#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''This module provides miscellaneous functions.
'''
from Bio.SeqFeature import SeqFeature
from Bio.SeqFeature import FeatureLocation
[docs]def eq(*args,**kwargs):
'''Compares two or more DNA sequences for equality i.e. they
represent the same DNA molecule. Comparisons are case insensitive.
Parameters
----------
args : iterable
iterable containing sequences
args can be strings, Biopython Seq or SeqRecord, Dseqrecord
or dsDNA objects.
circular : bool, optional
Consider all molecules circular or linear
linear : bool, optional
Consider all molecules circular or linear
Returns
-------
eq : bool
Returns True or False
Notes
-----
Compares two or more DNA sequences for equality i.e. if they
represent the same DNA molecule.
Two linear sequences are considiered equal if either:
* They have the same sequence (case insensitive)
* One sequence is the reverse complement of the other (case insensitive)
Two circular sequences are considiered equal if:
1. They have the same length.
AND
2. One sequence or its reverse complement can be found in the
concatenation of the other sequence with itself (they are circular
permutations).
The topology for the comparison can be set using one of the keywords
linear or circular to True or False.
If circular or linear is not set, it will be deduced from the topology of
each sequence for sequences that have a linear or circular attribute
(like Dseq and Dseqrecord).
Examples
--------
>>> from pydna import eq, Dseqrecord
>>> eq("aaa","AAA")
True
>>> eq("aaa","AAA","TTT")
True
>>> eq("aaa","AAA","TTT","tTt")
True
>>> eq("aaa","AAA","TTT","tTt", linear=True)
True
>>> eq("Taaa","aTaa", linear = True)
False
>>> eq("Taaa","aTaa", circular = True)
True
>>> a=Dseqrecord("Taaa")
>>> b=Dseqrecord("aTaa")
>>> eq(a,b)
False
>>> eq(a,b,circular=True)
True
>>> a=a.looped()
>>> b=b.looped()
>>> eq(a,b)
True
>>> eq(a,b,circular=False)
False
>>> eq(a,b,linear=True)
False
>>> eq(a,b,linear=False)
True
>>> eq("ggatcc","GGATCC")
True
>>> eq("ggatcca","GGATCCa")
True
>>> eq("ggatcca","tGGATCC")
True
'''
from Bio.Seq import reverse_complement
from Bio.SeqRecord import SeqRecord
import itertools
args=list(args)
for i, arg in enumerate(args):
if not hasattr(arg, "__iter__") or isinstance(arg, SeqRecord):
args[i] = (arg,)
args = list(itertools.chain.from_iterable(args))
topology = None
if "linear" in kwargs:
if kwargs["linear"]==True:
topology = "linear"
if kwargs["linear"]==False:
topology = "circular"
elif "circular" in kwargs:
if kwargs["circular"]==True:
topology = "circular"
if kwargs["circular"]==False:
topology = "linear"
else:
# topology keyword not set, look for topology associated to each sequence
# otherwise raise exception
topology = set([arg.circular if hasattr(arg, "circular") else None for arg in args])
if len(topology)!=1:
raise Exception("sequences have different topologies")
topology = topology.pop()
if topology in (False, None):
topology = "linear"
elif topology==True:
topology = "circular"
#args_string_list = [str(arg.seq).lower() if hasattr(arg,"seq") else str(arg).lower() for arg in args]
args = [arg.seq if hasattr(arg, "seq") else arg for arg in args]
args_string_list = [arg.watson.lower() if hasattr(arg, "watson") else str(arg).lower() for arg in args]
length = set((len(s) for s in args_string_list))
if len(length)!=1:
return False
same = True
if topology == "circular":
# force circular comparison of all given sequences
for s1, s2 in itertools.combinations(args_string_list, 2):
if not ( s1 in s2+s2 or reverse_complement(s1) in s2+s2):
same = False
elif topology == "linear":
# force linear comparison of all given sequences
for s1,s2 in itertools.combinations(args_string_list, 2):
if not ( s1==s2 or s1==reverse_complement(s2) ):
same = False
return same
[docs]def shift_origin(seq, shift):
'''Shift the origin of seq which is assumed to be a circular
sequence.
Parameters
----------
seq : string, Biopython Seq, Biopython SeqRecord, Dseq or Dseqrecord
sequence to be shifted.
Returns
-------
new_seq : string, Biopython Seq, Biopython SeqRecord, Dseq or Dseqrecord
sequence with a new origin.
