#!/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 drecord, for handling double stranded
DNA sequences. Dseq and drecord are subclasses of Biopythons
Seq and SeqRecord classes, respectively.These classes support the
notion of circular and linear DNA.
'''
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 reverse_complement as rc
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.find_sub_strings import common_sub_strings
[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 drecord object (see drecord).
There are three ways of creating a Dseq object directly:
Only one argument (string):
...........................
>>> import pydna
>>> pydna.Dseq("aaa")
Dseq(-3)
aaa
ttt
The give 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, int):
>>> 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 bot watson and crick
>>> 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 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
The default alphabet is set to Biopython IUPACAmbiguousDNA
##DNA topology
The topology 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'
>>> a.dsdata
'ttt'
'''
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)))
data= "".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.")
if (self.circular and
self.five_prime_end()[0] != "blunt" and
self.three_prime_end()[0] != "blunt"):
raise()
Seq.__init__(self, data, 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
'''
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 are switched
and inverted
'''
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 Sets the Dseq object to circular. This can only be done if the
two ends are 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!\n")
[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 _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 hs only DNA polymerase activity (such as exo-klenow)
and any combination of A, G, C or T. Default are all four
nucleotides together.
http://www.bio.net/bionet/mm/methods/1994-October/057457.html
>>> 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
tgctag 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 obj.T4() '''
return self.T4(*args,**kwargs)
[docs] def T4(self, nucleotides=None):
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)
[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 usage:
>>> 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
>>>
'''
frags=[self,]
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,)
newfrags=[]
for enzyme in enzymes:
for frag in frags:
if enzyme.search(Seq(frag.dsdata), linear = frag.linear):
s = zip([str(s) for s in enzyme.catalyze(Seq(frag.watson),linear = frag.linear)],
[str(s) for s in enzyme.catalyze(Seq(frag.crick), linear = frag.linear)[::-1]])
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=[]
return frags
@property
[docs] def ovhg(self):
return self._ovhg
@property
def linear(self):
return self._linear
@linear.setter
[docs] def linear(self, value):
if not value:
slask = self.looped()
self._circular = True
self._linear = False
else:
self._linear=True
self._circular=False
@property
def circular(self):
return self._circular
@circular.setter
[docs] def circular(self, value):
if value:
slask = self.looped()
self._circular = True
self._linear = False
else:
self._circular = False
self._linear = True
[docs]class drecord(SeqRecord):
'''Drecord is a double stranded version of the Biopython SeqRecord class.
The drecord object holds a Dseq object describing the sequence.
Additionally, drecord hold meta information about the sequence in the
from of a list of SeqFeatures, in the same way as the SeqRecord does.
The drecord can be initialized with a string, Seq, Dseq, SeqRecord
or another drecord. The sequence information will be stored in a
Dseq object in all cases. Drecord objects can be read or parsed
from sequences in fasta, embl or Genbank format.
Parameters
----------
record : string, Seq, SeqRecord, Dseq or other drecord object
This data wil 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
filter : bool, optional
If set to True, all non permitted characters will be
silently filtered from the sequence.
permitted letters are ACBEDGFIHKJMLONQPSRUTWVYXZ upper
or lowercase.
raw : string, optional
The string from which the object was parsed (if any).
parsed_from : string, optional
The format of the sequence from which the object was parsed
(if any).
Attributes
----------
filtered : bool
Sequence was filtered or not
parsed_from : string
The string from which the object was parsed (if any).
"not defined" by default.
raw : string
The string from which the object was parsed (if any).
default is 'not defined'
seq : Dseq
The seq property, which holds the actual sequence.
warnings : string
Any warnings issued during parsing.
Examples
--------
>>> from pydna import drecord
>>> a=drecord("aaa")
>>> a
drecord(-3)
>>> a.seq
Dseq(-3)
aaa
ttt
>>> from Bio.Seq import Seq
>>> b=drecord(Seq("aaa"))
>>> b
drecord(-3)
>>> b.seq
Dseq(-3)
aaa
ttt
>>> from Bio.SeqRecord import SeqRecord
>>> c=drecord(SeqRecord(Seq("aaa")))
>>> c
drecord(-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,
filter = False,
raw = "",
parsed_from = None,
*args, **kwargs):
self.raw = raw or "not set"
self.parsed_from = parsed_from or "not defined"
self.filtered = None
self._circular = None
self._linear = None
self.warnings = ""
if isinstance(record, basestring):
SeqRecord.__init__(self, Dseq(record, rc(record), 0), *args, **kwargs)
elif hasattr(record, "features"): # SeqRecord ?
for key, value in record.__dict__.items():
setattr(self, key, value )
if hasattr(self.seq, "watson"):
self.seq=copy.copy(self.seq)
else:
self.seq=Dseq(str(self.seq), str(rc(self.seq)), 0)
elif hasattr(record, "watson"): # Dseq ?
