### Navigation

- index
- modules |
- modules |
- Pydna 0.6.2 documentation »
- Module code »

# 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 StringIO
    import sys
    import textwrap
    import math
    import glob

    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, CompoundLocation
    from Bio.SeqUtils.CheckSum  import seguid
    from Bio.GenBank            import RecordParser
    from Bio.Data.CodonTable    import TranslationError

    from pydna.findsubstrings_suffix_arrays_python import common_sub_strings

    from pydna.utils import cseguid

    from prettytable import PrettyTable

    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).

        Parameters
        ----------

        watson : str
            a string representing the watson (sense) DNA strand.

        crick : str, optional
            a string representing the crick (antisense) DNA strand.

        ovhg : int, optional
            A positive or negative number to describe the stagger between the watson and crick strands.
            see below for a detailed explanation.

        linear : bool, optional
            True indicates that sequence is linear, False that it is circular.

        circular : bool, optional
            True indicates that sequence is circular, False that it is linear.

        alphabet : Bio.Alphabet, optional
            Bio.Alphabet.IUPAC.IUPACAmbiguousDNA from the Biopython package is set as default.

        Examples
        --------

        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 :class:`pydna.dsdna.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

        If the ovhg parameter is psecified a crick strand also needs to be supplied,
        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:

        1. linear   = False, True
        2. circular = True, False

        Note that both ends of the DNA fragment has to be compatible 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'

        A Dseq object can be longer that either the watson or crick strands.

        ::

            <-- 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
        >>>

        See also
        --------
        pydna.dsdna.Dseqrecord

        '''

        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].

            Returns -1 if the subsequence is NOT found.

            Parameters
            ----------

            sub : string or Seq object
                a string or another Seq object to look for.

            start : int, optional
                slice start.

            end : int, optional
                slice end.

            Examples
            --------
            >>> import pydna
            >>> seq = Dseq("atcgactgacgtgtt")
            >>> seq
            Dseq(-15)
            atcgactgacgtgtt
            tagctgactgcacaa
            >>> seq.find("gac")
            3
            >>> seq = pydna.Dseq(watson="agt",crick="actta",ovhg=-2)
            >>> seq
            Dseq(-7)
            agt
              attca
            >>> seq.find("taa")
            2
            """

            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 30 bp:

           Examples
           --------

           >>> import pydna
           >>> a=pydna.Dseq("atcgcttactagcgtactgatcatctgact")
           >>> a
           Dseq(-30)
           atcgcttactagcgtactgatcatctgact
           tagcgaatgatcgcatgactagtagactga
           >>> a+=Dseq("A")
           >>> a
           Dseq(-31)
           atcg..actA
           tagc..tgaT

           '''
            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.

            Examples
            --------
            >>> import pydna
            >>> a=pydna.Dseq("catcgatc")
            >>> a
            Dseq(-8)
            catcgatc
            gtagctag
            >>> b=a.reverse_complement()
            >>> b
            Dseq(-8)
            gatcgatg
            ctagctac
            >>>

           '''
            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

            Examples
            --------
            >>> 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')
            >>>

            See also
            --------
            pydna.dsdna.Dseq.three_prime_end

            '''
            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')
            >>>

            See also
            --------
            pydna.dsdna.Dseq.five_prime_end

            '''

            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,)
            elif not self:
                answer = copy.copy(other)
            elif not other:
                answer = copy.copy(self)
            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.

            Parameters
            ----------

            nucleotides : str

            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
            >>> c=pydna.Dseq("aaac", "tttg")
            >>> c
            Dseq(-5)
             aaac
            gttt
            >>> c.fill_in()
            Dseq(-5)
             aaac
            gttt
            >>>

            References
            ----------
            .. [#] http://en.wikipedia.org/wiki/Klenow_fragment#The_exo-_Klenow_fragment

            '''
            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

           References
           ----------
           .. [#] http://en.wikipedia.org/wiki/Mung_bean_nuclease

            '''
            return Dseq(self.dsdata)

        def t4(self,*args,**kwargs):
            '''Alias for the :func:`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 can be done in presence of any
           combination of the four A, G, C or T. Default are all four
           nucleotides together.

