#!/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 operator
import re
import itertools
import datetime
import copy
import os
import textwrap
import StringIO
import warnings
import string
import warnings
from Bio import Alphabet
from Bio import SeqIO
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio.Seq import Seq
from Bio.Seq import _maketrans
from Bio.Data.IUPACData import ambiguous_dna_complement as amb_compl
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature
from Bio.SeqFeature import FeatureLocation
from Bio.SeqUtils.CheckSum import seguid
from Bio.GenBank import RecordParser
from pydna.utils import eq
from pydna.findsubstrings_suffix_arrays_python import common_sub_strings
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).
Dseq is a subclass of the Biopython Seq object. It stores two
strings representing the watson (sense) and crick(antisense) strands.
two properties called linear and circular, and a numeric value ovhg
(overhang) describing the stagger for the watson and crick strand
in the 5' end of the fragment.
The most common usage is probably to create a Dseq object as a
part of a Dseqrecord object (see Dseqrecord).
There are three ways of creating a Dseq object directly:
Only one argument (string):
>>> import pydna
>>> pydna.Dseq("aaa")
Dseq(-3)
aaa
ttt
The given string will be interpreted as the watson strand of a
blunt, linear double stranded sequence object. The crick strand
is created automatically from the watson strand.
Two arguments (string, string):
>>> import pydna
>>> pydna.Dseq("gggaaat","ttt")
Dseq(-7)
gggaaat
ttt
If both watson and crick are given, but not ovhg an attempt
will be made to find the best annealing between the strands.
There are limitations to this! For long fragments it is quite
slow. The length of the annealing sequences have to be at least
half the length of the shortest of the strands.
Three arguments (string, string, ovhg=int):
The ovhg parameter controls the stagger at the five prime end::
ovhg=-2
XXXXX
XXXXX
ovhg=-1
XXXXX
XXXXX
ovhg=0
XXXXX
XXXXX
ovhg=1
XXXXX
XXXXX
ovhg=2
XXXXX
XXXXX
Example of creating Dseq objects with different amounts of stagger:
>>> pydna.Dseq(watson="agt",crick="actta",ovhg=-2)
Dseq(-7)
agt
attca
>>> pydna.Dseq(watson="agt",crick="actta",ovhg=-1)
Dseq(-6)
agt
attca
>>> pydna.Dseq(watson="agt",crick="actta",ovhg=0)
Dseq(-5)
agt
attca
>>> pydna.Dseq(watson="agt",crick="actta",ovhg=1)
Dseq(-5)
agt
attca
>>> pydna.Dseq(watson="agt",crick="actta",ovhg=2)
Dseq(-5)
agt
attca
the ovhg parameter has to be given with both watson and crick,
otherwise an exception is raised.
>>> pydna.Dseq(watson="agt",ovhg=2)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/dist-packages/pydna_/dsdna.py", line 169, in __init__
else:
Exception: ovhg defined without crick strand!
The default alphabet is set to Biopython IUPACAmbiguousDNA
The shape of the fragment is set by either:
linear = False, True
or
circular = True, False
Note that both ends of the DNA fragment has to be blunt to set
circular = True (or linear = False).
>>> pydna.Dseq("aaa","ttt")
Dseq(-3)
aaa
ttt
>>> pydna.Dseq("aaa","ttt",ovhg=0)
Dseq(-3)
aaa
ttt
>>> pydna.Dseq("aaa", "ttt", linear = False ,ovhg=0)
Dseq(o3)
aaa
ttt
>>> pydna.Dseq("aaa", "ttt", circular = True , ovhg=0)
Dseq(o3)
aaa
ttt
Coercing to string
>>> a=pydna.Dseq("tttcccc","aaacccc")
>>> a
Dseq(-11)
tttcccc
ccccaaa
>>> str(a)
'ggggtttcccc'
The double stranded part is accessible through the dsdata property:
>>> a.dsdata
'ttt'
Dseqrecord and Dseq share the same concept of length:
<-- length -->
GATCCTTT
AAAGCCTAG
'''
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()),
min( int(len(watson)/2), int(len(crick)/2))
)
try:
F,T,L = olaps.pop(0)
except IndexError:
raise Exception("Could not anneal the two 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 __getitem__(self, slc):
'''Returns a subsequence.
