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# Source code for pydna.dsdna

    #!/usr/bin/env python
    # -*- coding: utf-8 -*-
    # Copyright 2013 by Björn Johansson.  All rights reserved.
    # This code is part of the Python-dna distribution and governed by its
    # license.  Please see the LICENSE.txt file that should have been included
    # as part of this package.

    '''Provides two classes, Dseq and Dseqrecord, for handling double stranded
    DNA sequences. Dseq and Dseqrecord are subclasses of Biopythons
    Seq and SeqRecord classes, respectively. These classes support the
    notion of circular and linear DNA.

    '''

    import copy
    import datetime
    import itertools
    import operator
    import os
    import re
    import string
    import StringIO
    import sys
    import textwrap
    import warnings
    import math

    from Bio                    import Alphabet
    from Bio                    import SeqIO
    from Bio.Alphabet.IUPAC     import IUPACAmbiguousDNA
    from Bio.Seq                import Seq
    from Bio.Seq                import _maketrans
    from Bio.Data.IUPACData     import ambiguous_dna_complement as amb_compl
    from Bio.SeqRecord          import SeqRecord
    from Bio.SeqFeature         import SeqFeature
    from Bio.SeqFeature         import FeatureLocation
    from Bio.SeqUtils.CheckSum  import seguid
    from Bio.GenBank            import RecordParser
    from pydna.utils            import eq
    from pydna.findsubstrings_suffix_arrays_python import common_sub_strings
    from pydna.findterminaloverlap_indexof_python  import terminal_overlap

    amb_compl.update({"U":"A"})
    _complement_table = _maketrans(amb_compl)

    def rc(sequence):
        '''returns the reverse complement of sequence (string)
        accepts mixed DNA/RNA
        '''
        return sequence.translate(_complement_table)[::-1]

    class Dseq(Seq):
        '''Dseq is a class designed to hold information for a double stranded
        DNA fragment. Dseq also holds information describing the topology of
        the DNA fragment (linear or circular).

        Dseq is a subclass of the Biopython Seq object. It stores two
        strings representing the watson (sense) and crick(antisense) strands.
        two properties called linear and circular, and a numeric value ovhg
        (overhang) describing the stagger for the watson and crick strand
        in the 5' end of the fragment.

        The most common usage is probably to create a Dseq object as a
        part of a Dseqrecord object (see Dseqrecord).

        There are three ways of creating a Dseq object directly:

        Only one argument (string):

        >>> import pydna
        >>> pydna.Dseq("aaa")
        Dseq(-3)
        aaa
        ttt

        The given string will be interpreted as the watson strand of a
        blunt, linear double stranded sequence object. The crick strand
        is created automatically from the watson strand.

        Two arguments (string, string):

        >>> import pydna
        >>> pydna.Dseq("gggaaat","ttt")
        Dseq(-7)
        gggaaat
           ttt

        If both watson and crick are given, but not ovhg an attempt
        will be made to find the best annealing between the strands.
        There are limitations to this! For long fragments it is quite
        slow. The length of the annealing sequences have to be at least
        half the length of the shortest of the strands.

        Three arguments (string, string, ovhg=int):

        The ovhg parameter controls the stagger at the five prime end::

            ovhg=-2

            XXXXX
              XXXXX

            ovhg=-1

            XXXXX
             XXXXX

            ovhg=0

            XXXXX
            XXXXX

            ovhg=1

             XXXXX
            XXXXX

            ovhg=2

              XXXXX
            XXXXX

        Example of creating Dseq objects with different amounts of stagger:

        >>> pydna.Dseq(watson="agt",crick="actta",ovhg=-2)
        Dseq(-7)
        agt
          attca
        >>> pydna.Dseq(watson="agt",crick="actta",ovhg=-1)
        Dseq(-6)
        agt
         attca
        >>> pydna.Dseq(watson="agt",crick="actta",ovhg=0)
        Dseq(-5)
        agt
        attca
        >>> pydna.Dseq(watson="agt",crick="actta",ovhg=1)
        Dseq(-5)
         agt
        attca
        >>> pydna.Dseq(watson="agt",crick="actta",ovhg=2)
        Dseq(-5)
          agt
        attca

        the ovhg parameter has to be given with both watson and crick,
        otherwise an exception is raised.

        >>> pydna.Dseq(watson="agt",ovhg=2)
        Traceback (most recent call last):
          File "<stdin>", line 1, in <module>
          File "/usr/local/lib/python2.7/dist-packages/pydna_/dsdna.py", line 169, in __init__
            else:
        Exception: ovhg defined without crick strand!

        The default alphabet is set to Biopython IUPACAmbiguousDNA

        The shape of the fragment is set by either:

        linear   = False, True

        or

        circular = True, False

        Note that both ends of the DNA fragment has to be blunt to set
        circular = True (or linear = False).

        >>> pydna.Dseq("aaa","ttt")
        Dseq(-3)
        aaa
        ttt
        >>> pydna.Dseq("aaa","ttt",ovhg=0)
        Dseq(-3)
        aaa
        ttt
        >>> pydna.Dseq("aaa", "ttt", linear = False ,ovhg=0)
        Dseq(o3)
        aaa
        ttt
        >>> pydna.Dseq("aaa", "ttt", circular = True , ovhg=0)
        Dseq(o3)
        aaa
        ttt

        Coercing to string

        >>> a=pydna.Dseq("tttcccc","aaacccc")
        >>> a
        Dseq(-11)
            tttcccc
        ccccaaa

        >>> str(a)
        'ggggtttcccc'

        The double stranded part is accessible through the dsdata property:

        >>> a.dsdata
        'ttt'

        Dseqrecord and Dseq share the same concept of length
        ::

            <-- length -->
            GATCCTTT
                 AAAGCCTAG

        The slicing of a linear Dseq object works mostly as it does for a string.

        >>> s="ggatcc"
        >>> s[2:3]
        'a'
        >>> s[2:4]
        'at'
        >>> s[2:4:-1]
        ''
        >>> s[::2]
        'gac'
        >>> import pydna
        >>> d=pydna.Dseq(s, linear=True)
        >>> d[2:3]
        Dseq(-1)
        a
        t
        >>> d[2:4]
        Dseq(-2)
        at
        ta
        >>> d[2:4:-1]
        Dseq(-0)
        <BLANKLINE>
        <BLANKLINE>
        >>> d[::2]
        Dseq(-3)
        gac
        ctg

        The slicing of a circular Dseq object has a slightly different meaning.