           Alias for the :func:`t4` method

           Parameters
           ----------

           nucleotides : str

           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 are no cuts, an empty list is returned.

            Parameters
            ----------

            enzymes : enzyme object or iterable of such objects
                A Bio.Restriction.XXX restriction objects or iterable.

            Returns
            -------
            frags : list
                list of Dseq objects formed by the digestion

            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 []

            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()
        >>>

        References
        ----------

        .. [#] http://biopython.org/wiki/SeqRecord

        '''

        def __init__(self, record,
                           circular               = None,
                           linear                 = None,
                           n                      = 10E-12, # pmols
                           *args,
                           **kwargs):
            self.n = n
            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, so record is Dseqrecord
                    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, Dseq or Dseqrecord 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):
            '''The linear property'''
            return self.seq.linear

        @property
        def circular(self):
            '''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'

           References
           ----------

           .. [#] http://wiki.christophchamp.com/index.php/SEGUID

           '''
            return seguid(self.seq)

        def isorf(self, table=1):
            '''Detects if sequence is an open reading frame (orf) in the 5'-3' direction.
            Translation tables are numbers according to the NCBI numbering [#]_.

            Parameters
            ----------
            table  : int
                Sets the translation table, default is 1 (standard code)

            Returns
            -------
            bool
                True if sequence is an orf, False otherwise.

            Examples
            --------

            >>> from pydna import Dseqrecord
            >>> a=Dseqrecord("atgtaa")
            >>> a.isorf()
            True
            >>> b=Dseqrecord("atgaaa")
            >>> b.isorf()
            False
            >>> c=Dseqrecord("atttaa")
            >>> c.isorf()
            False

            References
            ----------

            .. [#] http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c

            '''

            try:
                self.seq.translate(table=table, cds=True)
            except TranslationError:
                return False
            else:
                return True

        def add_feature(self,x,y):
            '''Adds a feature of type misc to the feature list of the sequence.

            Parameters
            ----------
            x  : int
                Indicates start of the feature
            y  : int
                Indicates end of the feature

            Examples
            --------

            >>> from pydna import Dseqrecord
            >>> a=Dseqrecord("atgtaa")
            >>> a.features
            []
            >>> a.add_feature(2,4)
            >>> a.features
            [SeqFeature(FeatureLocation(ExactPosition(2), ExactPosition(4)), type='misc')]
            '''
            self.features.append( SeqFeature(FeatureLocation(x, y), type="misc" ))

        def extract_feature(self, n):
            '''Extracts a feature and creates a new Dseqrecord object.

            Parameters
            ----------
            n  : int
                Indicates the feature to extract

            Examples
            --------

            >>> from pydna import Dseqrecord
            >>> a=Dseqrecord("atgtaa")
            >>> a.add_feature(2,4)
            >>> b=a.extract_feature(0)
            >>> b
            Dseqrecord(-2)
            >>> b.seq
            Dseq(-2)
            gt
            ca

            '''
            return self.features[n].extract(self)

        def list_features(self):
            '''Prints an ASCII table with all features.

            Examples
            --------

            >>> from pydna import Dseqrecord
            >>> a=Dseqrecord("atgtaa")
            >>> a.add_feature(2,4)
            >>> a.list_features()
            +----------+-----------+-------+-----+--------+--------------+------+------+
            | Feature# | Direction | Start | End | Length | id           | type | orf? |
            +----------+-----------+-------+-----+--------+--------------+------+------+
            | 0        |    None   |   2   |  4  |      2 | <unknown id> | misc |  no  |
            +----------+-----------+-------+-----+--------+--------------+------+------+
            >>>
            '''