'''
sns = (self._ovhg*" " + self.watson)[slc]
asn = (-self._ovhg*" " + self.crick[::-1])[slc]
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)
def __eq__( self, other ):
'''Compare to another Dseq object OR an object thet implements
watson, crick and ovhg properties. This comarison 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 40 bp:
Examples
--------
>>> import pydna
>>> a=pydna.Dseq("atcgcttactagcgtactgatcatctgactgactagcgtga")
>>> a
Dseq(-41)
atcgcttactagcgtactga...catctgactgactagcgtga
tagcgaatgatcgcatgact...gtagactgactgatcgcact
>>>
'''
return self.__repr__()
def __repr__(self):
'''Returns a representation of the sequence, truncated if
longer than 40 bp'''
if len(self) > 40:
# (a)...(b)
# (a)...(b)
a = 20
b = 20
if self._ovhg > 0:
a = a - self._ovhg
ovhg3 = len(self.watson) - len(self.crick)+self._ovhg
return "{}({}{})\n{}...{}\n{}...{}".format(self.__class__.__name__,
{True:"-", False:"o"}[self.linear],
len(self),
(self._ovhg*" ")+str(self.watson)[:a],
str(self.watson)[-b:],
(-self._ovhg*" ")+str(self.crick)[::-1][:a-(-self._ovhg)],
str(self.crick)[:b-ovhg3][::-1])
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.
'''
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
>>> import pydna
>>> a=pydna.Dseq("aaa", "ttt")
>>> a
Dseq(-3)
aaa
ttt
>>> a.five_prime_end()
('blunt', '')
>>> a=pydna.Dseq("aaa", "ttt", ovhg=1)
>>> a
Dseq(-4)
aaa
ttt
>>> a.five_prime_end()
("3'", 't')
>>> a=pydna.Dseq("aaa", "ttt", ovhg=-1)
>>> a
Dseq(-4)
aaa
ttt
>>> a.five_prime_end()
("5'", 'a')
>>>
'''
if self.watson and not self.crick:
return "5'",self.watson.lower()
if not self.watson and self.crick:
return "3'",self.crick.lower()
if self._ovhg < 0:
sticky = self.watson[:-self._ovhg].lower()
type_ = "5'"
elif self._ovhg > 0:
sticky = self.crick[-self._ovhg:].lower()
type_ = "3'"
else:
sticky = ""
type_ = "blunt"
return type_, sticky
[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')
>>>
'''
ovhg = len(self.watson)-len(self.crick)+self._ovhg
if ovhg < 0:
sticky = self.crick[:-ovhg].lower()
type_ = "5'"
elif ovhg > 0:
sticky = self.watson[-ovhg:].lower()
type_ = "3'"
else:
sticky = ''
type_ = "blunt"
return type_, sticky
def __add__(self, other):
'''Simulates ligation between two DNA fragments.
Add other Dseq object at the end of the sequence.
Type error if all of the points below are fulfilled:
* either objects are circular
* if three prime sticky end of self is not the same type
(5' or 3') as the sticky end of other
* three prime sticky end of self complementary with five
prime sticky end of other.
Phosphorylation and dephosphorylation is not considered.
DNA is allways presumed to have the necessary 5' phospate
group necessary for ligation.
'''
# test for circular DNA
if self.circular:
raise TypeError("circular DNA cannot be ligated!")
try:
if other.circular:
raise TypeError("circular DNA cannot be ligated!")
except AttributeError:
pass
self_type, self_tail = self.three_prime_end()
other_type, other_tail = other.five_prime_end()
if (self_type == other_type and
str(self_tail) == str(rc(other_tail))):
answer = Dseq(self.watson + other.watson,
other.crick + self.crick,
self._ovhg,)
else:
raise TypeError("sticky ends not compatible!")
return answer
def __mul__(self, number):
if not isinstance(number, int):
raise TypeError("TypeError: can't multiply Dseq by non-int of type {}".format(type(number)))
if number<=0:
return self.__class__("")
new = copy.copy(self)
for i in range(number-1):
new += self
return new
def _fill_in_five_prime(self, nucleotides):
stuffer = ''
type, se = self.five_prime_end()
if type == "5'":
for n in rc(se):
if n in nucleotides:
stuffer+=n
else:
break
return self.crick+stuffer, self._ovhg+len(stuffer)
def _fill_in_three_prime(self, nucleotides):
stuffer = ''
type, se = self.three_prime_end()
if type == "5'":
for n in rc(se):
if n in nucleotides:
stuffer+=n
else:
break
return self.watson+stuffer
[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.
