet = Alphabet(), character = '?')
        >>> print my_nuc
        ????????
        >>> my_nuc.complement()
        UnknownSeq(8, alphabet = Alphabet(), character = '?')
        >>> print my_nuc.complement()
        ????????
        """
        if isinstance(Alphabet._get_base_alphabet(self.alphabet),
                      Alphabet.ProteinAlphabet) :
            raise ValueError("Proteins do not have complements!")
        return self

01014     def reverse_complement(self) :
        """The reverse complement of an unknown nucleotide equals itself.

        >>> my_nuc = UnknownSeq(10)
        >>> my_nuc
        UnknownSeq(10, alphabet = Alphabet(), character = '?')
        >>> print my_nuc
        ??????????
        >>> my_nuc.reverse_complement()
        UnknownSeq(10, alphabet = Alphabet(), character = '?')
        >>> print my_nuc.reverse_complement()
        ??????????
        """
        if isinstance(Alphabet._get_base_alphabet(self.alphabet),
                      Alphabet.ProteinAlphabet) :
            raise ValueError("Proteins do not have complements!")
        return self

01032     def transcribe(self) :
        """Returns unknown RNA sequence from an unknown DNA sequence.

        >>> my_dna = UnknownSeq(10, character="N")
        >>> my_dna
        UnknownSeq(10, alphabet = Alphabet(), character = 'N')
        >>> print my_dna
        NNNNNNNNNN
        >>> my_rna = my_dna.transcribe()
        >>> my_rna
        UnknownSeq(10, alphabet = RNAAlphabet(), character = 'N')
        >>> print my_rna
        NNNNNNNNNN
        """
        #Offload the alphabet stuff
        s = Seq(self._character, self.alphabet).transcribe()
        return UnknownSeq(self._length, s.alphabet, self._character)

01050     def back_transcribe(self) :
        """Returns unknown DNA sequence from an unknown RNA sequence.

        >>> my_rna = UnknownSeq(20, character="N")
        >>> my_rna
        UnknownSeq(20, alphabet = Alphabet(), character = 'N')
        >>> print my_rna
        NNNNNNNNNNNNNNNNNNNN
        >>> my_dna = my_rna.back_transcribe()
        >>> my_dna
        UnknownSeq(20, alphabet = DNAAlphabet(), character = 'N')
        >>> print my_dna
        NNNNNNNNNNNNNNNNNNNN
        """
        #Offload the alphabet stuff
        s = Seq(self._character, self.alphabet).back_transcribe()
        return UnknownSeq(self._length, s.alphabet, self._character)

01068     def translate(self, **kwargs) :
        """Translate an unknown nucleotide sequence into an unknown protein.

        e.g.

        >>> my_seq = UnknownSeq(11, character="N")
        >>> print my_seq
        NNNNNNNNNNN
        >>> my_protein = my_seq.translate()
        >>> my_protein
        UnknownSeq(3, alphabet = ProteinAlphabet(), character = 'X')
        >>> print my_protein
        XXX

        In comparison, using a normal Seq object:

        >>> my_seq = Seq("NNNNNNNNNNN")
        >>> print my_seq
        NNNNNNNNNNN
        >>> my_protein = my_seq.translate()
        >>> my_protein
        Seq('XXX', ExtendedIUPACProtein())
        >>> print my_protein
        XXX

        """
        if isinstance(Alphabet._get_base_alphabet(self.alphabet),
                      Alphabet.ProteinAlphabet) :
            raise ValueError("Proteins cannot be translated!")
        return UnknownSeq(self._length//3, Alphabet.generic_protein, "X")


01100 class MutableSeq(object):
    """An editable sequence object (with an alphabet).

    Unlike normal python strings and our basic sequence object (the Seq class)
    which are immuatable, the MutableSeq lets you edit the sequence in place.
    However, this means you cannot use a MutableSeq object as a dictionary key.