        >>> s="ggAtCc"
        >>> d=pydna.Dseq(s, circular=True)
        >>> d
        Dseq(o6)
        ggAtCc
        ccTaGg
        >>> d[4:3]
        Dseq(-5)
        CcggA
        GgccT

        The slice [X:X] produces an empty slice for a string, while this will return
        the linearized sequence starting at X:

        >>> s="ggatcc"
        >>> d=pydna.Dseq(s, circular=True)
        >>> d
        Dseq(o6)
        ggatcc
        cctagg
        >>> d[3:3]
        Dseq(-6)
        tccgga
        aggcct
        >>>

        '''

        def __init__(self,
                      watson,
                      crick         = None,
                      ovhg          = None,
                      linear        = None,
                      circular      = None,
                      alphabet      = IUPACAmbiguousDNA()):

            if ovhg is None:
                if crick is None:
                    self.crick = rc(watson)
                    self._ovhg = 0
                else:
                    olaps = common_sub_strings(str(watson).lower(),
                                               str(rc(crick).lower()),
                                               int(math.log(len(watson))/math.log(4)))
                    try:
                        F,T,L = olaps[0]
                    except IndexError:
                        raise Exception("Could not anneal the two strands! "
                                        "ovhg should be provided")
                    ovhgs = [ol[1]-ol[0] for ol in olaps if ol[2]==L]
                    if len(ovhgs)>1:
                        for o in ovhgs:
                            print o
                        raise Exception("More than one way of annealing the strands "
                                        "ovhg should be provided")

                    self._ovhg = T-F
                    self.crick = crick
            elif crick is None:
                raise Exception("ovhg defined without crick strand!")
            else:
                self._ovhg = ovhg
                self.crick = crick

            self.watson = watson

            sns = ((self._ovhg*" ")  + str(self.watson))
            asn = ((-self._ovhg*" ") + str(rc(self.crick)))

            self.todata = "".join([a.strip() or b.strip() for a,b in itertools.izip_longest(sns,asn, fillvalue=" ")])
            self.dsdata = "".join([a for a, b in itertools.izip_longest(sns,asn, fillvalue=" ") if a.lower()==b.lower()])

            if circular == None and linear in (True, False,):
                self._linear   = linear
                self._circular = not linear
            elif linear == None and circular in (True, False,):
                self._circular = circular
                self._linear   = not circular
            elif circular == linear == None:
                self._circular = False
                self._linear   = True
            elif linear in (True, False,) and circular in (True, False,) and circular != linear:
                self._circular = circular
                self._linear   = not circular
            else:
                raise Exception("circular and linear argument set to {} and {}, respectively\n".format(circular,linear)+
                                "circular and linear are each others opposites.")

            assert self._circular != self._linear

            if (self.circular and
                self.five_prime_end()[0]  != "blunt" and
                self.three_prime_end()[0] != "blunt"):
                raise Exception("DNA is circular, but has staggered ends!\n")

            Seq.__init__(self, self.todata, alphabet)

        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 self.linear:
                return Seq.find(self, sub, start, end)

            sub_str = self._get_seq_str_and_check_alphabet(sub)

            return (str(self)+str(self)).find(sub_str, start, end)

        def __getitem__(self, sl):
            '''Returns a subsequence.
            '''

            if self.linear:
                sns = (self._ovhg*" " + self.watson)[sl]
                asn = (-self._ovhg*" " + self.crick[::-1])[sl]
                ovhg = max((len(sns) - len(sns.lstrip()),
                            -len(asn) + len(asn.lstrip())),
                            key=abs)
                return Dseq(sns.strip(), asn[::-1].strip(), ovhg=ovhg, linear=True)
            else:
                sl = slice(sl.start or 0,
                           sl.stop  or len(self),
                           sl.step)

                if sl.start<sl.stop:
                    return Dseq(self.watson[sl],self.crick[::-1][sl][::-1], ovhg=0, linear=True)
                else:
                    #print sl.start,sl.stop, "<---"
                    try:
                        stp = abs(sl.step)
                    except TypeError:
                        stp = 1
                    start=sl.start
                    stop=sl.stop
                    if not start:
                        start=0
                    if not stop:
                        stop=len(self)

                    w = self.watson[(start or len(self))::stp] + self.watson[:(stop or 0):stp]
                    c = self.crick[len(self)-stop::stp] + self.crick[:len(self)-start:stp]

                    return Dseq(w, c, ovhg=0, linear=True)

        def __eq__( self, other ):
            '''Compare to another Dseq object OR an object that implements
            watson, crick and ovhg properties. This comparison is case
            insensitive.

            '''
            try:
                same = (other.watson.lower() == self.watson.lower() and
                        other.crick.lower()  == self.crick.lower()  and
                        other.ovhg == self._ovhg)
            except AttributeError:
                same = False
            return same

        def fig(self):
            '''Returns a representation of the sequence, truncated if
           longer than 40 bp:

           Examples
           --------

           >>> import pydna
           >>> a=pydna.Dseq("atcgcttactagcgtactgatcatctgactgactagcgtga")
           >>> a
           Dseq(-41)
           atcg..gtga
           tagc..cact
           >>>

           '''
            return self.__repr__()

        def __repr__(self):
            '''Returns a representation of the sequence, truncated if
            longer than 30 bp'''

            if len(self) > 30:

                if self.ovhg>0:
                    d = self.crick[-self.ovhg:][::-1]
                    hej = len(d)
                    if len(d)>10:
                        d = "{}..{}".format(d[:4], d[-4:])
                    a = len(d)*" "

                elif self.ovhg<0:
                    a = self.watson[:max(0,-self.ovhg)]
                    hej = len(a)
                    if len(a)>10:
                        a = "{}..{}".format(a[:4], a[-4:])
                    d = len(a)*" "
                else:
                    a = ""
                    d = ""
                    hej=0

                x = self.ovhg+len(self.watson)-len(self.crick)

                if x>0:
                    c=self.watson[len(self.crick)-self.ovhg:]
                    y=len(c)
                    if len(c)>10:
                        c = "{}..{}".format(c[:4], c[-4:])
                    f=len(c)*" "
                elif x<0:
                    f=self.crick[:-x][::-1]
                    y=len(f)
                    if len(f)>10:
                        f = "{}..{}".format(f[:4], f[-4:])
                    c=len(f)*" "
                else:
                    c = ""
                    f = ""
                    y=0

                L = len(self)-hej-y
                x1 = -min(0, self.ovhg)
                x2 = x1+L
                x3 = -min(0, x)
                x4 = x3+L

                b=self.watson[x1:x2]
                e=self.crick[x3:x4][::-1]
                if len(b)>10:
                    b = "{}..{}".format(b[:4], b[-4:])
                    e = "{}..{}".format(e[:4], e[-4:])

                #import sys;sys.exit()

                return ("{klass}({top}{size})\n"
                        "{a}{b}{c}\n"
                        "{d}{e}{f}").format(klass = self.__class__.__name__,
                                              top = {True:"-", False:"o"}[self.linear],
                                              size = len(self),
                                              a=a,
                                              b=b,
                                              c=c,
                                              d=d,
                                              e=e,
                                              f=f,)

            else:
                return "{}({}{})\n{}\n{}".format(self.__class__.__name__,
                                                    {True:"-", False:"o"}[self.linear],
                                                    len(self),
                                                    self._ovhg*" " + self.watson,
                                                   -self._ovhg*" "+ self.crick[::-1])

        def rc(self):
            '''Alias of the reverse_complement method'''
            return self.reverse_complement()

        def reverse_complement(self):
            '''Returns a Dseq object where watson and crick have switched
            places.

           '''
            ovhg = len(self.watson) - len(self.crick) + self._ovhg
            return Dseq(self.crick, self.watson, ovhg=ovhg, circular = self.circular)

        def looped(self):
            '''Returns a circularized Dseq object. This can only be done if the
           two ends are compatible, otherwise a TypeError is raised.