            x = PrettyTable(["Feature#", "Direction", "Start", "End", "Length", "id", "type", "orf?"])
            x.align["Feature#"] = "l" # Left align
            x.align["Length"] = "r"
            x.align["id"] = "l"
            x.align["type"] = "l"
            x.padding_width = 1 # One space between column edges and contents
            for i, sf in enumerate(self.features):
                x.add_row([ i,
                            {1:"-->", -1:"<--", 0:"---", None:"None"}[sf.strand],
                            sf.location.start,
                            sf.location.end,
                            len(sf), sf.id, sf.type,
                            {True:"yes",False:"no"}[self.extract_feature(i).isorf() or self.extract_feature(i).rc().isorf()]])
            print x
            return

        def cseguid(self):
            '''Returns the cSEGUID for the sequence. The cSEGUID is the SEGUID
            checksum calculated for the lexicographically minimal string rotation
            of the sequence or its reverse complement.

            Only defined for circular sequences.

            The cSEGUID checksum uniqely identifies a circular sequence.

            Examples
            --------

            >>> import pydna
            >>> a=pydna.Dseqrecord("aaat", circular=True)
            >>> a.cseguid()
            'oopV+6158nHJqedi8lsshIfcqYA'
            >>> a=pydna.Dseqrecord("ataa", circular=True)
            >>> a.cseguid()
            'oopV+6158nHJqedi8lsshIfcqYA'

           '''
            if self.linear:
                raise Exception("cseguid is only defined for circular sequences.")
            return cseguid(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).

            The stamp can be verified with :func:`verify_stamp`

            Examples
            --------

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

            See also
            --------
            pydna.dsdna.Dseqrecord.verify_stamp
            '''
            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
            >>>

           See also
           --------
           pydna.dsdna.Dseqrecord.stamp

           '''
            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)
            >>>

            See also
            --------
            pydna.dsdna.Dseq.looped
            '''
            new = copy.copy(self)
            for key, value in self.__dict__.items():
                setattr(new, key, value )
            new._seq = self.seq.looped()
            for fn, fo in zip(new.features, self.features):
                fn.qualifiers = fo.qualifiers

            return new

        def tolinear(self):
            '''
            Returns a linear, blunt copy 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 = copy.copy(self)
            for key, value in self.__dict__.items():
                setattr(new, key, value )
            new._seq = self.seq.tolinear()
            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
            //

            References
            ----------

            .. [#] http://biopython.org/wiki/SeqIO

            '''

            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 for writing [#]_. Default
            is "gb" which is short for Genbank. Note that Biopython SeqIO reads
            more formats than it writes.

            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>``

            Where <f> is "gb" by default. If the filename already exists and
            AND the sequence it contains is different, a new file name will be
            used so that the old file is not lost:

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

            References
            ----------
            .. [#] http://biopython.org/wiki/SeqIO

           '''
            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.features = [f._shift(offset) for f in other.features]
                #answer = self.__class__(SeqRecord.__add__(self, other))
                answer = Dseqrecord(SeqRecord.__add__(self, other))
                answer.n = min(self.n, other.n)
            else:
                #answer = self.__class__(SeqRecord.__add__(self, Dseqrecord(other)))
                answer = Dseqrecord(SeqRecord.__add__(self, Dseqrecord(other)))
                answer.n = self.n
            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)))
            if self.circular:
                raise TypeError("TypeError: can't multiply circular Dseqrecord")
            if number>0:
                new = copy.copy(self)
                for i in range(1, number):
                    new += self
                return new
            else:
                return self.__class__("")

        def __getitem__(self, sl):
            answer = copy.copy(self)
            answer.seq = answer.seq.__getitem__(sl)
            answer.seq.alphabet = self.seq.alphabet
            answer.features = SeqRecord.__getitem__(self, sl).features
            return answer

        def linearize(self, *enzymes):
            '''This method is similar to :func:`cut` but throws an exception if there
            is not excactly on cut i.e. none or more than one digestion products.