Examples
--------
>>> import pydna
>>> a=pydna.Dseq("aaa", "ttt")
>>> a
Dseq(-3)
aaa
ttt
>>> a.fill_in()
Dseq(-3)
aaa
ttt
>>> b=pydna.Dseq("caaa", "cttt")
>>> b
Dseq(-5)
caaa
tttc
>>> b.fill_in()
Dseq(-5)
caaag
gtttc
>>> b.fill_in("g")
Dseq(-5)
caaag
gtttc
>>> b.fill_in("tac")
Dseq(-5)
caaa
tttc
>>> b=pydna.Dseq("aaac", "tttg")
>>> c=pydna.Dseq("aaac", "tttg")
>>> c
Dseq(-5)
aaac
gttt
>>> c.fill_in()
Dseq(-5)
aaac
gttt
>>>
'''
if not nucleotides:
nucleotides = self.alphabet.letters
nucleotides = set(nucleotides.lower()+nucleotides.upper())
crick, ovhg = self._fill_in_five_prime(nucleotides)
watson = self._fill_in_three_prime(nucleotides)
return Dseq(watson, crick, ovhg)
[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
'''
return Dseq(self.dsdata)
[docs] def t4(self,*args,**kwargs):
'''Alias for the 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 in presence of any
combination of A, G, C or T. Default are all four
nucleotides together.
Examples
--------
>>> import pydna
>>> a=pydna.Dseq("gatcgatc")
>>> a
Dseq(-8)
gatcgatc
ctagctag
>>> a.T4()
Dseq(-8)
gatcgatc
ctagctag
>>> a.T4("t")
Dseq(-8)
gatcgat
tagctag
>>> a.T4("a")
Dseq(-8)
gatcga
agctag
>>> a.T4("g")
Dseq(-8)
gatcg
gctag
>>>
'''
if not nucleotides: nucleotides = self.alphabet.letters
nucleotides = set(nucleotides.lower() + nucleotides.upper())
type, se = self.five_prime_end()
crick = self.crick
if type == "5'":
crick, ovhg = self._fill_in_five_prime(nucleotides)
else:
if type == "3'":
ovhg = 0
crick = self.crick[:-len(se)]
x = len(crick)-1
while x>=0:
if crick[x] in nucleotides:
break
x-=1
ovhg = x-len(crick)+1
crick = crick[:x+1]
if not crick: ovhg=0
watson = self.watson
type, se = self.three_prime_end()
if type == "5'":
watson = self._fill_in_three_prime(nucleotides)
else:
if type == "3'":
watson = self.watson[:-len(se)]
x = len(watson)-1
while x>=0:
if watson[x] in nucleotides:
break
x-=1
watson=watson[:x+1]
return Dseq(watson, crick, ovhg)
def _cut(self, *enzymes):
output = []
stack = []
stack.extend(reversed(enzymes))
while stack:
top = stack.pop()
if hasattr(top, "__iter__"):
stack.extend(reversed(top))
else:
output.append(top)
enzymes = output
if not hasattr(enzymes, '__iter__'):
enzymes = (enzymes,)
if self.circular:
frags=[self.tolinear()*3,]
else:
frags=[self,]
newfrags=[]
enzymes = [e for (p,e) in sorted([(enzyme.search(Seq(frags[0].dsdata))[::-1], enzyme) for enzyme in enzymes], reverse=True) if p]
if not enzymes:
return [self,]
for enzyme in enzymes:
for frag in frags:
if enzyme.search(Seq(frag.dsdata)):
watson_fragments = [str(s) for s in enzyme.catalyze(Seq(frag.watson+"N"))]
crick_fragments = [str(s) for s in enzyme.catalyze(Seq(frag.crick+"N" ))[::-1]]
watson_fragments[-1] = watson_fragments[-1][:-1]
crick_fragments[0] = crick_fragments[0][:-1]
s = zip(watson_fragments, crick_fragments)
if frag.linear:
newfrags.append(Dseq(*s.pop(0),
ovhg = frag.ovhg,
linear = True))
for seqs in s:
newfrags.append(Dseq(*seqs,
ovhg = enzyme.ovhg,
linear = True))
else:
for seqs in s:
newfrags.append(Dseq(*seqs,
ovhg=enzyme.ovhg,
linear=True))
else:
newfrags.append(frag)
frags=newfrags
newfrags=[]
if self.circular:
swl = len(self.watson)
frags = frags[1:-1]
newfrags = [frags.pop(0),]
while sum(len(f.watson) for f in newfrags) < swl:
newfrags.append(frags.pop(0))
frags = newfrags
return frags
[docs] def cut(self, *enzymes):
'''Returns a list of linear Dseq fragments produced in the digestion.