    >>> from Bio.Seq import MutableSeq
    >>> from Bio.Alphabet import generic_dna
    >>> my_seq = MutableSeq("ACTCGTCGTCG", generic_dna)
    >>> my_seq
    MutableSeq('ACTCGTCGTCG', DNAAlphabet())
    >>> my_seq[5]
    'T'
    >>> my_seq[5] = "A"
    >>> my_seq
    MutableSeq('ACTCGACGTCG', DNAAlphabet())
    >>> my_seq[5]
    'A'
    >>> my_seq[5:8] = "NNN"
    >>> my_seq
    MutableSeq('ACTCGNNNTCG', DNAAlphabet())
    >>> len(my_seq)
    11

    Note that the MutableSeq object does not support as many string-like
    or biological methods as the Seq object.
    """
    def __init__(self, data, alphabet = Alphabet.generic_alphabet):
        if type(data) == type(""):
            self.data = array.array("c", data)
        else:
            self.data = data   # assumes the input is an array
        self.alphabet = alphabet
    
01135     def __repr__(self):
        """Returns a (truncated) representation of the sequence for debugging."""
        if len(self) > 60 :
            #Shows the last three letters as it is often useful to see if there
            #is a stop codon at the end of a sequence.
            #Note total length is 54+3+3=60
            return "%s('%s...%s', %s)" % (self.__class__.__name__,
                                   str(self[:54]), str(self[-3:]),
                                   repr(self.alphabet))
        else :
            return "%s('%s', %s)" % (self.__class__.__name__,
                                   str(self),
                                   repr(self.alphabet))

01149     def __str__(self):
        """Returns the full sequence as a python string.

        Note that Biopython 1.44 and earlier would give a truncated
        version of repr(my_seq) for str(my_seq).  If you are writing code
        which needs to be backwards compatible with old Biopython, you
        should continue to use my_seq.tostring() rather than str(my_seq).
        """
        #See test_GAQueens.py for an historic usage of a non-string alphabet!
        return "".join(self.data)

01160     def __cmp__(self, other):
        """Compare the sequence for to another sequence or a string.

        If compared to another sequence the alphabets must be compatible.
        Comparing DNA to RNA, or Nucleotide to Protein will raise an
        exception.

        Otherwise only the sequence itself is compared, not the precise
        alphabet.

        This method indirectly supports ==, < , etc."""
        if hasattr(other, "alphabet") :
            #other should be a Seq or a MutableSeq
            if not Alphabet._check_type_compatible([self.alphabet,
                                                    other.alphabet]) :
                raise TypeError("Incompatable alphabets %s and %s" \
                                % (repr(self.alphabet), repr(other.alphabet)))
            #They should be the same sequence type (or one of them is generic)
            if isinstance(other, MutableSeq):
                #See test_GAQueens.py for an historic usage of a non-string
                #alphabet!  Comparing the arrays supports this.
                return cmp(self.data, other.data)
            else :
                return cmp(str(self), str(other))
        elif isinstance(other, basestring) :
            return cmp(str(self), other)
        else :
            raise TypeError

    def __len__(self): return len(self.data)

    def __getitem__(self, index) :
        #Note since Python 2.0, __getslice__ is deprecated
        #and __getitem__ is used instead.
        #See http://docs.python.org/ref/sequence-methods.html
        if isinstance(index, int) :
            #Return a single letter as a string
            return self.data[index]
        else :
            #Return the (sub)sequence as another Seq object
            return MutableSeq(self.data[index], self.alphabet)

    def __setitem__(self, index, value):
        #Note since Python 2.0, __setslice__ is deprecated
        #and __setitem__ is used instead.
        #See http://docs.python.org/ref/sequence-methods.html
        if isinstance(index, int) :
            #Replacing a single letter with a new string
            self.data[index] = value
        else :
            #Replacing a sub-sequence
            if isinstance(value, MutableSeq):
                self.data[index] = value.data
            elif isinstance(value, type(self.data)):
                self.data[index] = value
            else:
                self.data[index] = array.array("c", str(value))

    def __delitem__(self, index):
        #Note since Python 2.0, __delslice__ is deprecated
        #and __delitem__ is used instead.
        #See http://docs.python.org/ref/sequence-methods.html
        
        #Could be deleting a single letter, or a slice
        del self.data[index]
    
01226     def __add__(self, other):
        """Add another sequence or string to this sequence.