           Examples
           --------

           >>> import pydna
           >>> a=pydna.Dseq("catcgatc")
           >>> a
           Dseq(-8)
           catcgatc
           gtagctag
           >>> a.looped()
           Dseq(o8)
           catcgatc
           gtagctag
           >>> a.T4("t")
           Dseq(-8)
           catcgat
            tagctag
           >>> a.T4("t").looped()
           Dseq(o7)
           catcgat
           gtagcta
           >>> a.T4("a")
           Dseq(-8)
           catcga
             agctag
           >>> a.T4("a").looped()
           Traceback (most recent call last):
             File "<stdin>", line 1, in <module>
             File "/usr/local/lib/python2.7/dist-packages/pydna/dsdna.py", line 357, in looped
               if type5 == type3 and str(sticky5) == str(rc(sticky3)):
           TypeError: DNA cannot be circularized.
           5' and 3' sticky ends not compatible!
           >>>

           '''
            if self.circular:
                return self
            type5, sticky5 = self.five_prime_end()
            type3, sticky3 = self.three_prime_end()
            if type5 == type3 and str(sticky5) == str(rc(sticky3)):
                nseq = Dseq(self.watson, self.crick[-self._ovhg:] + self.crick[:-self._ovhg], 0, circular=True)
                assert len(nseq.crick) == len(nseq.watson)
                return nseq
            else:
                raise TypeError("DNA cannot be circularized.\n"
                                 "5' and 3' sticky ends not compatible!")

        def tolinear(self):
            '''Returns a blunt, linear copy of a circular Dseq object. This can
           only be done if the Dseq object is circular, otherwise a
           TypeError is raised.

           Examples
           --------

           >>> import pydna
           >>> a=pydna.Dseq("catcgatc", circular=True)
           >>> a
           Dseq(o8)
           catcgatc
           gtagctag
           >>> a.tolinear()
           Dseq(-8)
           catcgatc
           gtagctag
           >>>

           '''

            if self.linear:
                raise TypeError("DNA is not circular.\n")
            return self.__class__(self.watson, self.crick, ovhg=0, linear=True)

        def five_prime_end(self):
            '''Returns a tuple describing the structure of the 5' end of
            the DNA fragment

            >>> import pydna
            >>> a=pydna.Dseq("aaa", "ttt")
            >>> a
            Dseq(-3)
            aaa
            ttt
            >>> a.five_prime_end()
            ('blunt', '')
            >>> a=pydna.Dseq("aaa", "ttt", ovhg=1)
            >>> a
            Dseq(-4)
             aaa
            ttt
            >>> a.five_prime_end()
            ("3'", 't')
            >>> a=pydna.Dseq("aaa", "ttt", ovhg=-1)
            >>> a
            Dseq(-4)
            aaa
             ttt
            >>> a.five_prime_end()
            ("5'", 'a')
            >>>

            '''
            if self.watson and not self.crick:
                return "5'",self.watson.lower()
            if not self.watson and self.crick:
                return "3'",self.crick.lower()
            if self._ovhg < 0:
                sticky = self.watson[:-self._ovhg].lower()
                type_ = "5'"
            elif self._ovhg > 0:
                sticky = self.crick[-self._ovhg:].lower()
                type_ = "3'"
            else:
                sticky = ""
                type_ = "blunt"
            return type_, sticky

        def three_prime_end(self):
            '''Returns a tuple describing the structure of the 5' end of
            the DNA fragment

            >>> import pydna
            >>> a=pydna.Dseq("aaa", "ttt")
            >>> a
            Dseq(-3)
            aaa
            ttt
            >>> a.three_prime_end()
            ('blunt', '')
            >>> a=pydna.Dseq("aaa", "ttt", ovhg=1)
            >>> a
            Dseq(-4)
             aaa
            ttt
            >>> a.three_prime_end()
            ("3'", 'a')
            >>> a=pydna.Dseq("aaa", "ttt", ovhg=-1)
            >>> a
            Dseq(-4)
            aaa
             ttt
            >>> a.three_prime_end()
            ("5'", 't')
            >>>

            '''

            ovhg = len(self.watson)-len(self.crick)+self._ovhg

            if ovhg < 0:
                sticky = self.crick[:-ovhg].lower()
                type_ = "5'"
            elif ovhg > 0:
                sticky = self.watson[-ovhg:].lower()
                type_ = "3'"
            else:
                sticky = ''
                type_ = "blunt"
            return type_, sticky

        def __add__(self, other):
            '''Simulates ligation between two DNA fragments.

            Add other Dseq object at the end of the sequence.
            Type error if all of the points below are fulfilled:

            * either objects are circular
            * if three prime sticky end of self is not the same type
              (5' or 3') as the sticky end of other
            * three prime sticky end of self complementary with five
              prime sticky end of other.

            Phosphorylation and dephosphorylation is not considered.
            DNA is allways presumed to have the necessary 5' phospate
            group necessary for ligation.

           '''
            # test for circular DNA
            if self.circular:
                raise TypeError("circular DNA cannot be ligated!")
            try:
                if other.circular:
                    raise TypeError("circular DNA cannot be ligated!")
            except AttributeError:
                pass

            self_type,  self_tail  = self.three_prime_end()
            other_type, other_tail = other.five_prime_end()
            if  (self_type == other_type and
                str(self_tail) == str(rc(other_tail))):
                answer = Dseq(self.watson + other.watson,
                              other.crick + self.crick,
                              self._ovhg,)
            else:
                raise TypeError("sticky ends not compatible!")
            return answer

        def __mul__(self, number):
            if not isinstance(number, int):
                raise TypeError("TypeError: can't multiply Dseq by non-int of type {}".format(type(number)))
            if number<=0:
                return self.__class__("")
            new = copy.copy(self)
            for i in range(number-1):
                new += self
            return new

        def _fill_in_five_prime(self, nucleotides):
            stuffer = ''
            type, se = self.five_prime_end()
            if type == "5'":
                for n in rc(se):
                    if n in nucleotides:
                        stuffer+=n
                    else:
                        break
            return self.crick+stuffer, self._ovhg+len(stuffer)

        def _fill_in_three_prime(self, nucleotides):
            stuffer = ''
            type, se = self.three_prime_end()
            if type == "5'":
                for n in rc(se):
                    if n in nucleotides:
                        stuffer+=n
                    else:
                        break
            return self.watson+stuffer

        def fill_in(self, nucleotides=None):
            '''Fill in of five prime protruding end with a DNA polymerase
            that has only DNA polymerase activity (such as exo-klenow)
            and any combination of A, G, C or T. Default are all four
            nucleotides together.

            Examples
            --------

            >>> import pydna
            >>> a=pydna.Dseq("aaa", "ttt")
            >>> a
            Dseq(-3)
            aaa
            ttt
            >>> a.fill_in()
            Dseq(-3)
            aaa
            ttt
            >>> b=pydna.Dseq("caaa", "cttt")
            >>> b
            Dseq(-5)
            caaa
             tttc
            >>> b.fill_in()
            Dseq(-5)
            caaag
            gtttc
            >>> b.fill_in("g")
            Dseq(-5)
            caaag
            gtttc
            >>> b.fill_in("tac")
            Dseq(-5)
            caaa
             tttc
            >>> b=pydna.Dseq("aaac", "tttg")
            >>> c=pydna.Dseq("aaac", "tttg")
            >>> c
            Dseq(-5)
             aaac
            gttt
            >>> c.fill_in()
            Dseq(-5)
             aaac
            gttt
            >>>

            '''
            if not nucleotides:
                nucleotides = self.alphabet.letters
            nucleotides = set(nucleotides.lower()+nucleotides.upper())
            crick, ovhg = self._fill_in_five_prime(nucleotides)
            watson = self._fill_in_three_prime(nucleotides)
            return Dseq(watson, crick, ovhg)

        def mung(self):
            '''
           Simulates treatment a nuclease with 5'-3' and 3'-5' single
           strand specific exonuclease activity (such as mung bean nuclease)::

                ggatcc    ->     gatcc
                 ctaggg          ctagg

                 ggatcc   ->      ggatc
                tcctag            cctag

            >>> import pydna
            >>> b=pydna.Dseq("caaa", "cttt")
            >>> b
            Dseq(-5)
            caaa
             tttc
            >>> b.mung()
            Dseq(-3)
            aaa
            ttt
            >>> c=pydna.Dseq("aaac", "tttg")
            >>> c
            Dseq(-5)
             aaac
            gttt
            >>> c.mung()
            Dseq(-3)
            aaa
            ttt
            '''
            return Dseq(self.dsdata)

        def t4(self,*args,**kwargs):
            '''Alias for the T4 method'''
            return self.T4(*args,**kwargs)

        def T4(self, nucleotides=None):
            '''Fill in of five prime protruding ends and chewing back of
           three prime protruding ends by a DNA polymerase providing both
           5'-3' DNA polymerase activity and 3'-5' nuclease acitivty
           (such as T4 DNA polymerase). This in presence of any
           combination of A, G, C or T. Default are all four
           nucleotides together.