SeqRecord.__init__(self, record, *args, **kwargs)
elif isinstance(record, Seq): # Seq ?
SeqRecord.__init__(self, Dseq(str(record),str(record.reverse_complement()),0), *args, **kwargs)
else:
raise TypeError(("record argument needs to be a string,"
"Seq, SeqRecord or Dseq object,"
" got {}").format(type(record)))
if filter:
IUPAC_single_alphabet_letters = ("ACBEDGFIHKJMLONQPSRUTWVYXZ"
"acbedgfihkjmlonqpsrutwvyxz")
filtered_out = "".join([c for c in self.seq if c not in IUPAC_single_alphabet_letters])
if filtered_out:
filtered = "".join([c for c in self.seq if c in IUPAC_single_alphabet_letters])
self.seq = Seq(filtered, self.seq.alphabet)
self.filtered = filtered_out
self.warnings += u"{} non-permitted chars were filtered from the sequence!\n".format(", ".join(set(filtered_out)))
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()})
if circular == None and linear in (True, False,):
self.linear = linear
elif linear == None and circular in (True, False,):
self.circular = circular
@property
def linear(self):
'''Not really a method, but the linear property'''
return self.seq.linear
@linear.setter
[docs] def linear(self, value):
self.seq.linear = bool(value)
@property
def circular(self):
'''Not really a method, but the circular property'''
return self.seq.circular
@circular.setter
[docs] def circular(self, value):
self.seq.circular = bool(value)
[docs] def seguid(self):
'''
Returns the SEGUID for the sequence
>>> import pydna
>>> a=pydna.drecord("aaa")
>>> a.seguid()
'YG7G6b2Kj/KtFOX63j8mRHHoIlE'
'''
return seguid(self.seq)
[docs] def stamp(self):
'''Adds a stamp
SEGUID <seguid>
to the description attribute of the drecord
object (string).
>>> import pydna
>>> a=pydna.drecord("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 if the SEGUID stamp is valid.
returns True if stamp is present and match the
sequid calculated from the sequence
'''
pattern = "(SEGUID|seguid)\s*\S{27}"
try:
stamp = re.search(pattern, self.description).group()
except AttributeError:
return False
return seguid(self.seq) == stamp[-27:]
[docs] def looped(self):
'''
Returns a circular version of the drecord object. The
underlying Dseq object has to have compatible ends.
>>> import pydna
>>> a=pydna.drecord("aaa")
>>> a
drecord(-3)
>>> b=a.looped()
>>> b
drecord(o3)
>>>
'''
new = copy.deepcopy(self)
new.circular = True
for fn, fo in zip(new.features, self.features):
fn.qualifiers = fo.qualifiers
return new
[docs] def write(self, filename="", f="gb"):
if not filename:
filename=self.description+"."+f
if isinstance(filename, basestring):
if os.path.isfile(filename):
seguid_new = self.seguid()
seguid_old = read(filename).seguid()
if seguid_new == seguid_old:
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 ("drecord\n"
"circular: {}\n"
"size: {}\n").format(self.circular, len(self))+SeqRecord.__str__(self)
def __repr__(self):
return "drecord({}{})".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 = drecord(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 = drecord(SeqRecord.__add__(self, other))
else:
answer = drecord(SeqRecord.__add__(self, drecord(other)))
answer.circular = False
return answer
# def __radd__(self, other):
# other = copy.copy(other)
# other = drecord(other)
# answer = drecord(other.__add__(self))
# answer.circular = False
# return answer
def __getitem__(self, index):
answer = drecord(SeqRecord.__getitem__(self, index))
answer.seq.alphabet = self.seq.alphabet
return answer
[docs] def cut(self, *enzymes):
'''Digest the drecord object with one or more restriction enzymes.
