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
import colorsys
import shelve

from prettytable import PrettyTable

from Bio                    import SeqIO
from Bio.Alphabet.IUPAC     import IUPACAmbiguousDNA
from Bio.Seq                import Seq
from Bio.Seq                import translate
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.SeqFeature         import CompoundLocation
from Bio.SeqUtils.CheckSum  import seguid
from Bio.SeqUtils           import GC
from Bio.GenBank            import RecordParser
from Bio.Data.CodonTable    import TranslationError

from _sequencetrace         import SequenceTraceFactory

from pydna.findsubstrings_suffix_arrays_python import common_sub_strings
from pydna.utils import cseguid
from pydna.pretty import pretty_str, pretty_string, pretty_unicode




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

[docs]def rc(sequence): '''returns the reverse complement of sequence (string) accepts mixed DNA/RNA ''' return sequence.translate(_complement_table)[::-1]
[docs]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()): watson = "".join(watson.split()) if ovhg is None: if crick is None: self.crick = rc(watson) self._ovhg = 0 else: crick = "".join(crick.split()) 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 = "".join(crick.split()) 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)
[docs] 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: 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
[docs] 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])
[docs] def rc(self): '''Alias of the reverse_complement method''' return self.reverse_complement()
[docs] 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)
[docs] 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!")
[docs] 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)
[docs] 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
[docs] 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
[docs] 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)
[docs] 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)
[docs] def t4(self,*args,**kwargs): '''Alias for the :func:`T4` method ''' return self.T4(*args,**kwargs)
[docs] 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
[docs] 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
[docs] def ovhg(self): '''The ovhg property''' return self._ovhg
@property
[docs] def linear(self): '''The linear property''' return self._linear
@property
[docs] def circular(self): '''The circular property''' return self._circular
[docs]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 try: record.letter_annotations = {} except AttributeError: pass 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))) self.name = self.name[:16] 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()}) self.map_target = None @property
[docs] def linear(self): '''The linear property''' return self.seq.linear
@property
[docs] def circular(self): '''The circular property''' return self.seq.circular
[docs] 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 pretty_string(seguid(self.seq))
[docs] 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
[docs] def add_feature(self, x=None, y=None, seq=None, label=None, type="misc", **kwargs): '''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')] ''' qualifiers = {"label": label} if seq: seq = Dseqrecord(seq) x = self.seq.lower().find(seq.seq.lower()) if x==-1: return y = x + len(seq) self.features.append( SeqFeature(FeatureLocation(x, y), type=type, qualifiers = qualifiers, **kwargs)) ''' In [11]: a.seq.translate() Out[11]: Seq('K', ExtendedIUPACProtein()) In [12]: '''
[docs] 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)
[docs] def spread_ape_colors(self): ''' This method assigns random colors compatible with the ApE editor to features. ''' def get_N_HexCol(N): HSV_tuples = [(x*1.0/N, 0.5, 0.5) for x in xrange(N)] hex_out = [] for rgb in HSV_tuples: rgb = map(lambda x: int(x*255),colorsys.hsv_to_rgb(*rgb)) hex_out.append("".join(map(lambda x: chr(x).encode('hex'),rgb))) return hex_out for i, color in enumerate(get_N_HexCol(len(self.features))): self.features[i].qualifiers['ApEinfo_fwdcolor'] = "#"+color self.features[i].qualifiers['ApEinfo_revcolor'] = "#"+color
[docs] def olaps(self, other, *args, **kwargs): other = Dseqrecord(other) olaps = common_sub_strings(str(self.seq).lower(), str(other.seq).lower(), **kwargs) return [ self[olap[0]:olap[0]+olap[2]] for olap in olaps ]
[docs] def list_features(self): '''Prints an ASCII table with all features. Examples -------- >>> from pydna import Dseqrecord >>> a=Dseqrecord("atgtaa") >>> a.add_feature(2,4) >>> print 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()]]) return pretty_str(x)
[docs] def gc(self): '''Returns GC content ''' return pretty_string(round(GC(str(self.seq)), 1))
[docs] 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 regardless of where the origin is set. 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)
[docs] 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
[docs] 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:]
[docs] 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
[docs] 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
[docs] 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 ''' #r = self #r.id = r.id[:7] s = SeqRecord.format(self, f).strip() if f in ("genbank","gb"): if self.circular: return pretty_string(s[:55]+"circular"+s[63:]) else: return pretty_string(s[:55]+"linear"+s[61:]) else: return pretty_string(s)