If there is not cut, the whole sequence is returned.
Example
-------
>>> from pydna import Dseq
>>> seq=Dseq("ggatccnnngaattc")
>>> seq
Dseq(-15)
ggatccnnngaattc
cctaggnnncttaag
>>> from Bio.Restriction import BamHI,EcoRI
>>> type(seq.cut(BamHI))
<type 'list'>
>>> for frag in seq.cut(BamHI):
... print frag.fig()
Dseq(-5)
g
cctag
Dseq(-14)
gatccnnngaattc
gnnncttaag
>>> seq.cut(EcoRI, BamHI) == seq.cut(BamHI, EcoRI)
True
>>> a,b,c = seq.cut(EcoRI, BamHI)
>>> a+b+c
Dseq(-15)
ggatccnnngaattc
cctaggnnncttaag
>>>
'''
output = []
stack = []
stack.extend(reversed(enzymes))
while stack:
top = stack.pop()
if hasattr(top, "__iter__"):
stack.extend(reversed(top))
else:
output.append(top)
enzymes = output
if not hasattr(enzymes, '__iter__'):
enzymes = (enzymes,)
if self.circular:
frags=[self.tolinear()*3,]
else:
frags=[self,]
newfrags=[]
enzymes = [e for (p,e) in sorted([(enzyme.search(Seq(frags[0].dsdata))[::-1], enzyme) for enzyme in enzymes], reverse=True) if p]
if not enzymes:
return [self,]
for enz in enzymes:
for frag in frags:
ws = [x-1 for x in enz.search(Seq(frag.watson)+"N")] #, linear = frag.linear
cs = [x-1 for x in enz.search(Seq(frag.crick) +"N")] #, linear = frag.linear
sitepairs = [(sw, sc) for sw, sc in zip(ws,cs[::-1])
if (sw + max(0, frag.ovhg) -
max(0, enz.ovhg)
==
len(frag.crick)-sc -
min(0, frag.ovhg) +
min(0, enz.ovhg))]
sitepairs = sitepairs + [(len(frag.watson), 0)]
w2, c1 = sitepairs[0]
nwat = frag.watson[:w2]
ncrk = frag.crick[c1:]
newfrags.append(Dseq(nwat, ncrk, ovhg=frag.ovhg))
for (w1, c2), (w2, c1) in zip(sitepairs[:-1], sitepairs[1:]):
nwat = frag.watson[w1:w2]
ncrk = frag.crick[c1:c2]
newfrag = Dseq(nwat, ncrk, ovhg = enz.ovhg)
newfrags.append(newfrag)
if not newfrags:
newfrags.append(frag)
frags=newfrags
newfrags=[]
if self.circular:
swl = len(self.watson)
frags = frags[1:-1]
newfrags = [frags.pop(0),]
while sum(len(f.watson) for f in newfrags) < swl:
newfrags.append(frags.pop(0))
frags = newfrags[-1:] + newfrags[:-1]
return frags
@property
[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()
>>>
'''
def __init__(self, record,
circular = None,
linear = None,
*args, **kwargs):
if circular == None and linear in (True, False,):
circular = not linear
elif linear == None and circular in (True, False,):
linear = not circular
if isinstance(record, basestring): # record is a string
SeqRecord.__init__(self,
Dseq(record,
rc(record),
ovhg=0 ,
linear=linear,
circular=circular),
*args,
**kwargs)
elif hasattr(record, "features"): # record is SeqRecord or Dseqrecord?
for key, value in record.__dict__.items():
setattr(self, key, value )
if hasattr(record.seq, "watson"): # record.seq is a Dseq
new_seq = copy.copy(record.seq)
if new_seq.circular and linear:
new_seq = new_seq.tolinear()
if new_seq.linear and circular:
new_seq = new_seq.looped()
self.seq=new_seq
else: # record is Bio.SeqRecord
self.seq=Dseq(str(self.seq),
rc(str(self.seq)),
ovhg=0 ,
linear=linear,
circular=circular)
elif hasattr(record, "watson"): # record is Dseq ?
if record.circular and linear:
record = record.tolinear()
if record.linear and circular:
record = record.looped()
SeqRecord.__init__(self, record, *args, **kwargs)
elif isinstance(record, Seq): # record is Bio.Seq ?