Parameters
----------
enzymes : iterable object
iterable containing Biopython
restriction enzyme objects
Returns
-------
fragments : list
list of drecord objects formed by the digestion
Examples
--------
>>> import pydna
>>> a=pydna.drecord("ggatcc")
>>> from Bio.Restriction import BamHI
>>> a.cut(BamHI)
[drecord(-5), drecord(-5)]
>>> frag1, frag2 = a.cut(BamHI)
>>> frag1.seq
Dseq(-5)
g
cctag
>>> frag2.seq
Dseq(-5)
gatcc
g
'''
frags=[self,]
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,)
newfrags=[]
for enz in enzymes:
for frag in frags:
wts = Seq(frag.seq.watson)
crk = Seq(frag.seq.crick)
if frag.linear:
wts+="N"
crk+="N"
ws = [x-1 for x in enz.search(wts, linear = frag.linear)]
cs = [x-1 for x in enz.search(crk, linear = frag.linear)]
sitepairs = [(sw, sc) for sw, sc in zip(ws,cs[::-1])
if (sw + max(0, frag.seq.ovhg) -
max(0, enz.ovhg)
==
len(frag.seq.crick)-sc -
min(0, frag.seq.ovhg) +
min(0, enz.ovhg))]
sitepairs = sitepairs + [(len(frag.seq.watson), 0)]
w2, c1 = sitepairs[0]
nwat = frag.seq.watson[:w2]
ncrk = frag.seq.crick[c1:]
newfrag=drecord(Dseq(nwat, ncrk, ovhg=frag.seq.ovhg))
feature_lim = max(len(newfrag.seq.watson)+newfrag.seq.ovhg , len(newfrag.seq.crick)-newfrag.seq.ovhg)
newfrag.features = frag[:feature_lim].features
newfrags.append(newfrag)
for (w1, c2), (w2, c1) in zip(sitepairs[:-1], sitepairs[1:]):
nwat = frag.seq.watson[w1:w2]
ncrk = frag.seq.crick[c1:c2]
newfrag = drecord(Dseq(nwat,ncrk, ovhg=enz.ovhg))
newfrag.features = frag[min(w1, len(frag.seq.crick)-c2):max(w2,len(frag.seq.crick)-c1)].features
newfrags.append(newfrag)
#if str(enz)=="KpnI":
# print enz
# print newfrag.fig()
# print min(w1, len(frag.seq.crick)-c2), "==>",max(w2,len(frag.seq.crick)-c1)
# #print w1, len(frag.seq.crick)-c1 ,"-->",w2,len(frag.seq.dsdata)-c2
# print
# print "----"
#print min(w1, len(frag.seq.dsdata)-c1),"-->",max(w2,len(frag.seq.dsdata)-c2)
if frag.circular:
newfrag=newfrags.pop()+newfrags.pop(0)
newfrags.append(newfrag)
if not newfrags:
newfrags.append(frag)
frags=newfrags
newfrags=[]
for f in frags:
f.description = self.description+"_"+"_".join(str(e) for e in enzymes)
return frags
[docs] def reverse_complement(self):
'''Returns a new drecord object which is the reverse complement'''
return self.rc()
[docs] def rc(self):
'''Returns a new drecord object which is the reverse complement'''
answer = drecord(SeqRecord.reverse_complement(self))
answer.circular = self.circular
return answer
[docs] def shifted(self, shift):
'''Returns a circular drecord with a new origin <shift>.
This only works on circular drecords. If we consider the following
circular sequence:
AAAT <-- watson strand
TAAA <-- crick strand
The last T on the watson strand is linked to the first A and the
first and the last nucleotide of the crick strand as well.