           Examples
           --------

           >>> import pydna
           >>> a=pydna.Dseq("gatcgatc")
           >>> a
           Dseq(-8)
           gatcgatc
           ctagctag
           >>> a.T4()
           Dseq(-8)
           gatcgatc
           ctagctag
           >>> a.T4("t")
           Dseq(-8)
           gatcgat
            tagctag
           >>> a.T4("a")
           Dseq(-8)
           gatcga
             agctag
           >>> a.T4("g")
           Dseq(-8)
           gatcg
              gctag
           >>>

           '''

            if not nucleotides: nucleotides = self.alphabet.letters
            nucleotides = set(nucleotides.lower() + nucleotides.upper())
            type, se = self.five_prime_end()
            crick = self.crick
            if type == "5'":
                crick, ovhg = self._fill_in_five_prime(nucleotides)
            else:
                if type == "3'":
                    ovhg = 0
                    crick = self.crick[:-len(se)]
            x = len(crick)-1
            while x>=0:
                if crick[x] in nucleotides:
                    break
                x-=1
            ovhg = x-len(crick)+1
            crick = crick[:x+1]
            if not crick: ovhg=0
            watson = self.watson
            type, se = self.three_prime_end()
            if type == "5'":
                watson = self._fill_in_three_prime(nucleotides)
            else:
                if type == "3'":
                    watson = self.watson[:-len(se)]
            x = len(watson)-1
            while x>=0:
                if watson[x] in nucleotides:
                    break
                x-=1
            watson=watson[:x+1]
            return Dseq(watson, crick, ovhg)

        def _cut(self, *enzymes):

            output = []
            stack = []
            stack.extend(reversed(enzymes))
            while stack:
                top = stack.pop()
                if hasattr(top, "__iter__"):
                    stack.extend(reversed(top))
                else:
                    output.append(top)
            enzymes = output

            if not hasattr(enzymes, '__iter__'):
                enzymes = (enzymes,)

            if self.circular:
                frags=[self.tolinear()*3,]
            else:
                frags=[self,]

            newfrags=[]

            enzymes = [e for (p,e) in sorted([(enzyme.search(Seq(frags[0].dsdata))[::-1], enzyme) for enzyme in enzymes], reverse=True) if p]

            if not enzymes:
                return [self,]

            for enzyme in enzymes:
                for frag in frags:

                    if enzyme.search(Seq(frag.dsdata)):

                        watson_fragments = [str(s) for s in enzyme.catalyze(Seq(frag.watson+"N"))]
                        crick_fragments  = [str(s) for s in enzyme.catalyze(Seq(frag.crick+"N" ))[::-1]]

                        watson_fragments[-1] = watson_fragments[-1][:-1]
                        crick_fragments[0]   = crick_fragments[0][:-1]

                        s = zip(watson_fragments, crick_fragments)

                        if frag.linear:
                            newfrags.append(Dseq(*s.pop(0),
                                                 ovhg = frag.ovhg,
                                                 linear = True))
                            for seqs in s:
                                newfrags.append(Dseq(*seqs,
                                                     ovhg = enzyme.ovhg,
                                                     linear = True))
                        else:
                            for seqs in s:
                                newfrags.append(Dseq(*seqs,
                                                     ovhg=enzyme.ovhg,
                                                     linear=True))
                    else:
                        newfrags.append(frag)
                frags=newfrags
                newfrags=[]

            if self.circular:
                swl = len(self.watson)
                frags = frags[1:-1]
                newfrags = [frags.pop(0),]
                while sum(len(f.watson) for f in newfrags) < swl:
                    newfrags.append(frags.pop(0))
                frags = newfrags

            return frags

        def cut(self, *enzymes):
            '''Returns a list of linear Dseq fragments produced in the digestion.
            If there is not cut, the whole sequence is returned.

            Examples
            --------

            >>> from pydna import Dseq
            >>> seq=Dseq("ggatccnnngaattc")
            >>> seq
            Dseq(-15)
            ggatccnnngaattc
            cctaggnnncttaag
            >>> from Bio.Restriction import BamHI,EcoRI
            >>> type(seq.cut(BamHI))
            <type 'list'>
            >>> for frag in seq.cut(BamHI):
            ...     print frag.fig()
            Dseq(-5)
            g
            cctag
            Dseq(-14)
            gatccnnngaattc
                gnnncttaag
            >>> seq.cut(EcoRI, BamHI) ==  seq.cut(BamHI, EcoRI)
            True
            >>> a,b,c = seq.cut(EcoRI, BamHI)
            >>> a+b+c
            Dseq(-15)
            ggatccnnngaattc
            cctaggnnncttaag
            >>>

            '''
            output = []
            stack = []
            stack.extend(reversed(enzymes))
            while stack:
                top = stack.pop()
                if hasattr(top, "__iter__"):
                    stack.extend(reversed(top))
                else:
                    output.append(top)
            enzymes = output
            if not hasattr(enzymes, '__iter__'):
                enzymes = (enzymes,)

            if self.circular:
                frags=[self.tolinear()*3,]
            else:
                frags=[self,]

            newfrags=[]

            enzymes = [e for (p,e) in sorted([(enzyme.search(Seq(frags[0].dsdata))[::-1], enzyme) for enzyme in enzymes], reverse=True) if p]

            if not enzymes:
                return [self,]

            for enz in enzymes:
                for frag in frags:

                    ws = [x-1 for x in enz.search(Seq(frag.watson)+"N")] #, linear = frag.linear
                    cs = [x-1 for x in enz.search(Seq(frag.crick) +"N")] #, linear = frag.linear

                    sitepairs = [(sw, sc) for sw, sc in zip(ws,cs[::-1])
                                 if (sw + max(0, frag.ovhg) -
                                 max(0, enz.ovhg)
                                 ==
                                 len(frag.crick)-sc -
                                 min(0, frag.ovhg) +
                                 min(0, enz.ovhg))]

                    sitepairs = sitepairs + [(len(frag.watson), 0)]

                    w2, c1 = sitepairs[0]

                    nwat = frag.watson[:w2]
                    ncrk = frag.crick[c1:]

                    newfrags.append(Dseq(nwat, ncrk, ovhg=frag.ovhg))

                    for (w1, c2), (w2, c1)  in zip(sitepairs[:-1], sitepairs[1:]):
                        nwat = frag.watson[w1:w2]
                        ncrk = frag.crick[c1:c2]
                        newfrag = Dseq(nwat, ncrk, ovhg = enz.ovhg)
                        newfrags.append(newfrag)

                    if not newfrags:
                        newfrags.append(frag)

                frags=newfrags
                newfrags=[]

            if self.circular:
                swl = len(self.watson)
                frags = frags[1:-1]
                newfrags = [frags.pop(0),]
                while sum(len(f.watson) for f in newfrags) < swl:
                    newfrags.append(frags.pop(0))
                frags = newfrags[-1:] + newfrags[:-1]

            return frags

        @property
        def ovhg(self):
            '''The ovhg property'''
            return self._ovhg

        @property
        def linear(self):
            '''The linear property'''
            return self._linear

        @property
        def circular(self):
            '''The circular property'''
            return self._circular

    class Dseqrecord(SeqRecord):
        '''Dseqrecord is a double stranded version of the Biopython SeqRecord class.
        The Dseqrecord object holds a Dseq object describing the sequence.
        Additionally, Dseqrecord hold meta information about the sequence in the
        from of a list of SeqFeatures, in the same way as the SeqRecord does.
        The Dseqrecord can be initialized with a string, Seq, Dseq, SeqRecord
        or another Dseqrecord. The sequence information will be stored in a
        Dseq object in all cases. Dseqrecord objects can be read or parsed
        from sequences in Fasta, Embl or Genbank format.