Examples
--------
>>> import pydna
>>> pydna.shift_origin("taaa",1)
'aaat'
>>> pydna.shift_origin("taaa",0)
'taaa'
>>> pydna.shift_origin("taaa",2)
'aata'
>>> pydna.shift_origin("gatc",2)
'tcga'
'''
from Bio.SeqFeature import SeqFeature
from Bio.SeqFeature import FeatureLocation
from Bio.SeqRecord import SeqRecord
import copy
length=len(seq)
if not 0<=shift<length:
raise(ValueError("shift ({}) has to be 0<=shift<length({})",format((shift,length,))))
if hasattr(seq, "linear"):
new = seq.tolinear()
else:
new = seq
new = (new+new)[shift:shift+length]
def wraparound(feature):
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)
return c
if hasattr(seq, "features"):
for feature in seq.features:
if shift in feature:
new.features.append(wraparound(feature))
if hasattr(seq, "linear"):
new = new.looped()
return new
[docs]def sync(seq, ref):
'''Synchronize two circular sequences.
Parameters
----------
seq : string, Biopython Seq, Biopython SeqRecord, Dseq or Dseqrecord
sequence to be shifted.
ref : string, Biopython Seq, Biopython SeqRecord, Dseq or Dseqrecord
The reference sequence.
Returns
-------
sequence : string, Biopython Seq, Biopython SeqRecord, Dseq or Dseqrecord
sequence with a new origin.
This function tries to rotate the circular sequence seq
so that it has a maximum overlap with ref.
Examples
--------
>>> import pydna
>>> pydna.sync("taaatc","aaataa")
'aaatct'
>>> pydna.sync("taaatc","aaataa")
'aaatct'
>>> pydna.sync("taaat","aaataa")
'aaatt'
'''
import itertools
import copy
from Bio.Seq import reverse_complement
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from findsubstrings_suffix_arrays_python import common_sub_strings
from utils import eq
if hasattr(seq, "linear"):
sequence = seq.tolinear()
else:
sequence = copy.deepcopy(seq)
if hasattr(sequence, "seq"):
sequence = sequence.seq
if hasattr(sequence, "watson"):
a = str(sequence.watson).lower()
a_rc = str(sequence.crick).lower()
sequence_rc = sequence.reverse_complement()
double_sequence = sequence+sequence
else:
a = str(sequence.lower())
a_rc = str(sequence.reverse_complement()).lower()
sequence_rc = sequence.reverse_complement()
double_sequence = sequence+sequence
else:
a = str(sequence).lower()
a_rc = str(reverse_complement(sequence)).lower()
sequence_rc = reverse_complement(sequence)
double_sequence = a+a
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(25, 25*(len(a)/25)+1))
d = common_sub_strings(a_rc+a_rc, b, limit = min(25, 25*(len(a)/25)+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("no overlap !")
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
sequence = shift_origin(seq, ofs)
try:
sequence.circular=True
except AttributeError:
pass
if hasattr(seq, "watson"):
assert eq(seq.watson, sequence, circular =True)
return dsdna(sequence)
assert eq(seq, sequence, circular =True)
return sequence
[docs]def copy_features(source_sr, target_sr, limit = 10):
'''This function tries to copy all features in source_seq and copy
them to target_seq. Source_sr and target_sr are objects with
a features property, such as Dseqrecord or Biopython SeqRecord.
Parameters
----------
source_seq : SeqRecord or Dseqrecord
The sequence to copy features from
target_seq : SeqRecord or Dseqrecord
The sequence to copy features to
Returns
-------
bool : True
This function acts on target_seq in place.
No data is returned.
'''
import re
from Bio.Seq import reverse_complement as rc
target_length = len(target_sr)
target_string = str(target_sr.seq).upper()
try:
circular = bool(target_sr.circular)
except AttributeError:
circular=False
newfeatures=[]
trgt_string = target_string
trgt_string_rc = rc(trgt_string)
for feature in [f for f in source_sr.features if len(f)>limit]:
fsr = feature.extract(source_sr).upper()
featurelength = 0# len(fsr)
if circular:
trgt_string = target_string+target_string[:featurelength]
trgt_string_rc = rc(trgt_string)
positions = (
[(m.start(), m.end(), 1,) for m in re.finditer(str(fsr.seq),trgt_string)]
+
[(len(trgt_string_rc)-m.end(),len(trgt_string_rc)-m.start(),-1,)
for m in re.finditer(str(fsr.seq),trgt_string_rc)])
for begin, end, strand in positions:
if circular and begin<target_length<end:
end = end-len(
target_sr)
sf1 = SeqFeature(FeatureLocation(begin, trgt_length),
type=feature.type,
location_operator=feature.location_operator,
strand=strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=None,)
sf2 = SeqFeature(FeatureLocation(0, end),
type=feature.type,
location_operator=feature.location_operator,
strand=strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=None,)
nf = SeqFeature(FeatureLocation(begin, end),
type=feature.type,
location_operator="join",
strand=strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=[sf1,sf2],)
else:
nf = SeqFeature(FeatureLocation(begin,end),
type=feature.type,
location_operator=feature.location_operator,
strand=strand,
id=feature.id,
qualifiers=feature.qualifiers,
sub_features=None)
newfeatures.append(nf)
target_sr.features.extend(newfeatures)
return True
if __name__=="__main__":
import doctest
doctest.testmod()