shift
if shift is 1, this indicates a new origin at position 1:
new origin
|
A|AAT
T|AAA
new sequence:
AATA
AAAT
Shift is always positive and 0<shift<length, so in this example
permissible values of shift are 1,2 and 3
>>> import pydna
>>> a=pydna.drecord("aaa",circular=True)
>>> a
drecord(o3)
>>> a=pydna.drecord("aaat",circular=True)
>>> a
drecord(o4)
>>> a.seq
Dseq(o4)
aaat
ttta
>>> b=a.shifted(1)
>>> b
drecord(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 ({}) has to be 0<=shift<length({})".format((shift, length,)))
new = copy.deepcopy(self)
new.circular = True
for fn, fo in zip(new.features, self.features):
fn.qualifiers = fo.qualifiers
new.linear = True
new = (new+new)[shift:shift+length]
new.circular = True
new.features = []
for feature in self.features:
if not shift in feature:
new.features.append(feature)
else:
new_start = length -(shift-feature.location.start)
new_end = feature.location.end-shift
a = SeqFeature(FeatureLocation(0, new_end),
type=feature.type,
location_operator=feature.location_operator,
strand=feature.strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=None)
b = SeqFeature(FeatureLocation(new_start, length),
type=feature.type,
location_operator=feature.location_operator,
strand=feature.strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=None)
c = SeqFeature(FeatureLocation(new_start, new_end),
type=feature.type,
location_operator="join",
strand=feature.strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=[a,b])
sub_features=[]
for sf in feature.sub_features:
if feature.location.end<shift:
sub_features.append(SeqFeature(FeatureLocation(length-feature.location.start,
length-feature.location.end),
type=feature.type,
location_operator=feature.location_operator,
strand=feature.strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=None))
elif feature.location.start>shift:
sub_features.append(SeqFeature(FeatureLocation(feature.location.start-shift,
feature.location.end-shift),
type=feature.type,
location_operator=feature.location_operator,
strand=feature.strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=None))
else:
sub_features.extend() #wraparound(sf))
c.sub_features.extend(sub_features)
new.features.append(c)
return new
[docs] def synced(self, ref, limit = 25):
'''This function returns a new circular sequence, 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 or SeqRecord object or
another drecord object.
The reason for using this might be to rotate a recombinant plasmid so
that it starts at the same position after cloning.
>>> import pydna
>>> a=pydna.drecord("gaat",circular=True)
>>> a.seq
Dseq(o4)
gaat
ctta
>>> d = a[2:] + a[:2]
>>> d.seq
Dseq(-4)
atga
tact
>>> insert=pydna.drecord("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 = copy.copy(self.seq)
sequence.linear = True
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, obj="drecord"):
'''This function returns the first sequence found in data. At least one
sequence is required.
read(data, filter = False) --> drecord object
data 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
if filter == True, sequences will be silently filtered
for allowed characters (see docs for drecord)
'''
results = parse(data, filter, obj)
try:
results = results.pop()
except IndexError:
raise ValueError("No sequences found in data ({})".format(data[:20]))
return results
[docs]def parse(data, filter = False, obj = "drecord"):
'''This function returns *all* sequences found in data. If no
sequences are found, an empty list is returned.
parse(data, filter = False) --> list of drecord objects
data 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
if filter == True, sequences will be silently filtered
for allowed characters (see docs for drecord)
'''
raw=""
if not hasattr(data, '__iter__'):
data = (data,)
for item in data:
if isinstance(item, basestring):
raw+=textwrap.dedent(item).strip()
else:
continue
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+=item
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 obj == "drecord":
sequences.append( drecord( 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 Bio.Restriction import Acc65I, KpnI, NlaIV, EcoRI, EcoRV
import pydna
a = pydna.Dseq('CACANGGTACCNGGTACCNGCGGATATC', 'AATTGTGTNCCATGGNCCATGGNCGCCTATAGatgc'[::-1], 4)
print a.fig()
b = Dseq( 'CACANGGTACCNGGTACCNGCGGATATC',
'AATTGTGTNCCATGGNCCATGGNCGCCTATAG'[::-1], 4)
a=pydna.read("../tests/pUC19.gb")
a=a.synced("cggtgatgacggtgaaaacctctgacacat")
#raise SystemExit
print a.seq[0:60]
a = (drecord( Dseq( 'AATTCACANGGTACCNGGTACCNGCGGATATC',
'GTGTNCCATGGNCCATGGNCGCCTATAG'[::-1], -4)),
drecord( Dseq( 'CACANGGTACCNGGTACCNGCGGATATC',
'GTGTNCCATGGNCCATGGNCGCCTATAG'[::-1], 0)),
drecord( Dseq( 'CACANGGTACCNGGTACCNGCGGATATC',
'AATTGTGTNCCATGGNCCATGGNCGCCTATAG'[::-1], 4)),)
enzymes = [Acc65I, NlaIV, KpnI]
for enz in enzymes:
for f in a:
b,c,d = f.cut(enz)
e=b+c+d
assert str(e.seq).lower() == str(f.seq).lower()
a=pydna.read('''
LOCUS New_DNA 33 bp ds-DNA linear 08-NOV-2012
DEFINITION .