            '''

            if self.seq._linear:
                raise Exception("Can only linearize circular molecules!")
            fragments = self.cut(*enzymes)
            if len(fragments)>1:
                raise Exception("More than one fragment is formed!")
            if not fragments:
                raise Exception("The enzyme(s) do not cut!")
            return fragments.pop()

        def cut(self, *enzymes):
            '''Digest the Dseqrecord object with one or more restriction enzymes.
            returns a list of linear Dseqrecords. If there are no cuts, an empty
            list is returned.

            See also :func:`Dseq.cut`

            Parameters
            ----------

            enzymes : enzyme object or iterable of such objects
                A Bio.Restriction.XXX restriction object or iterable of such.

            Returns
            -------
            Dseqrecord_frags : 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 not frags:
                return []

            if self.linear:
                last_pos=0
                #template = self.__class__(self, linear=True)
                #template = copy.copy(self)
                template = self
            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 not last_pos:
                    return [self]
                if 0 in last_pos:
                    last_pos=0
                else:
                    last_pos = last_pos.pop()
                template = self._multiply_circular(3)

            Dseqrecord_frags = []
            start = last_pos

            for f in frags:
                end = start + len(str(f))
                Dseqrecord_frag = Dseqrecord(f, linear=True, n=self.n)
                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)

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

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

            return Dseqrecord_frags

        def reverse_complement(self):
            '''Returns 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
            >>>

            See also
            --------
            pydna.dsdna.Dseq.reverse_complement

            '''

            return self.rc()

        def rc(self):
            '''alias of the reverse_complement method'''
            answer = Dseqrecord(super(Dseqrecord, self).reverse_complement())
            assert answer.circular == self.circular
            answer.name       = "{}_rc".format(self.name[:13])
            answer.description= self.description+"_rc"
            answer.id         = self.id+"_rc"
            return answer
            #return Dseqrecord(self.seq.rc())

        def _multiply_circular(self, multiplier):
            '''returns a linearised version of a circular sequence multiplied by
           multiplier '''

            if self.linear:
                raise TypeError("sequence has to be circular!")
            if not isinstance(multiplier, int):
                raise TypeError("TypeError: can't multiply Dseq by non-int of type {}".format(type(multiplier)))
            if multiplier<=0:
                return self.__class__("")

            new_features = []

            for feature in self.features:
                new_feature = copy.deepcopy(feature)
                if len(new_feature.location.parts)>1:    # CompoundFeature
                    j=0
                    while (j+1)<=len(new_feature.location.parts):
                        if new_feature.location.parts[j].end == len(self) and new_feature.location.parts[j+1].start==0:
                            new_feature.location.parts[j] = FeatureLocation(new_feature.location.parts[j].start,
                                                                            new_feature.location.parts[j].end+len(new_feature.location.parts[j+1]))
                            del new_feature.location.parts[j+1]
                        j+=1
                    slask = [new_feature.location.parts.pop(0)]
                    for fl in new_feature.location.parts:
                        if fl.start < slask[-1].start:
                            slask.append(fl+len(self))
                        else:
                            slask.append(fl)
                    if len(slask)>1:
                        new_feature.location.parts=slask
                    else:
                        new_feature.location=slask[0]
                new_features.append(new_feature)

            sequence = self.tolinear()
            sequence.features = new_features
            sequence = sequence * multiplier

            sequence.features = [f for f in sequence.features if f.location.end <= len(sequence)]
            sequence.features.sort(key = operator.attrgetter('location.start'))

            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 at the | symbol:
             |
             | ``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

             Examples
             --------

             >>> 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 for 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)[shift:]

            features_to_fold = [f for f in new.features if f.location.start<length<f.location.end]

            folded_features = []

            for feature in features_to_fold:

                if len(feature.location.parts)>1: # CompoundFeature
                    nps=[]
                    for part in feature.location.parts:

                        if part.start<part.end<=length:
                            nps.append(part)

                        elif part.start<length<part.end:
                            nps.append(FeatureLocation(part.start,length))
                            nps.append(FeatureLocation(0, part.end-length))