        There is a short representation associated with the Dseqrecord.
        ``Dseqrecord(-3)`` represents a linear sequence of length 2
        while ``Dseqrecord(o7)``
        represents a circular sequence of length 7.

        Dseqrecord and Dseq share the same concept of length
        ::

            <-- length -->
            GATCCTTT
                 AAAGCCTAG

        Parameters
        ----------
        record  : string, Seq, SeqRecord, Dseq or other Dseqrecord object
            This data will be used to form the seq property

        circular : bool, optional
            True or False reflecting the shape of the DNA molecule

        linear : bool, optional
            True or False reflecting the shape of the DNA molecule

        Examples
        --------

        >>> from pydna import Dseqrecord
        >>> a=Dseqrecord("aaa")
        >>> a
        Dseqrecord(-3)
        >>> a.seq
        Dseq(-3)
        aaa
        ttt
        >>> from Bio.Seq import Seq
        >>> b=Dseqrecord(Seq("aaa"))
        >>> b
        Dseqrecord(-3)
        >>> b.seq
        Dseq(-3)
        aaa
        ttt
        >>> from Bio.SeqRecord import SeqRecord
        >>> c=Dseqrecord(SeqRecord(Seq("aaa")))
        >>> c
        Dseqrecord(-3)
        >>> c.seq
        Dseq(-3)
        aaa
        ttt
        >>> a.seq.alphabet
        IUPACAmbiguousDNA()
        >>> b.seq.alphabet
        IUPACAmbiguousDNA()
        >>> c.seq.alphabet
        IUPACAmbiguousDNA()
        >>>

        '''

        def __init__(self, record,
                             circular               = None,
                             linear                 = None,
                             *args, **kwargs):

            if circular == None and linear in (True, False,):
                circular = not linear
            elif linear == None and circular in (True, False,):
                linear   = not circular

            if isinstance(record, basestring):  # record is a string
                SeqRecord.__init__(self,
                                   Dseq(record,
                                        rc(record),
                                        ovhg=0 ,
                                        linear=linear,
                                        circular=circular),
                                   *args,
                                   **kwargs)
            elif hasattr(record, "features"): # record is SeqRecord or Dseqrecord?
                for key, value in record.__dict__.items():
                    setattr(self, key, value )
                if hasattr(record.seq, "watson"): # record.seq is a Dseq
                    new_seq = copy.copy(record.seq)
                    if new_seq.circular and linear:
                        new_seq = new_seq.tolinear()
                    if new_seq.linear and circular:
                        new_seq = new_seq.looped()
                    self.seq=new_seq
                else:                             # record is Bio.SeqRecord
                    self.seq=Dseq(str(self.seq),
                                  rc(str(self.seq)),
                                  ovhg=0 ,
                                  linear=linear,
                                  circular=circular)
            elif hasattr(record, "watson"):      # record is Dseq ?
                if record.circular and linear:
                    record = record.tolinear()
                if record.linear and circular:
                    record = record.looped()
                SeqRecord.__init__(self, record, *args, **kwargs)
            elif isinstance(record, Seq):         # record is Bio.Seq ?
                SeqRecord.__init__(self, Dseq(str(record),
                                              str(record.reverse_complement()),
                                              ovhg=0 ,
                                              linear=linear,
                                              circular=circular),
                                              *args,
                                              **kwargs)
            else:
                raise TypeError(("record argument needs to be a string,"
                                  "Seq, SeqRecord or Dseq object,"
                                  " got {}").format(type(record)))

            if self.id in ("","."):
                self.id = self.name[:7]

            if self.description ==".":
                self.description = ""

            if not 'date' in self.annotations:
                self.annotations.update({"date": datetime.date.today().strftime("%d-%b-%Y").upper()})

        @property
        def linear(self):
            '''Not really a method, but the linear property'''
            return self.seq.linear

        @property
        def circular(self):
            '''Not really a method, but the circular property'''
            return self.seq.circular

        def seguid(self):
            '''Returns the SEGUID for the sequence

           Examples
           --------

           >>> import pydna
           >>> a=pydna.Dseqrecord("aaa")
           >>> a.seguid()
           'YG7G6b2Kj/KtFOX63j8mRHHoIlE'

           '''
            return seguid(self.seq)

        def stamp(self):
            '''Adds a seguid stamp to the description property. This will
            show in the genbank format. The following string:

            ``SEGUID <seguid>``

            will be appended to the description property of the Dseqrecord
            object (string).

            Examples
            --------

            >>> import pydna
            >>> a=pydna.Dseqrecord("aaa")
            >>> a.stamp()
            >>> a.description
            '<unknown description> SEGUID YG7G6b2Kj/KtFOX63j8mRHHoIlE'
            >>> a.verify_stamp()
            True

            '''
            pattern = "(SEGUID|seguid)\s*\S{27}"
            try:
                stamp = re.search(pattern, self.description).group()
            except AttributeError:
                stamp = "SEGUID {}".format(seguid(self.seq))

            if not self.description:
                self.description = stamp
            elif not re.search(pattern, self.description):
                self.description += " "+stamp

        def verify_stamp(self):
            '''Verifies the SEGUID stamp in the description property is
           valid. True if stamp match the sequid calculated from the sequence.
           Exception raised if no stamp can be found.

            >>> import pydna
            >>> a=pydna.Dseqrecord("aaa")
            >>> a.annotations['date'] = '02-FEB-2013'
            >>> a.seguid()
            'YG7G6b2Kj/KtFOX63j8mRHHoIlE'
            >>> print a.format("gb")
            LOCUS       .                          3 bp    DNA     linear   UNK 02-FEB-2013
            DEFINITION  .
            ACCESSION   <unknown id>
            VERSION     <unknown id>
            KEYWORDS    .
            SOURCE      .
              ORGANISM  .
                        .
            FEATURES             Location/Qualifiers
            ORIGIN
                    1 aaa
            //
            >>> a.stamp()
            >>> a
            Dseqrecord(-3)
            >>> print a.format("gb")
            LOCUS       .                          3 bp    DNA     linear   UNK 02-FEB-2013
            DEFINITION  <unknown description> SEGUID YG7G6b2Kj/KtFOX63j8mRHHoIlE
            ACCESSION   <unknown id>
            VERSION     <unknown id>
            KEYWORDS    .
            SOURCE      .
              ORGANISM  .
                        .
            FEATURES             Location/Qualifiers
            ORIGIN
                    1 aaa
            //
            >>> a.verify_stamp()
            True
            >>>

           '''
            pattern = "(SEGUID|seguid)\s*\S{27}"
            try:
                stamp = re.search(pattern, self.description).group()
            except AttributeError:
                raise Exception("No stamp present in the description property.")
            return seguid(self.seq) == stamp[-27:]

        def looped(self):
            '''
            Returns a circular version of the Dseqrecord object. The
            underlying Dseq object has to have compatible ends.