SeqRecord.__init__(self, Dseq(str(record),
str(record.reverse_complement()),
ovhg=0 ,
linear=linear,
circular=circular),
*args,
**kwargs)
else:
raise TypeError(("record argument needs to be a string,"
"Seq, SeqRecord or Dseq object,"
" got {}").format(type(record)))
if self.id in ("","."):
self.id = self.name[:7]
if self.description ==".":
self.description = ""
if not 'date' in self.annotations:
self.annotations.update({"date": datetime.date.today().strftime("%d-%b-%Y").upper()})
@property
[docs] def linear(self):
'''Not really a method, but the linear property'''
return self.seq.linear
@property
[docs] def circular(self):
'''Not really a method, but 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'
'''
return seguid(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).
Examples
--------
>>> import pydna
>>> a=pydna.Dseqrecord("aaa")
>>> a.stamp()
>>> a.description
'<unknown description> SEGUID YG7G6b2Kj/KtFOX63j8mRHHoIlE'
>>> a.verify_stamp()
True
'''
pattern = "(SEGUID|seguid)\s*\S{27}"
try:
stamp = re.search(pattern, self.description).group()
except AttributeError:
stamp = "SEGUID {}".format(seguid(self.seq))
if not self.description:
self.description = stamp
elif not re.search(pattern, self.description):
self.description += " "+stamp
[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
>>>
'''
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)
>>>
'''
new = self.__class__(self.seq.looped())
new.features = self.features
for fn, fo in zip(new.features, self.features):
fn.qualifiers = fo.qualifiers
return new
[docs] def tolinear(self):
'''
Returns a linear, blunt of a circular Dseqrecord object. The
underlying Dseq object has to be circular.
Examples
--------
>>> import pydna
>>> a=pydna.Dseqrecord("aaa", circular = True)
>>> a
Dseqrecord(o3)
>>> b=a.tolinear()
>>> b
Dseqrecord(-3)
>>>
'''
new = self.__class__(self.seq.tolinear())
new.features = [copy.copy(f) for f in self.features]
return new
[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. Default is "gb"
which is short for Genbank.
Filename is the path to the file where the sequece is to be
written. The filename is optional, if it is not given, the
description property (string) is used together with the format:
If obj is the Dseqrecord object, the default file name will be:
``<obj.description>.<f>``
If the filename already exists and the sequence it contains
is different, a new file name will be used:
``<obj.description>_NEW.<f>``
'''
if not filename:
filename = self.description + "." + f
if isinstance(filename, basestring):
if os.path.isfile(filename):
seguid_new=self.seguid()
old_file = read(filename)
seguid_old = old_file.seguid()
if seguid_new == seguid_old and self.circular == old_file.circular:
os.utime(filename, None)
else:
name, ext = os.path.splitext(filename)
new_filename = "{}_NEW{}".format(name, ext)
print("\n\nseguid(old) = {} in file {}"
"\nseguid(new) = {} in file {}\n").format(seguid_old, filename, seguid_new, new_filename)
with open(new_filename, "w") as fp:
fp.write(self.format(f))
else:
with open(filename, "w") as fp:
fp.write(self.format(f))
else:
with filename as fp:
fp.write(self.format(f))
def __str__(self):
return ("Dseqrecord\n"
"circular: {}\n"
"size: {}\n").format(self.circular, len(self))+SeqRecord.__str__(self)
def __repr__(self):
return "Dseqrecord({}{})".format({True:"-", False:"o"}[self.linear],len(self))
def __add__(self, other):
if hasattr(other, "seq") and hasattr(other.seq, "watson"):
offset = other.seq.ovhg
other = Dseqrecord(other.seq,
id = self.id,
name = self.name,
description = self.description,
features = [f._shift(offset) for f in other.features],
annotations = self.annotations.copy(),
dbxrefs = self.dbxrefs[:])
answer = Dseqrecord(SeqRecord.__add__(self, other))
else:
answer = Dseqrecord(SeqRecord.__add__(self, Dseqrecord(other)))
assert answer.circular == False
return answer
# def __mul__(self, number):
# if not isinstance(number, int):
# raise TypeError("TypeError: can't multiply Dseqrecord by non-int of type {}".format(type(number)))
# number-=1
# if number>0:
# new = copy.copy(self)
# for i in range(number):
# new += self
# return new
# else:
# return self.__class__("")
def __getitem__(self, index):
answer = Dseqrecord(SeqRecord.__getitem__(self, index))
answer.seq.alphabet = self.seq.alphabet
return answer
[docs] def cut(self, *enzymes):
'''Digest the Dseqrecord object with one or more restriction enzymes.
returns a list of linear Dseqrecords.
