return _pretty_str("Assembly\n"
"fragments..: {sequences}\n"
"limit(bp)..: {limit}\n"
"G.nodes....: {nodes}\n"
"algorithm..: {al}".format(
sequences=" ".join(
"{}bp".format(len(x["mixed"]))
for x in self.fragments),
limit=self.limit,
nodes=self.G.order(),
al=self.algorithm.__name__,
))
example_fragments = (
_Dseqrecord("AacgatCAtgctcc", name="a"),
_Dseqrecord("TtgctccTAAattctgc", name="b"),
_Dseqrecord("CattctgcGAGGacgatG", name="c"),
)
linear_results = (
_Dseqrecord("AacgatCAtgctccTAAattctgcGAGGacgatG", name="abc"),
_Dseqrecord("ggagcaTGatcgtCCTCgcagaatG", name="ac_rc"),
_Dseqrecord("AacgatG", name="ac"),
)
circular_results = (
_Dseqrecord("acgatCAtgctccTAAattctgcGAGG", name="abc", circular=True),
_Dseqrecord("ggagcaTGatcgtCCTCgcagaatTTA", name="abc_rc", circular=True),
)
def pcr(*args, **kwargs):
"""pcr is a convenience function for the Anneal class to simplify its
usage, especially from the command line. If more than one or no PCR
product is formed, a ValueError is raised.
args is any iterable of Dseqrecords or an iterable of iterables of
Dseqrecords. args will be greedily flattened.
Parameters
----------
args : iterable containing sequence objects
Several arguments are also accepted.
limit : int = 13, optional
limit length of the annealing part of the primers.
Notes
-----
sequences in args could be of type:
* string
* Seq
* SeqRecord (or subclass)
* Dseqrecord (or sublcass)
The last sequence will be assumed to be the template while
all preceeding sequences will be assumed to be primers.
This is a powerful function, use with care!
Returns
-------
product : Amplicon
An :class:`pydna.amplicon.Amplicon` object representing the PCR
product. The direction of the PCR product will be the same as for
the template sequence.
Examples
--------
>>> from pydna.dseqrecord import Dseqrecord
>>> from pydna.readers import read
>>> from pydna.amplify import pcr
>>> from pydna.primer import Primer
>>> template = Dseqrecord("tacactcaccgtctatcattatctac\
tatcgactgtatcatctgatagcac")
>>> from Bio.SeqRecord import SeqRecord
>>> p1 = Primer("tacactcaccgtctatcattatc")
>>> p2 = Primer("cgactgtatcatctgatagcac").reverse_complement()
>>> pcr(p1, p2, template)
Amplicon(51)
>>> pcr([p1, p2], template)
Amplicon(51)
>>> pcr((p1,p2,), template)
Amplicon(51)
>>>
"""
output = _flatten(args) # flatten
new = []
for s in output:
if hasattr(s, "watson"):
s = _SeqRecord(_Seq(s.watson))
elif hasattr(s, "transcribe"):
s = _SeqRecord(s)
elif isinstance(s, str):
s = _SeqRecord(_Seq(s))
elif hasattr(s, "features"):
pass
else:
raise TypeError("arguments need to be a string, Bio.Seq, SeqRecord"
", Primer, Dseqrecord or Amplicon object")
new.append(s)
# A single Amplicon object
if len(new) == 1 and hasattr(new[0], "forward_primer"):
new = [new[0].forward_primer, new[0].reverse_primer, new[0]]
if not hasattr(new[-1].seq, "watson"):
new[-1] = _Dseqrecord(s)
anneal_primers = Anneal(new[:-1], new[-1], **kwargs)
if len(anneal_primers.products) == 1:
return anneal_primers.products[0]
elif len(anneal_primers.products) == 0:
raise ValueError("No PCR product! {}".format(anneal_primers.report()))
raise ValueError("PCR not specific! {}".format(anneal_primers.report()))
def products(self):
if self._products:
return self._products
self._products = []
for fp in self.forward_primers:
for rp in self.reverse_primers:
if self.template.circular:
tmpl = self.template.shifted(fp.position - fp._fp)
tmpl = tmpl[:] * 2
for f in tmpl.features:
for x, y in zip(f.location.parts,
f.location.parts[1:]):
if x.end == y.start + len(self.template):
f.location = _FeatureLocation(
x.start,
y.end + len(self.template),
strand=f.location.strand,
)
if fp.position > rp.position:
tmpl = tmpl[:len(self.template) - fp.position +
rp.position + rp._fp + fp._fp]
else:
tmpl = tmpl[:rp.position + rp._fp -
(fp.position - fp._fp)]