[docs] 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 # invent a name if note given if isinstance(filename, basestring): if os.path.isfile(filename): seguid_new = self.seguid() old_file = read(filename) seguid_old = old_file.seguid() # if seguids and topology are the same, nothing is written if seguid_new == seguid_old and self.circular == old_file.circular: os.utime(filename, None) # update last change time else: name, ext = os.path.splitext(filename) old_filename = "{}_OLD{}".format(name, ext) os.rename(filename, old_filename) print('Sequence change\n' '{} {} bp seguid {}\n' '{} {} bp seguid {}\n').format(old_filename, len(old_file), seguid_old, filename, len(self), seguid_new ) with open(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 __contains__(self, other): if other.lower() in str(self.seq).lower(): return True else: s = self.seq.watson.replace(" ","") ln = len(s) spc = 3-ln%3 if ln%3 else 0 s = "n" * spc + s + "nnn" for frame in range(3): if other.lower() in translate(s[frame:frame+spc+ln]).lower(): return True #s = self.seq.crick.replace(" ","") #ln=len(s) #spc = 3-ln%3 if ln%3 else 0 #s = "n" * spc + s + "nnn" #for frame in range(3): # if other.lower() in translate(s[frame:frame+spc+ln]).lower(): # return True return False
[docs] def find_aa(self, other): return self.find_aminoacids(other)
[docs] def find_aminoacids(self, other): ''' >>> import pydna >>> s=pydna.Dseqrecord("atgtacgatcgtatgctggttatattttag") >>> s.seq.translate() Seq('MYDRMLVIF*', HasStopCodon(ExtendedIUPACProtein(), '*')) >>> "RML" in s True >>> "MMM" in s False >>> s.seq.rc().translate() Seq('LKYNQHTIVH', ExtendedIUPACProtein()) >>> "QHT" in s.rc() True >>> "QHT" in s False >>> slc = s.find_aa("RML") >>> slc slice(9, 18, None) >>> s[slc] Dseqrecord(-9) >>> code = s[slc].seq >>> code Dseq(-9) cgtatgctg gcatacgac >>> code.translate() Seq('RML', ExtendedIUPACProtein()) ''' other = str(other).lower() assert self.seq.watson == "".join(self.seq.watson.split()) s = self.seq.watson ln = len(s) spc = 3-ln%3 if ln%3 else 0 s = s + "n"*spc + "nnn" start = None for frame in range(3): try: start = translate(s[frame:frame+ln+spc]).lower().index(other) break except ValueError: pass oh = self.seq.ovhg if self.seq.ovhg>0 else 0 if start == None: return None else: return slice(frame+start*3+oh, frame+(start+len(other))*3+oh)
[docs] def map_trace_files(self, pth): import glob traces = [] stf = SequenceTraceFactory() for name in glob.glob(pth): traces.append( stf.loadTraceFile( name )) if not traces: raise(Exception("no trace files found!")) if hasattr( self.map_target, "step" ): area = self.map_target elif hasattr( self.map_target, "extract" ): area = slice(self.map_target.location.start, self.map_target.location.end) else: area = None if area: self.matching_reads = [] self.not_matching_reads = [] target = str(self[area].seq).lower() target_rc = str(self[area].seq.rc()).lower() for trace in traces: if target in str(trace.basecalls).lower() or target_rc in str(trace.basecalls).lower(): self.matching_reads.append(trace) else: self.not_matching_reads.append(trace) reads = self.matching_reads else: self.matching_reads = None self.not_matching_reads = None reads = traces for read in reads: matches = common_sub_strings(str(self.seq).lower(), read.basecalls.lower(), 25) if len(matches)>1: newmatches = [matches[0],] for i, x in enumerate(matches[1:]): g,f,h = matches[i] if g+h < x[0] and f+h < x[1]: newmatches.append(x) elif len(matches)==1: newmatches = matches else: continue if len(newmatches)>1: ms = [] for m in newmatches: ms.append(FeatureLocation(m[0], m[0]+m[2])) loc = CompoundLocation(ms) else: a,b,c = newmatches[0] loc = FeatureLocation(a,a+c) self.features.append( SeqFeature(loc, qualifiers = {"label": read.getFileName()}, type="trace") ) return [x.getFileName() for x in reads]
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 if self.linear or sl.start<sl.stop: answer.features = SeqRecord.__getitem__(self, sl).features else: try: answer.features = self.shifted(sl.stop).features except Exception: answer.features = self.features answer.features = [f for f in answer.features if f.location.parts == sorted(f.location.parts)] return answer
[docs] 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()
[docs] 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
[docs] def number_of_cuts(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,) return sum([len(enzyme.search(self.seq)) for enzyme in enzymes])
[docs] 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()
[docs] 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
[docs] 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
[docs] 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!") try: rs = ref.seguid() except AttributeError: rs = seguid(ref) refresh = False cached = None csh = os.environ["pydna_cache"] key = str(self.seguid())+"|"+rs+"|"+str(limit) cache = shelve.open(os.path.join(os.environ["datadir"],"synced.shelf"), protocol=2, writeback=False) if csh in ("compare", "cached"): try: cached = cache[str(key)] except KeyError: if os.environ["pydna_cache"] == "compare": raise Exception("no result for this key!") else: refresh = True if refresh or os.environ["pydna_cache"] in ("compare", "refresh", "nocache"): 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: result = newseq else: result = newseq.shifted(start) if os.environ["pydna_cache"] == "compare": if result!=cached: module_logger.warning('dsdna error') if refresh or os.environ["pydna_cache"] == "refresh": cache[key] = result elif cached and os.environ["pydna_cache"] not in ("nocache", "refresh"): result = cached cache.close() return result
[docs]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
[docs]def parse2(data, ds = True): '''experimental''' 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
[docs]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,) drs = [os.getcwd().decode()] if os.environ["pydna_dna_dirs"]: drs+= os.environ["pydna_dna_dirs"].split(os.pathsep) for item in data: for dr in drs: #print "####", type(item), type(dr), type(item.encode("utf-8"))#, item.encode("utf-8") #print "###", os.path.join(dr, item) try: with open(os.path.join(dr, item), 'r') as f: raw+= f.read() break except IOError: pass 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()