ACCESSION
VERSION
SOURCE .
ORGANISM .
COMMENT
COMMENT ApEinfo:methylated:1
FEATURES Location/Qualifiers
misc_feature 1..11
/label=Acc65I-1
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 12..18
/label=Acc65I-2
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 19..33
/label=Acc65I-3
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 1..15
/label=KpnI-1
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 16..22
/label=KpnI-2
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 23..33
/label=KpnI-3
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 1..13
/label=NlaIV-1
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 14..20
/label=NlaIV-2
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
misc_feature 21..33
/label=NlaIV-3
/ApEinfo_fwdcolor=cyan
/ApEinfo_revcolor=green
/ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}
width 5 offset 0
ORIGIN
1 GAATTCacan ggtaccnGGT ACCngcgGAT ATC
//
''')
assert a.seguid()=="di3hL8t2G4iQQsxlm/CtvnUMBz8"
assert ([x.qualifiers["label"][0] for x in a.features] ==
['Acc65I-1', 'Acc65I-2', 'Acc65I-3', 'KpnI-1', 'KpnI-2',
'KpnI-3', 'NlaIV-1', 'NlaIV-2', 'NlaIV-3'])
b,c,d = a.cut(Acc65I)
print [x.qualifiers["label"][0] for x in b.features] == ['Acc65I-1', 'KpnI-1', 'NlaIV-1']
print [x.qualifiers["label"][0] for x in c.features] == ['Acc65I-2', 'KpnI-2', 'NlaIV-2']
print [x.qualifiers["label"][0] for x in d.features] == ['Acc65I-3', 'KpnI-3', 'NlaIV-3']
e = b+c+d
print sorted([x.qualifiers["label"][0] for x in e.features]) == [x.qualifiers["label"][0] for x in a.features]
assert str(a.seq)==str(e.seq)
b,c,d = a.cut(KpnI)
print [x.qualifiers["label"][0] for x in b.features] == ['Acc65I-1', 'KpnI-1', 'NlaIV-1']
print [x.qualifiers["label"][0] for x in c.features] == ['Acc65I-2', 'KpnI-2', 'NlaIV-2']
print [x.qualifiers["label"][0] for x in d.features] == ['Acc65I-3', 'KpnI-3', 'NlaIV-3']
e = b+c+d
print sorted([x.qualifiers["label"][0] for x in e.features]) == [x.qualifiers["label"][0] for x in a.features]
b,c,d = a.cut(NlaIV)
print [x.qualifiers["label"][0] for x in b.features] == ['Acc65I-1', 'NlaIV-1']
print [x.qualifiers["label"][0] for x in c.features] == ['NlaIV-2']
print [x.qualifiers["label"][0] for x in d.features] == [ 'KpnI-3', 'NlaIV-3']
e = b+c+d
assert str(a.seq)==str(e.seq)
b,c = a.cut(EcoRI)
e = b+c
assert str(a.seq)==str(e.seq)
b,c = a.cut(EcoRV)
e = b+c
assert str(a.seq)==str(e.seq)
b,c,d = a.cut(EcoRI,EcoRV)
e = b+c+d
assert str(a.seq)==str(e.seq)
b,c,d, f = a.cut(Acc65I,EcoRI)
e = b+c+d+f
assert str(a.seq)==str(e.seq)
b,c,d, f = a.cut(EcoRI,Acc65I)
e = b+c+d+f
assert str(a.seq)==str(e.seq)
print "done!"
seqs = parse('../tests/RefDataBjorn.fas', filter=False)
assert len(seqs) == 771
assert list(set([len (a) for a in seqs])) == [901]
for i,s in enumerate(seqs):
a = s.description
b = a.split("|")
c = "|".join([b[0],b[1],b[3]])
s.id = b[2].replace(" ","_")+"_"+str(i)
s.description = ""
if b[3]=="Zenion hololepis":
s.id = b[3].replace(" ","_")+"_"+str(i)
s.seq.alphabet = IUPACAmbiguousDNA()
print "done! II"