Parameters
----------
enzymes : iterable object
iterable containing Biopython
restriction enzyme objects
Returns
-------
fragments : list
list of Dseqrecord objects formed by the digestion
Examples
--------
>>> import pydna
>>> a=pydna.Dseqrecord("ggatcc")
>>> from Bio.Restriction import BamHI
>>> a.cut(BamHI)
[Dseqrecord(-5), Dseqrecord(-5)]
>>> frag1, frag2 = a.cut(BamHI)
>>> frag1.seq
Dseq(-5)
g
cctag
>>> frag2.seq
Dseq(-5)
gatcc
g
'''
output, stack = [], []
stack.extend(reversed(enzymes))
while stack:
top = stack.pop()
if hasattr(top, "__iter__"):
stack.extend(reversed(top))
else:
output.append(top)
enzymes = output
if not hasattr(enzymes, '__iter__'):
enzymes = (enzymes,)
frags = self.seq.cut(enzymes)
if self.linear:
last_pos=0
template = self.__class__(self, linear=True)
else:
last_pos = [p.pop(0)-max(0,enzyme.ovhg)-1 for (p,e) in
sorted([(enzyme.search(Seq(self.seq.dsdata),
linear = self.linear)[::-1],
enzyme) for enzyme in enzymes]) if p]
if 0 in last_pos:
last_pos=0
else:
last_pos = last_pos.pop()
template = self._multiply_circular(3)
Dseqrecord_frags = []
start = last_pos
#from pydna_helper import ape; ape(template)
#raw_input("!")
for f in frags:
end = start + len(str(f))
Dseqrecord_frag = Dseqrecord(f, linear=True)
Dseqrecord_frag.features = template[start:end].features
#ape(template[start:end])
#print Dseqrecord_frag.seq.fig()
Dseqrecord_frag.description = self.description+"_"+"_".join(str(e) for e in enzymes)
#ape(Dseqrecord_frag);
#raw_input("xx")
Dseqrecord_frags.append(Dseqrecord_frag)
start = end
start-= len(f.three_prime_end()[1])
return Dseqrecord_frags
[docs] def reverse_complement(self):
'''Returns a new Dseqrecord object which is the reverse complement.
Examples
--------
>>> import pydna
>>> a=pydna.Dseqrecord("ggaatt")
>>> a
Dseqrecord(-6)
>>> a.seq
Dseq(-6)
ggaatt
ccttaa
>>> a.reverse_complement().seq
Dseq(-6)
aattcc
ttaagg
>>>
'''
return self.rc()
[docs] def rc(self):
'''alias of the reverse_complement method'''
answer = Dseqrecord(SeqRecord.reverse_complement(self))
assert answer.circular == self.circular
return answer
#return Dseqrecord(self.seq.rc())
def _multiply_circular(self, number):
'''returns a linearised version of self multiplied by
number '''
if self.linear:
raise TypeError("self has to be circular!")