        Returns a new MutableSeq object."""
        if hasattr(other, "alphabet") :
            #other should be a Seq or a MutableSeq
            if not Alphabet._check_type_compatible([self.alphabet,
                                                    other.alphabet]) :
                raise TypeError("Incompatable alphabets %s and %s" \
                                % (repr(self.alphabet), repr(other.alphabet)))
            #They should be the same sequence type (or one of them is generic)
            a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
            if isinstance(other, MutableSeq):
                #See test_GAQueens.py for an historic usage of a non-string
                #alphabet!  Adding the arrays should support this.
                return self.__class__(self.data + other.data, a)
            else :
                return self.__class__(str(self) + str(other), a)
        elif isinstance(other, basestring) :
            #other is a plain string - use the current alphabet
            return self.__class__(str(self) + str(other), self.alphabet)
        else :
            raise TypeError

    def __radd__(self, other):
        if hasattr(other, "alphabet") :
            #other should be a Seq or a MutableSeq
            if not Alphabet._check_type_compatible([self.alphabet,
                                                    other.alphabet]) :
                raise TypeError("Incompatable alphabets %s and %s" \
                                % (repr(self.alphabet), repr(other.alphabet)))
            #They should be the same sequence type (or one of them is generic)
            a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
            if isinstance(other, MutableSeq):
                #See test_GAQueens.py for an historic usage of a non-string
                #alphabet!  Adding the arrays should support this.
                return self.__class__(other.data + self.data, a)
            else :
                return self.__class__(str(other) + str(self), a)
        elif isinstance(other, basestring) :
            #other is a plain string - use the current alphabet
            return self.__class__(str(other) + str(self), self.alphabet)
        else :
            raise TypeError

    def append(self, c):
        self.data.append(c)

    def insert(self, i, c):
        self.data.insert(i, c)

    def pop(self, i = (-1)):
        c = self.data[i]
        del self.data[i]
        return c

    def remove(self, item):
        for i in range(len(self.data)):
            if self.data[i] == item:
                del self.data[i]
                return
        raise ValueError("MutableSeq.remove(x): x not in list")

01289     def count(self, sub, start=0, end=sys.maxint):
        """Non-overlapping count method, like that of a python string.

        This behaves like the python string method of the same name,
        which does a non-overlapping count!

        Returns an integer, the number of occurrences of substring
        argument sub in the (sub)sequence given by [start:end].
        Optional arguments start and end are interpreted as in slice
        notation.
    
        Arguments:
         - sub - a string or another Seq object to look for
         - start - optional integer, slice start
         - end - optional integer, slice end

        e.g.
        
        >>> from Bio.Seq import MutableSeq
        >>> my_mseq = MutableSeq("AAAATGA")
        >>> print my_mseq.count("A")
        5
        >>> print my_mseq.count("ATG")
        1
        >>> print my_mseq.count(Seq("AT"))
        1
        >>> print my_mseq.count("AT", 2, -1)
        1
        
        HOWEVER, please note because that python strings, Seq objects and
        MutableSeq objects do a non-overlapping search, this may not give
        the answer you expect:

        >>> "AAAA".count("AA")
        2
        >>> print MutableSeq("AAAA").count("AA")
        2

        A non-overlapping search would give the answer as three!
        """
        try :
            #TODO - Should we check the alphabet?
            search = sub.tostring()
        except AttributeError :
            search = sub

        if not isinstance(search, basestring) :
            raise TypeError("expected a string, Seq or MutableSeq")

        if len(search) == 1 :
            #Try and be efficient and work directly from the array.
            count = 0
            for c in self.data[start:end]:
                if c == search: count += 1
            return count
        else :
            #TODO - Can we do this more efficiently?
            return self.tostring().count(search, start, end)

    def index(self, item):
        for i in range(len(self.data)):
            if self.data[i] == item:
                return i
        raise ValueError("MutableSeq.index(x): x not in list")

01354     def reverse(self):
        """Modify the mutable sequence to reverse itself.

        No return value.
        """
        self.data.reverse()

01361     def complement(self):
        """Modify the mutable sequence to take on its complement.