            Examples
            --------
            >>> import pydna
            >>> a=pydna.Dseqrecord("aaa")
            >>> a
            Dseqrecord(-3)
            >>> b=a.looped()
            >>> b
            Dseqrecord(o3)
            >>>
            '''
            new = self.__class__(self.seq.looped())

            new.features            = copy.copy(self.features)
            new.annotations         = copy.copy(self.annotations)
            new.name                = copy.copy(self.name)
            new.dbxrefs             = copy.copy(self.dbxrefs)
            new.id                  = copy.copy(self.id)
            new.description         = copy.copy(self.description)
            new.letter_annotations  = copy.copy(self.letter_annotations)

            for fn, fo in zip(new.features, self.features):
                fn.qualifiers = fo.qualifiers

            return new

        def tolinear(self):
            '''
            Returns a linear, blunt of a circular Dseqrecord object. The
            underlying Dseq object has to be circular.

            Examples
            --------
            >>> import pydna
            >>> a=pydna.Dseqrecord("aaa", circular = True)
            >>> a
            Dseqrecord(o3)
            >>> b=a.tolinear()
            >>> b
            Dseqrecord(-3)
            >>>
            '''
            new = self.__class__(self.seq.tolinear())
            #new.features = [copy.copy(f) for f in self.features]
            new.features            = copy.copy(self.features)
            new.annotations         = copy.copy(self.annotations)
            new.name                = copy.copy(self.name)
            new.dbxrefs             = copy.copy(self.dbxrefs)
            new.id                  = copy.copy(self.id)
            new.description         = copy.copy(self.description)
            new.letter_annotations  = copy.copy(self.letter_annotations)
            for fn, fo in zip(new.features, self.features):
                fn.qualifiers = fo.qualifiers

            return new

        def format(self, f="gb"):
            '''Returns the sequence as a string using a format supported by Biopython
            SeqIO. Default is "gb" which is short for Genbank.

            Examples
            --------
            >>> import pydna
            >>> a=pydna.Dseqrecord("aaa")
            >>> a.annotations['date'] = '02-FEB-2013'
            >>> a
            Dseqrecord(-3)
            >>> print a.format()
            LOCUS       .                          3 bp    DNA     linear   UNK 02-FEB-2013
            DEFINITION  .
            ACCESSION   <unknown id>
            VERSION     <unknown id>
            KEYWORDS    .
            SOURCE      .
              ORGANISM  .
                        .
            FEATURES             Location/Qualifiers
            ORIGIN
                    1 aaa
            //

            '''

            s = SeqRecord.format(self, f).strip()
            if f in ("genbank","gb"):
                if self.circular:
                    return s[:55]+"circular"+s[63:]
                else:
                    return s[:55]+"linear"+s[61:]
            else:
                return s

        def write(self, filename=None, f="gb"):
            '''Writes the Dseqrecord to a file using the format f, which must
            be a format supported by Biopython SeqIO. Default is "gb"
            which is short for Genbank.

            Filename is the path to the file where the sequece is to be
            written. The filename is optional, if it is not given, the
            description property (string) is used together with the format:

            If obj is the Dseqrecord object, the default file name will be:

            ``<obj.description>.<f>``

            If the filename already exists and the sequence it contains
            is different, a new file name will be used:

            ``<obj.description>_NEW.<f>``

           '''
            if not filename:
                filename = self.description + "." + f
            if isinstance(filename, basestring):
                if os.path.isfile(filename):
                    seguid_new=self.seguid()
                    old_file = read(filename)
                    seguid_old = old_file.seguid()
                    if  seguid_new == seguid_old and self.circular == old_file.circular:
                        os.utime(filename, None)
                    else:
                        name, ext = os.path.splitext(filename)
                        new_filename = "{}_NEW{}".format(name, ext)
                        print("\n\nseguid(old) = {} in file {}"
                               "\nseguid(new) = {} in file {}\n").format(seguid_old, filename, seguid_new, new_filename)
                        with open(new_filename, "w") as fp:
                            fp.write(self.format(f))

                else:
                    with open(filename, "w") as fp:
                        fp.write(self.format(f))
            else:
                with filename as fp:
                    fp.write(self.format(f))

        def __str__(self):
            return ("Dseqrecord\n"
                     "circular: {}\n"
                     "size: {}\n").format(self.circular, len(self))+SeqRecord.__str__(self)

        def __repr__(self):
            return "Dseqrecord({}{})".format({True:"-", False:"o"}[self.linear],len(self))

        def __add__(self, other):
            if hasattr(other, "seq") and hasattr(other.seq, "watson"):
                offset = other.seq.ovhg
                other = Dseqrecord(other.seq,
                                id = self.id,
                                name = self.name,
                                description = self.description,
                                features = [f._shift(offset) for f in other.features],
                                annotations = self.annotations.copy(),
                                dbxrefs = self.dbxrefs[:])
                answer = Dseqrecord(SeqRecord.__add__(self, other))

            else:
                answer = Dseqrecord(SeqRecord.__add__(self, Dseqrecord(other)))
                assert answer.circular == False
            return answer

    #    def __mul__(self, number):
    #        if not isinstance(number, int):
    #            raise TypeError("TypeError: can't multiply Dseqrecord by non-int of type {}".format(type(number)))
    #        number-=1
    #        if number>0:
    #            new = copy.copy(self)
    #            for i in range(number):
    #                new += self
    #            return new
    #        else:
    #            return self.__class__("")

        def __getitem__(self, sl):
            answer = Dseqrecord(Dseq.__getitem__(self.seq, sl))
            answer.seq.alphabet = self.seq.alphabet

            answer.features = SeqRecord.__getitem__(self, sl).features

            return answer

        def cut(self, *enzymes):
            '''Digest the Dseqrecord object with one or more restriction enzymes.
           returns a list of linear Dseqrecords.

           Parameters
           ----------
           enzymes : iterable object
                iterable containing Biopython
                restriction enzyme objects

           Returns
           -------
           fragments : list
                list of Dseqrecord objects formed by the digestion

           Examples
           --------

           >>> import pydna
           >>> a=pydna.Dseqrecord("ggatcc")
           >>> from Bio.Restriction import BamHI
           >>> a.cut(BamHI)
           [Dseqrecord(-5), Dseqrecord(-5)]
           >>> frag1, frag2 = a.cut(BamHI)
           >>> frag1.seq
           Dseq(-5)
           g
           cctag
           >>> frag2.seq
           Dseq(-5)
           gatcc
               g

           '''
            output, stack = [], []
            stack.extend(reversed(enzymes))
            while stack:
                top = stack.pop()
                if hasattr(top, "__iter__"):
                    stack.extend(reversed(top))
                else:
                    output.append(top)
            enzymes = output
            if not hasattr(enzymes, '__iter__'):
                enzymes = (enzymes,)

            frags = self.seq.cut(enzymes)

            if self.linear:
                last_pos=0
                template = self.__class__(self, linear=True)
            else:
                last_pos = [p.pop(0)-max(0,enzyme.ovhg)-1 for (p,e) in
                             sorted([(enzyme.search(Seq(self.seq.dsdata),
                                                    linear = self.linear)[::-1],
                                       enzyme) for enzyme in enzymes]) if p]
                if 0 in last_pos:
                    last_pos=0
                else:
                    last_pos = last_pos.pop()
                template = self._multiply_circular(3)