if not isinstance(number, int):
raise TypeError("TypeError: can't multiply Dseq by non-int of type {}".format(type(number)))
if number<=0:
return self.__class__("")
new_features = [copy.copy(f) for f in self.features if not len(self)-1 in f or not 0 in f]
wrap_around_features = [copy.copy(f) for f in self.features if len(self)-1 in f and 0 in f]
new_locs = [ FeatureLocation(f.location.start, f.location.start+len(f)) for f in wrap_around_features]
for feat, newl in zip(wrap_around_features, new_locs):
feat.location = newl
feat.location_operator = None
feat.sub_features=[]
new_feature_sets = []
sequence = self.tolinear()
sequence.features=[]
for i in range(0, number-1):
sequence += self.tolinear()
new_feature_sets.extend( [copy.copy(f)._shift(len(self)*i) for f in new_features] )
new_feature_sets.extend( [copy.copy(f)._shift(len(self)*i) for f in wrap_around_features] )
new_feature_sets.extend( [copy.copy(f)._shift(len(self)*(number-1)) for f in new_features] )
sequence.features = new_feature_sets
return sequence
[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
|
| ``G|AAAT``
| ``C|TTTA``
new sequence:
| ``AAATG``
| ``TTTAC``
Shift is always positive and 0<shift<length, so in the example
below, permissible values of shift are 1,2 and 3
>>> import pydna
>>> a=pydna.Dseqrecord("aaat",circular=True)
>>> a
Dseqrecord(o4)
>>> a.seq
Dseq(o4)
aaat
ttta
>>> b=a.shifted(1)
>>> b
Dseqrecord(o4)
>>> b.seq
Dseq(o4)
aata
ttat
'''
if self.linear:
raise Exception("Sequence is linear.\n"
"The origin can only be\n"
"shifted on a circular sequence!\n")
length=len(self)
if not 0<shift<length:
raise Exception("shift is {}, has to be 0<shift<{}".format(shift, length))
new = self._multiply_circular(3)
#from pydna_helper import ape; ape(new)
#print [f for f in new.features if shift+length in f]
features_to_fold = [f for f in new.features if shift+length in f and f.location.start<shift+length]
folded_features = []
for feature in features_to_fold:
subfl1 = FeatureLocation(feature.location.start-shift, length)
subfl2 = FeatureLocation(0, len(feature)-len(subfl1))
sub1 = SeqFeature(subfl1,
type=feature.type,
location_operator=feature.location_operator,
strand=feature.strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=None)
sub2 = SeqFeature(subfl2,
type=feature.type,
location_operator=feature.location_operator,
strand=feature.strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=None)
pf = SeqFeature(FeatureLocation(subfl1.start, subfl2.end),
type=feature.type,
location_operator="join",
strand=feature.strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=[sub1,sub2])
folded_features.append(pf)
new = new[shift:shift+length]
new = new.looped()
new.features.extend(folded_features)
new.features.sort(key = operator.attrgetter('location.start'))
new.description = "{}_shifted ori {}".format(self.description, shift)
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!")
sequence = self.seq.tolinear()
a = str(sequence.watson).lower()
a_rc = str(sequence.crick).lower()
sequence_rc = sequence.reverse_complement()
double_sequence = sequence+sequence
if hasattr(ref, "seq"):
b=ref.seq
if hasattr(ref, "watson"):
b = str(b.watson).lower()
else:
b = str(b).lower()
else:
b = str(ref.lower())
b=b[:len(a)]
c = common_sub_strings(a+a, b, limit = min(limit, limit*(len(a)/limit)+1))
d = common_sub_strings(a_rc+a_rc, b, limit = min(limit, limit*(len(a)/limit)+1))
if c:
starta, startb, length = c.pop(0)
else:
starta, startb, length = 0,0,0
if d:
starta_rc, startb_rc, length_rc = d.pop(0)
else:
starta_rc, startb_rc, length_rc = 0,0,0
if not c and not d:
raise Exception("There is no overlap between sequences!")
if length_rc>length:
starta, startb = starta_rc, startb_rc
sequence = sequence_rc
if starta>startb:
if len(a)<len(b):
ofs = starta-startb + len(b)-len(a)
else:
ofs = starta-startb
elif starta<startb:
ofs = startb-starta + len(a)-len(b)
ofs = len(a)-ofs
elif starta==startb:
ofs=0
return self.shifted(ofs)
[docs]def read(data, filter = False, ds = True):
'''This function is similar the parse funtion but returns only
the first sequence found.
Parameters
----------
data : string
see below
filter : bool
if filter == True, sequences will be silently filtered
for allowed characters (see docs for Dseqrecord)
ds : bool
Double stranded or single stranded DNA, Return
"Dseqrecord" or "SeqRecord" objects.
Returns
-------
Dseqrecord
contains the first Dseqrecord or SeqRecord object parsed.
Notes
-----
The data parameter is similar to the data parameter for parse.
See Also
--------
parse
'''
results = parse(data, filter, ds)
try:
results = results.pop()
except IndexError:
raise ValueError("No sequences found in data ({})".format(data[:20]))
return results
[docs]def parse(data, filter = False, ds = True):
'''This function returns *all* DNA sequences found in data. If no
sequences are found, an empty list is returned. This is a greedy
function, use carefully.