                        elif length<=part.start<part.end:
                            nps.append(FeatureLocation(part.start-length, part.end-length))

                    folded_features.append(SeqFeature(CompoundLocation(nps),
                                                      qualifiers = feature.qualifiers,
                                                      type=feature.type))

                else:
                    folded_features.append(SeqFeature(CompoundLocation([FeatureLocation(feature.location.start, length),
                                                                        FeatureLocation(0, feature.location.end-length)]),
                                                      qualifiers = feature.qualifiers,
                                                      type=feature.type))

            new = new[:length].looped()
            new.features.extend(folded_features)
            new.features.sort(key = operator.attrgetter('location.start'))
            new.description = self.description #!
            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!")

            newseq = copy.copy(self)

            s    = str(self.seq.watson).lower()
            s_rc = str(self.seq.crick).lower()

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

            try:
                circular_ref = ref.circular
            except AttributeError:
                circular_ref = False

            lim = min(limit, limit*(len(s)/limit)+1)

            c = common_sub_strings(s+s,       r, limit = lim)
            d = common_sub_strings(s_rc+s_rc, r, limit = lim)

            c =  [(x[0],x[2]) for x in c if x[1]==0]
            d =  [(x[0],x[2]) for x in d if x[1]==0]

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

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

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

            if length_rc>length:
                start = start_rc
                newseq = newseq.rc()

            if start == 0:
                return newseq
            else:
                return newseq.shifted(start)

    def read(data, ds = True):
        '''This function is similar the :func:`parse` function but expects one and only
        one sequence or and exception is thrown.

        Parameters
        ----------
        data : string
            see below
        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 :func:`parse`.

        See Also
        --------
        parse

        '''

        results = parse(data, ds)
        try:
            results = results.pop()
        except IndexError:
            raise ValueError("No sequences found in data ({})".format(data[:30]))
        return results

    def parse_new(data, ds = True):
        pattern =  r"(?:>.+\n^(?:^[^>]+?)(?=\n\n|>|LOCUS|ID))|(?:(?:LOCUS|ID)(?:(?:.|\n)+?)^//)"

        def extract_seqs(raw):
            raw = textwrap.dedent(raw).strip()
            raw = raw.replace( '\r\n', '\n')
            raw = raw.replace( '\r',   '\n')
            return re.findall(pattern, textwrap.dedent(raw+ "\n\n"),re.MULTILINE)

        files=[]
        rawseqs=[]

        if not hasattr(data, '__iter__'):
            data = (data,)
        for item in data:
            for pth in glob.glob(item):
                if os.path.isfile(pth):
                    files.append(os.path.abspath(pth))
                else:
                    for dirpath,_,filenames in os.walk(pth):
                        for f in filenames:
                            files.append( os.path.abspath(os.path.join(dirpath, f)))
                for file_ in files:
                    with open(file_,'r') as f:
                        rawseqs.extend(extract_seqs(f.read()))
                files=[]
            else:
                rawseqs.extend(extract_seqs(item))
        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())
                        if "circular" in rawseq.splitlines()[0]:
                            circular = True
                    except ValueError:
                        continue

            if ds:
                sequences.append(Dseqrecord(parsed, circular = circular))
            else:
                sequences.append(parsed)
            handle.close()
        return sequences

    def parse(data, 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
            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

        ds : bool
            If True double stranded :class:`Dseqrecord` objects are returned.
            If False single stranded :class:`Bio.SeqRecord` [#]_ objects are returned.

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

        References
        ----------

        .. [#] http://biopython.org/wiki/SeqRecord

        See Also
        --------
        read

        '''
        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, circular = circular))
            else:
                sequences.append(parsed)
            handle.close()
        #sequences[0].features[8].qualifiers['label'][0] = u'björn'
        return sequences

        #http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?
        #db=nuccore&
        #id=21614549&
        #strand=1&
        #seq_start=1&
        #seq_stop=100&
        #rettype=gb&
        #retmode=text

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

### Navigation

- index
- modules |
- modules |
- Pydna 0.6.2 documentation »
- Module code »