            Dseqrecord_frags = []
            start = last_pos

            #from pydna_helper import ape; ape(template)

            #raw_input("!")

            for f in frags:
                end = start + len(str(f))
                Dseqrecord_frag = Dseqrecord(f, linear=True)
                Dseqrecord_frag.features = template[start:end].features

                Dseqrecord_frag.annotations         = copy.copy(self[start:end].annotations)
                Dseqrecord_frag.name                = copy.copy(self.name)
                Dseqrecord_frag.dbxrefs             = copy.copy(self[start:end].dbxrefs)
                Dseqrecord_frag.id                  = copy.copy(self.id)
                Dseqrecord_frag.letter_annotations  = copy.copy(self[start:end].letter_annotations)

                #ape(template[start:end])
                #print Dseqrecord_frag.seq.fig()

                Dseqrecord_frag.description = self.description+"_"+"_".join(str(e) for e in enzymes)

                #ape(Dseqrecord_frag);
                #raw_input("xx")

                Dseqrecord_frags.append(Dseqrecord_frag)
                start = end
                start-= len(f.three_prime_end()[1])

            return Dseqrecord_frags

        def reverse_complement(self):
            '''Returns a new Dseqrecord object which is the reverse complement.

           Examples
           --------
           >>> import pydna
           >>> a=pydna.Dseqrecord("ggaatt")
           >>> a
           Dseqrecord(-6)
           >>> a.seq
           Dseq(-6)
           ggaatt
           ccttaa
           >>> a.reverse_complement().seq
           Dseq(-6)
           aattcc
           ttaagg
           >>>
           '''

            return self.rc()

        def rc(self):
            '''alias of the reverse_complement method'''
            answer = Dseqrecord(SeqRecord.reverse_complement(self))
            assert answer.circular == self.circular
            answer.id = self.id+"_rc"
            return answer
            #return Dseqrecord(self.seq.rc())

        def _multiply_circular(self, number):
            '''returns a linearised version of self multiplied by
           number '''

            if self.linear:
                raise TypeError("sequence has to be circular!")

            if not isinstance(number, int):
                raise TypeError("TypeError: can't multiply Dseq by non-int of type {}".format(type(number)))

            if number<=0:
                return self.__class__("")

            new_features = [copy.copy(f) for f in self.features if not len(self)-1 in f or not 0 in f]
            wrap_around_features =  [copy.copy(f) for f in self.features if len(self)-1 in f and 0 in f]
            new_locs = [ FeatureLocation(f.location.start, f.location.start+len(f)) for f in wrap_around_features]

            for feat, newl in zip(wrap_around_features, new_locs):
                feat.location = newl
                feat.location_operator = None
                feat.sub_features=[]

            new_feature_sets = []
            sequence = self.tolinear()
            sequence.features=[]

            for i in range(0, number-1):
                sequence += self.tolinear()
                new_feature_sets.extend( [copy.copy(f)._shift(len(self)*i) for f in new_features] )
                new_feature_sets.extend( [copy.copy(f)._shift(len(self)*i) for f in wrap_around_features] )
            new_feature_sets.extend( [copy.copy(f)._shift(len(self)*(number-1)) for f in new_features] )

            sequence.features = new_feature_sets
            return sequence

        def shifted(self, shift):
            '''Returns a circular Dseqrecord with a new origin <shift>.
            This only works on circular Dseqrecords. If we consider the following
            circular sequence:

            | ``GAAAT   <-- watson strand``
            | ``CTTTA   <-- crick strand``

            The T and the G on the watson strand are linked together as well
            as the A and the C of the of the crick strand.

            if ``shift`` is 1, this indicates a new origin at position 1:

            |    new origin
            |
            | ``G|AAAT``
            | ``C|TTTA``

            new sequence:

            | ``AAATG``
            | ``TTTAC``

            Shift is always positive and 0<shift<length, so in the example
            below, permissible values of shift are 1,2 and 3

            >>> import pydna
            >>> a=pydna.Dseqrecord("aaat",circular=True)
            >>> a
            Dseqrecord(o4)
            >>> a.seq
            Dseq(o4)
            aaat
            ttta
            >>> b=a.shifted(1)
            >>> b
            Dseqrecord(o4)
            >>> b.seq
            Dseq(o4)
            aata
            ttat

            '''
            if self.linear:
                raise Exception("Sequence is linear.\n"
                                 "The origin can only be\n"
                                 "shifted on a circular sequence!\n")
            length=len(self)
            if not 0<shift<length:
                raise Exception("shift is {}, has to be 0<shift<{}".format(shift, length))

            new = self._multiply_circular(3)

            #from pydna_helper import ape; ape(new)

            features_to_fold = [f for f in new.features if shift+length in f and f.location.start<shift+length]

            folded_features = []

            for feature in features_to_fold:

                subfl1 =  FeatureLocation(feature.location.start-shift, length)
                subfl2 =  FeatureLocation(0, len(feature)-len(subfl1))

                sub1 = SeqFeature(subfl1,
                                  type=feature.type,
                                  location_operator=feature.location_operator,
                                  strand=feature.strand,
                                  id=feature.id,
                                  qualifiers=feature.qualifiers,
                                  sub_features=None)
                sub2 = SeqFeature(subfl2,
                                  type=feature.type,
                                  location_operator=feature.location_operator,
                                  strand=feature.strand,
                                  id=feature.id,
                                  qualifiers=feature.qualifiers,
                                  sub_features=None)
                pf =    SeqFeature(FeatureLocation(subfl1.start, subfl2.end),
                                  type=feature.type,
                                  location_operator="join",
                                  strand=feature.strand,
                                  id=feature.id,
                                  qualifiers=feature.qualifiers,
                                  sub_features=[sub1,sub2])
                folded_features.append(pf)

            new = new[shift:shift+length].looped()
            new.features.extend(folded_features)
            new.features.sort(key = operator.attrgetter('location.start'))

            new.description = "{}_shifted ori {}".format(self.description, shift)
            return new

        def synced(self, ref, limit = 25):
            '''This function returns a new circular sequence (Dseqrecord object), which has ben rotated
            in such a way that there is maximum overlap between the sequence and
            ref, which may be a string, Biopython Seq, SeqRecord object or
            another Dseqrecord object.