Parameters
----------
data : string or iterable
see below
filter : bool
if filter == True, sequences will be silently filtered
for allowed characters (see docs for Dseqrecord)
ds : bool
Double stranded or single stranded DNA, Return
"Dseqrecord" or "SeqRecord" objects.
Returns
-------
list
contains Dseqrecord or SeqRecord objects
Notes
-----
The data parameter is a string containing:
1. an absolute path to a local file.
The file will be read in text
mode and parsed for EMBL, FASTA
and Genbank sequences.
2. an absolute path to a local directory.
all files in the directory will be
read and parsed as in 1.
3. a string containing one or more
sequences in EMBL, GENBANK,
or FASTA format. Mixed formats
are allowed.
4. data can be a list or other iterable of 1 - 3
'''
raw=""
if not hasattr(data, '__iter__'):
data = (data,)
for item in data:
if os.path.isdir(item):
for file_ in os.listdir(item):
with open(file_,'r') as f:
raw+="\n\n"+f.read()
elif os.path.isfile(os.path.join(os.getcwd(),item)):
with open(item,'r') as f:
raw+= f.read()
else:
raw+=textwrap.dedent(item).strip()
pattern = r"(?:>.+\n^(?:^[^>]+?)(?=\n\n|>|LOCUS|ID))|(?:(?:LOCUS|ID)(?:(?:.|\n)+?)^//)"
raw = raw.replace( '\r\n', '\n')
raw = raw.replace( '\r', '\n')
rawseqs = re.findall(pattern,textwrap.dedent(raw+"\n\n"),re.MULTILINE)
sequences=[]
while rawseqs:
circular = False
rawseq = rawseqs.pop(0)
handle = StringIO.StringIO(rawseq)
try:
parsed = SeqIO.read(handle, "embl", alphabet=IUPACAmbiguousDNA())
original_format = "embl"
if "circular" in rawseq.splitlines()[0]:
circular = True
except ValueError:
handle.seek(0)
try:
parsed = SeqIO.read(handle, "genbank", alphabet=IUPACAmbiguousDNA())
original_format = "genbank"
handle.seek(0)
parser = RecordParser()
residue_type = parser.parse(handle).residue_type
if "circular" in residue_type:
circular = True
except ValueError:
handle.seek(0)
try:
parsed = SeqIO.read(handle, "fasta", alphabet=IUPACAmbiguousDNA())
original_format = "fasta"
if "circular" in rawseq.splitlines()[0]:
circular = True
except ValueError:
continue
if ds:
sequences.append( Dseqrecord( parsed,
parsed_from = original_format,
raw_string = rawseq,
circular = circular,
filter = filter ))
else:
sequences.append(parsed)
handle.close()
return sequences
if __name__=="__main__":
import doctest
doctest.testmod()
from pydna import *
s = read('''
LOCUS New_DNA 21 bp ds-DNA circular 03-APR-2013
DEFINITION a
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature join(18..21,1..4)
/label=bb
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 5..17
/label=ins
/ApEinfo_fwdcolor=#e03c2b
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
ORIGIN
1 aaaGGTACCt ttGGATCCggg
//
''')# ----################----
for i in range(1,len(s)):
assert s.features[0].extract(s).seq.tostring() == "CGGGAAAG"
assert s.features[1].extract(s).seq.tostring() == "GTACCTTTGGATC"
b = s.shifted(i)
assert set([b.features[0].extract(b).seq.tostring(), b.features[1].extract(b).seq.tostring()]) == set(["CGGGAAAG", "GTACCTTTGGATC"])
from Bio.Restriction import Acc65I,KpnI, BamHI
bb1, ins1 = sorted(s.cut(Acc65I, BamHI), key=len, reverse=True)
for i in range(1,len(s)):
b = s.shifted(i)
from pydna_helper import ape
bb, ins = sorted(b.cut(Acc65I, BamHI), key=len, reverse=True)
assert eq(bb1, bb)
assert eq(ins1,ins)
assert bb.features[0].extract(bb).seq.watson == "CGGGAAAG"
assert bb.features[0].extract(bb).seq.crick == "CTTTCCCG"
assert eq(bb.features[0].extract(bb), s.features[0].extract(s) )
assert ins.features[0].extract(ins).seq.watson == "GTACCTTTG"
assert ins.features[0].extract(ins).seq.crick == "GATCCAAAG"
assert ins.features[0].extract(ins).seq.tostring() == s.features[1].extract(s).seq.tostring()