        Trying to complement a protein sequence raises an exception.

        No return value.
        """
        if isinstance(Alphabet._get_base_alphabet(self.alphabet),
                      Alphabet.ProteinAlphabet) :
            raise ValueError("Proteins do not have complements!")
        if self.alphabet in (IUPAC.ambiguous_dna, IUPAC.unambiguous_dna):
            d = ambiguous_dna_complement
        elif self.alphabet in (IUPAC.ambiguous_rna, IUPAC.unambiguous_rna):
            d = ambiguous_rna_complement
        elif 'U' in self.data and 'T' in self.data :
            #TODO - Handle this cleanly?
            raise ValueError("Mixed RNA/DNA found")
        elif 'U' in self.data:
            d = ambiguous_rna_complement
        else:
            d = ambiguous_dna_complement
        c = dict([(x.lower(), y.lower()) for x,y in d.iteritems()])
        d.update(c)
        self.data = map(lambda c: d[c], self.data)
        self.data = array.array('c', self.data)
        
01387     def reverse_complement(self):
        """Modify the mutable sequence to take on its reverse complement.

        Trying to reverse complement a protein sequence raises an exception.

        No return value.
        """
        self.complement()
        self.data.reverse()

    ## Sorting a sequence makes no sense.
    # def sort(self, *args): self.data.sort(*args)
    
01400     def extend(self, other):
        if isinstance(other, MutableSeq):
            for c in other.data:
                self.data.append(c)
        else:
            for c in other:
                self.data.append(c)

01408     def tostring(self):
        """Returns the full sequence as a python string.

        Although not formally deprecated, you are now encouraged to use
        str(my_seq) instead of my_seq.tostring().

        Because str(my_seq) will give you the full sequence as a python string,
        there is often no need to make an explicit conversion.  For example,
        
        print "ID={%s}, sequence={%s}" % (my_name, my_seq)

        On Biopython 1.44 or older you would have to have done this:

        print "ID={%s}, sequence={%s}" % (my_name, my_seq.tostring())
        """
        return "".join(self.data)

01425     def toseq(self):
        """Returns the full sequence as a new immutable Seq object.

        >>> from Bio.Seq import Seq
        >>> from Bio.Alphabet import IUPAC
        >>> my_mseq = MutableSeq("MKQHKAMIVALIVICITAVVAAL", \
                                 IUPAC.protein)
        >>> my_mseq
        MutableSeq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
        >>> my_mseq.toseq()
        Seq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())

        Note that the alphabet is preserved.
        """
        return Seq("".join(self.data), self.alphabet)

# The transcribe, backward_transcribe, and translate functions are
# user-friendly versions of the corresponding functions in Bio.Transcribe
# and Bio.Translate. The functions work both on Seq objects, and on strings.

def transcribe(dna):
    """Transcribes a DNA sequence into RNA.

    If given a string, returns a new string object.

    Given a Seq or MutableSeq, returns a new Seq object with an RNA alphabet.

    Trying to transcribe a protein or RNA sequence raises an exception.

    e.g.
    
    >>> transcribe("ACTGN")
    'ACUGN'
    """
    if isinstance(dna, Seq) :
        return dna.transcribe()
    elif isinstance(dna, MutableSeq):
        return dna.toseq().transcribe()
    else:
        return dna.replace('T','U').replace('t','u')

def back_transcribe(rna):
    """Back-transcribes an RNA sequence into DNA.

    If given a string, returns a new string object.
    
    Given a Seq or MutableSeq, returns a new Seq object with an RNA alphabet.

    Trying to transcribe a protein or DNA sequence raises an exception.

    e.g.

    >>> back_transcribe("ACUGN")
    'ACTGN'
    """
    if isinstance(rna, Seq) :
        return rna.back_transcribe()
    elif isinstance(rna, MutableSeq):
        return rna.toseq().back_transcribe()
    else:
        return rna.replace('U','T').replace('u','t')
    
def _translate_str(sequence, table, stop_symbol="*", to_stop=False,
                   cds=False, pos_stop="X") :
    """Helper function to translate a nucleotide string (PRIVATE).