            The reason for using this could be to rotate a recombinant plasmid so
            that it starts at the same position after cloning. See the example below:

            Examples
            --------

            >>> import pydna
            >>> a=pydna.Dseqrecord("gaat",circular=True)
            >>> a.seq
            Dseq(o4)
            gaat
            ctta
            >>> d = a[2:] + a[:2]
            >>> d.seq
            Dseq(-4)
            atga
            tact
            >>> insert=pydna.Dseqrecord("CCC")
            >>> recombinant = (d+insert).looped()
            >>> recombinant.seq
            Dseq(o7)
            atgaCCC
            tactGGG
            >>> recombinant.synced(a).seq
            Dseq(o7)
            gaCCCat
            ctGGGta

            '''
            if self.linear:
                raise Exception("Only circular DNA can be synced!")

            sequence = self.seq.tolinear()

            a    = str(sequence.watson).lower()
            a_rc = str(sequence.crick).lower()
            sequence_rc = sequence.reverse_complement()
            double_sequence = sequence+sequence

            if hasattr(ref, "seq"):
                b=ref.seq
                if hasattr(ref, "watson"):
                    b = str(b.watson).lower()
                else:
                    b = str(b).lower()
            else:
                b = str(ref.lower())

            b=b[:len(a)]

            c = common_sub_strings(a+a, b, limit = min(len(ref),limit, limit*(len(a)/limit)+1))
            d = common_sub_strings(a_rc+a_rc, b, limit = min(len(ref), limit, limit*(len(a)/limit)+1))

            if c:
                starta, startb, length = c.pop(0)
            else:
                starta, startb, length = 0,0,0

            if d:
                starta_rc, startb_rc, length_rc = d.pop(0)
            else:
                starta_rc, startb_rc, length_rc = 0,0,0

            if not c and not d:
                raise Exception("There is no overlap between sequences!")

            if length_rc>length:
                starta, startb = starta_rc, startb_rc
                sequence = sequence_rc

            if starta>startb:
                if len(a)<len(b):
                    ofs = starta-startb + len(b)-len(a)
                else:
                    ofs = starta-startb
            elif starta<startb:
                ofs = startb-starta + len(a)-len(b)
                ofs = len(a)-ofs
            elif starta==startb:
                ofs=0
            return self.shifted(ofs)

    def read(data, filter = False, ds = True):
        '''This function is similar the parse funtion but returns only
        the first sequence found.

        Parameters
        ----------
        data : string
            see below
        filter : bool
            if filter == True, sequences will be silently filtered
            for allowed characters (see docs for Dseqrecord)
        ds : bool
            Double stranded or single stranded DNA, Return
            "Dseqrecord" or "SeqRecord" objects.

        Returns
        -------
        Dseqrecord
            contains the first Dseqrecord or SeqRecord object parsed.

        Notes
        -----

        The data parameter is similar to the data parameter for parse.

        See Also
        --------
        parse

        '''

        results = parse(data, filter, ds)
        try:
            results = results.pop()
        except IndexError:
            raise ValueError("No sequences found in data ({})".format(data[:20]))
        return results

    def parse(data, filter = False, ds = True):
        '''This function returns *all* DNA sequences found in data. If no
        sequences are found, an empty list is returned. This is a greedy
        function, use carefully.

        Parameters
        ----------
        data : string or iterable
            see below
        filter : bool
            if filter == True, sequences will be silently filtered
            for allowed characters (see docs for Dseqrecord)
        ds : bool
            Double stranded or single stranded DNA, Return
            "Dseqrecord" or "SeqRecord" objects.

        Returns
        -------
        list
            contains Dseqrecord or SeqRecord objects

        Notes
        -----

        The data parameter is a string containing:

        1. an absolute path to a local file.
           The file will be read in text
           mode and parsed for EMBL, FASTA
           and Genbank sequences.

        2. an absolute path to a local directory.
           all files in the directory will be
           read and parsed as in 1.

        3. a string containing one or more
           sequences in EMBL, GENBANK,
           or FASTA format. Mixed formats
           are allowed.

        4. data can be a list or other iterable of 1 - 3

        '''
        raw=""
        if not hasattr(data, '__iter__'):
            data = (data,)
        for item in data:
            if os.path.isdir(item):
                for file_ in os.listdir(item):
                    with open(file_,'r') as f:
                        raw+="\n\n"+f.read()
            elif os.path.isfile(os.path.join(os.getcwd(),item)):
                with open(item,'r') as f:
                    raw+= f.read()
            else:
                raw+=textwrap.dedent(item).strip()

        pattern =  r"(?:>.+\n^(?:^[^>]+?)(?=\n\n|>|LOCUS|ID))|(?:(?:LOCUS|ID)(?:(?:.|\n)+?)^//)"
        raw = raw.replace( '\r\n', '\n')
        raw = raw.replace( '\r',   '\n')
        rawseqs = re.findall(pattern,textwrap.dedent(raw+"\n\n"),re.MULTILINE)
        sequences=[]

        while rawseqs:
            circular = False
            rawseq = rawseqs.pop(0)
            handle = StringIO.StringIO(rawseq)
            try:
                parsed = SeqIO.read(handle, "embl", alphabet=IUPACAmbiguousDNA())
                original_format = "embl"
                if "circular" in rawseq.splitlines()[0]:
                    circular = True
            except ValueError:
                handle.seek(0)
                try:
                    parsed = SeqIO.read(handle, "genbank", alphabet=IUPACAmbiguousDNA())
                    original_format = "genbank"
                    handle.seek(0)
                    parser = RecordParser()
                    residue_type = parser.parse(handle).residue_type
                    if "circular" in residue_type:
                        circular = True
                except ValueError:
                    handle.seek(0)
                    try:
                        parsed = SeqIO.read(handle, "fasta", alphabet=IUPACAmbiguousDNA())
                        original_format = "fasta"
                        if "circular" in rawseq.splitlines()[0]:
                            circular = True
                    except ValueError:
                        continue

            if ds:
                sequences.append( Dseqrecord( parsed,
                                           parsed_from = original_format,
                                           raw_string  = rawseq,
                                           circular    = circular,
                                           filter      = filter ))
            else:
                sequences.append(parsed)
            handle.close()
        return sequences

    if __name__=="__main__":
        import doctest
        doctest.testmod()

        from pydna import *

        s = read('''

                LOCUS       New_DNA                   21 bp ds-DNA     circular     03-APR-2013
                DEFINITION  a
                ACCESSION
                VERSION
                SOURCE      .
                  ORGANISM  .
                COMMENT
                COMMENT     ApEinfo:methylated:1
                FEATURES             Location/Qualifiers
                     misc_feature    join(18..21,1..4)
                                     /label=bb
                                     /ApEinfo_fwdcolor=cyan
                                     /ApEinfo_revcolor=green
                                     /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                                     width 5 offset 0
                     misc_feature    5..17
                                     /label=ins
                                     /ApEinfo_fwdcolor=#e03c2b
                                     /ApEinfo_revcolor=green
                                     /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
                                     width 5 offset 0
                ORIGIN
                        1 aaaGGTACCt ttGGATCCggg
                //
            ''')#           ----################----

        for i in range(1, len(s)):
            assert s.features[0].extract(s).seq.tostring()  == "CGGGAAAG"
            assert s.features[1].extract(s).seq.tostring()  == "GTACCTTTGGATC"
            b = s.shifted(i)
            assert set([b.features[0].extract(b).seq.tostring(), b.features[1].extract(b).seq.tostring()]) == set(["CGGGAAAG", "GTACCTTTGGATC"])

        from Bio.Restriction import Acc65I,KpnI, BamHI

        bb1, ins1 = sorted(s.cut(Acc65I, BamHI), key=len, reverse=True)

        for i in range(1, len(s)):
            b = s.shifted(i)
            from pydna_helper import ape
            bb, ins = sorted(b.cut(Acc65I, BamHI), key=len, reverse=True)

            assert eq(bb1, bb)
            assert eq(ins1,ins)

            assert bb.features[0].extract(bb).seq.watson == "CGGGAAAG"
            assert bb.features[0].extract(bb).seq.crick  == "CTTTCCCG"

            assert eq(bb.features[0].extract(bb), s.features[0].extract(s) )

            assert ins.features[0].extract(ins).seq.watson == "GTACCTTTG"
            assert ins.features[0].extract(ins).seq.crick  == "GATCCAAAG"

            assert ins.features[0].extract(ins).seq.tostring() == s.features[1].extract(s).seq.tostring()

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