    Arguments:
     - sequence    - a string
     - table       - a CodonTable object (NOT a table name or id number)
     - stop_symbol - a single character string, what to use for terminators.
     - to_stop     - boolean, should translation terminate at the first
                     in frame stop codon?  If there is no in-frame stop codon
                     then translation continues to the end.
     - pos_stop    - a single character string for a possible stop codon
                     (e.g. TAN or NNN)
     - cds - Boolean, indicates this is a complete CDS.  If True, this
             checks the sequence starts with a valid alternative start
             codon (which will be translated as methionine, M), that the
             sequence length is a multiple of three, and that there is a
             single in frame stop codon at the end (this will be excluded
             from the protein sequence, regardless of the to_stop option).
             If these tests fail, an exception is raised.

    Returns a string.

    e.g.

    >>> from Bio.Data import CodonTable
    >>> table = CodonTable.ambiguous_dna_by_id[1]
    >>> _translate_str("AAA", table)
    'K'
    >>> _translate_str("TAR", table)
    '*'
    >>> _translate_str("TAN", table)
    'X'
    >>> _translate_str("TAN", table, pos_stop="@")
    '@'
    >>> _translate_str("TA?", table)
    Traceback (most recent call last):
       ...
    TranslationError: Codon 'TA?' is invalid
    >>> _translate_str("ATGCCCTAG", table, cds=True)
    'MP'
    >>> _translate_str("AAACCCTAG", table, cds=True)
    Traceback (most recent call last):
       ...
    TranslationError: First codon 'AAA' is not a start codon
    >>> _translate_str("ATGCCCTAGCCCTAG", table, cds=True)
    Traceback (most recent call last):
       ...
    TranslationError: Extra in frame stop codon found.
    """
    sequence = sequence.upper()
    amino_acids = []
    forward_table = table.forward_table
    stop_codons = table.stop_codons
    if table.nucleotide_alphabet.letters is not None :
        valid_letters = set(table.nucleotide_alphabet.letters.upper())
    else :
        #Assume the worst case, ambiguous DNA or RNA:
        valid_letters = set(IUPAC.ambiguous_dna.letters.upper() + \
                            IUPAC.ambiguous_rna.letters.upper())
    if cds :
        if str(sequence[:3]).upper() not in table.start_codons :
            raise CodonTable.TranslationError(\
                "First codon '%s' is not a start codon" % sequence[:3])
        if len(sequence) % 3 != 0 :
            raise CodonTable.TranslationError(\
                "Sequence length %i is not a multiple of three" % len(sequence))
        if str(sequence[-3:]).upper() not in stop_codons :
            raise CodonTable.TranslationError(\
                "Final codon '%s' is not a stop codon" % sequence[-3:])
        #Don't translate the stop symbol, and manually translate the M
        sequence = sequence[3:-3]
        amino_acids = ["M"]
    n = len(sequence)
    for i in xrange(0,n-n%3,3) :
        codon = sequence[i:i+3]
        try :
            amino_acids.append(forward_table[codon])
        except (KeyError, CodonTable.TranslationError) :
            #Todo? Treat "---" as a special case (gapped translation)
            if codon in table.stop_codons :
                if cds :
                    raise CodonTable.TranslationError(\
                        "Extra in frame stop codon found.")
                if to_stop : break
                amino_acids.append(stop_symbol)
            elif valid_letters.issuperset(set(codon)) :
                #Possible stop codon (e.g. NNN or TAN)
                amino_acids.append(pos_stop)
            else :
                raise CodonTable.TranslationError(\
                    "Codon '%s' is invalid" % codon)
    return "".join(amino_acids)

def translate(sequence, table="Standard", stop_symbol="*", to_stop=False,
              cds=False):
    """Translate a nucleotide sequence into amino acids.

    If given a string, returns a new string object. Given a Seq or
    MutableSeq, returns a Seq object with a protein alphabet.

    Arguments:
     - table - Which codon table to use?  This can be either a name
               (string) or an NCBI identifier (integer).  Defaults
               to the "Standard" table.
     - stop_symbol - Single character string, what to use for any
                     terminators, defaults to the asterisk, "*".
     - to_stop - Boolean, defaults to False meaning do a full
                 translation continuing on past any stop codons
                 (translated as the specified stop_symbol).  If
                 True, translation is terminated at the first in
                 frame stop codon (and the stop_symbol is not
                 appended to the returned protein sequence).
     - cds - Boolean, indicates this is a complete CDS.  If True, this
                 checks the sequence starts with a valid alternative start
                 codon (which will be translated as methionine, M), that the
                 sequence length is a multiple of three, and that there is a
                 single in frame stop codon at the end (this will be excluded
                 from the protein sequence, regardless of the to_stop option).
                 If these tests fail, an exception is raised.
    
    A simple string example using the default (standard) genetic code:
    
    >>> coding_dna = "GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG"
    >>> translate(coding_dna)
    'VAIVMGR*KGAR*'
    >>> translate(coding_dna, stop_symbol="@")
    'VAIVMGR@KGAR@'
    >>> translate(coding_dna, to_stop=True)
    'VAIVMGR'
     
    Now using NCBI table 2, where TGA is not a stop codon:

    >>> translate(coding_dna, table=2)
    'VAIVMGRWKGAR*'
    >>> translate(coding_dna, table=2, to_stop=True)
    'VAIVMGRWKGAR'

    In fact this example uses an alternative start codon valid under NCBI table 2,
    GTG, which means this example is a complete valid CDS which when translated
    should really start with methionine (not valine):
    
    >>> translate(coding_dna, table=2, cds=True)
    'MAIVMGRWKGAR'

    Note that if the sequence has no in-frame stop codon, then the to_stop
    argument has no effect:

    >>> coding_dna2 = "GTGGCCATTGTAATGGGCCGC"
    >>> translate(coding_dna2)
    'VAIVMGR'
    >>> translate(coding_dna2, to_stop=True)
    'VAIVMGR'
    
    NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid
    or a stop codon.  These are translated as "X".  Any invalid codon
    (e.g. "TA?" or "T-A") will throw a TranslationError.

    NOTE - Does NOT support gapped sequences.
    
    It will however translate either DNA or RNA.
    """
    if isinstance(sequence, Seq) :
        return sequence.translate(table, stop_symbol, to_stop, cds)
    elif isinstance(sequence, MutableSeq):
        #Return a Seq object
        return sequence.toseq().translate(table, stop_symbol, to_stop, cds)
    else:
        #Assume its a string, return a string
        try :
            codon_table = CodonTable.ambiguous_generic_by_id[int(table)]
        except ValueError :
            codon_table = CodonTable.ambiguous_generic_by_name[table]
        return _translate_str(sequence, codon_table, stop_symbol, to_stop, cds)
      
def reverse_complement(sequence):
    """Returns the reverse complement sequence of a nucleotide string.

    If given a string, returns a new string object.
    Given a Seq or a MutableSeq, returns a new Seq object with the same alphabet.

    Supports unambiguous and ambiguous nucleotide sequences.

    e.g.

    >>> reverse_complement("ACTG-NH")
    'DN-CAGT'
    """
    if isinstance(sequence, Seq) :
        #Return a Seq
        return sequence.reverse_complement()
    elif isinstance(sequence, MutableSeq) :
        #Return a Seq
        #Don't use the MutableSeq reverse_complement method as it is 'in place'.
        return sequence.toseq().reverse_complement()

    #Assume its a string.
    #In order to avoid some code duplication, the old code would turn the string
    #into a Seq, use the reverse_complement method, and convert back to a string.
    #This worked, but is over five times slower on short sequences!
    if ('U' in sequence or 'u' in sequence) \
    and ('T' in sequence or 't' in sequence):
        raise ValueError("Mixed RNA/DNA found")
    elif 'U' in sequence or 'u' in sequence:
        ttable = _rna_complement_table
    else:
        ttable = _dna_complement_table
    return sequence.translate(ttable)[::-1]

def _test():
    """Run the Bio.Seq module's doctests."""
    print "Runing doctests..."
    import doctest
    doctest.testmod()
    print "Done"

if __name__ == "__main__":
    _test()

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