else:
tmpl = self.template[fp.position - fp._fp:rp.position +
rp._fp]
prd = (_Dseqrecord(fp.tail) + tmpl +
_Dseqrecord(rp.tail).reverse_complement())
full_tmpl_features = [
f for f in tmpl.features
if f.location.start == 0 and f.location.end == len(tmpl)
]
new_identifier = ""
if full_tmpl_features:
ft = full_tmpl_features[0]
if "label" in ft.qualifiers:
new_identifier = " ".join(ft.qualifiers["label"])
elif "note" in ft.qualifiers:
new_identifier = " ".join(ft.qualifiers["note"])
from pydna.utils import (
identifier_from_string as _identifier_from_string,
) # TODO: clean this up
prd.name = (_identifier_from_string(new_identifier)[:16]
or self.kwargs.get("name")
or "{}bp_PCR_prod".format(len(prd))[:16])
prd.id = (_identifier_from_string(new_identifier)[:16]
or self.kwargs.get("id") or "{}bp {}".format(
str(len(prd))[:14], prd.seguid()))
prd.description = self.kwargs.get(
"description") or "pcr product_{}_{}".format(
fp.description, rp.description)
amplicon = _Amplicon(prd,
template=self.template,
forward_primer=fp,
reverse_primer=rp,
**self.kwargs)
# amplicon.forward_primer.amplicon = amplicon
# amplicon.reverse_primer.amplicon = amplicon
self._products.append(amplicon)
return self._products
def assembly_fragments(f, overlap=35, maxlink=40):
'''This function return a list of :mod:`pydna.amplicon.Amplicon` objects where
primers have been modified with tails so that the fragments can be fused in
the order they appear in the list by for example Gibson assembly or homologous
recombination.
Given that we have two linear :mod:`pydna.amplicon.Amplicon` objects a and b
we can modify the reverse primer of a and forward primer of b with tails to allow
fusion by fusion PCR, Gibson assembly or in-vivo homologous recombination.
The basic requirements for the primers for the three techniques are the same.
::
<-->
_________ a _________ __________ b ________
/ \\ / \\
agcctatcatcttggtctctgca TTTATATCGCATGACTCTTCTTT
||||||||||||||||||||||| |||||||||||||||||||||||
<gacgt <AGAAA
agcct> TTTAT>
||||||||||||||||||||||| |||||||||||||||||||||||
tcggatagtagaaccagagacgt AAATATAGCGTACTGAGAAGAAA
agcctatcatcttggtctctgcaTTTATATCGCATGACTCTTCTTT
||||||||||||||||||||||||||||||||||||||||||||||
tcggatagtagaaccagagacgtAAATATAGCGTACTGAGAAGAAA
\\___________________ c ______________________/
Design tailed primers incorporating a part of the next or previous fragment to be assembled.
::
agcctatcatcttggtctctgca
|||||||||||||||||||||||
gagacgtAAATATA
|||||||||||||||||||||||
tcggatagtagaaccagagacgt
TTTATATCGCATGACTCTTCTTT
|||||||||||||||||||||||
ctctgcaTTTATAT
|||||||||||||||||||||||
AAATATAGCGTACTGAGAAGAAA
PCR products with flanking sequences are formed in the PCR process.
::
agcctatcatcttggtctctgcaTTTATAT
||||||||||||||||||||||||||||||
tcggatagtagaaccagagacgtAAATATA
\\____________/
identical
sequences
____________
/ \\
ctctgcaTTTATATCGCATGACTCTTCTTT
||||||||||||||||||||||||||||||
gagacgtAAATATAGCGTACTGAGAAGAAA
The fragments can be fused by any of the techniques mentioned earlier to form c:
::
agcctatcatcttggtctctgcaTTTATATCGCATGACTCTTCTTT
||||||||||||||||||||||||||||||||||||||||||||||
tcggatagtagaaccagagacgtAAATATAGCGTACTGAGAAGAAA
The first argument of this function is a list of sequence objects containing
Amplicons and other similar objects.
**At least every second sequence object needs to be an Amplicon**
This rule exists because if a sequence object is that is not a PCR product
is to be fused with another fragment, that other fragment needs to be an Amplicon
so that the primer of the other object can be modified to include the whole stretch
of sequence homology needed for the fusion. See the example below where a is a
non-amplicon (a linear plasmid vector for instance)
::
_________ a _________ __________ b ________
/ \\ / \\
agcctatcatcttggtctctgca <--> TTTATATCGCATGACTCTTCTTT
||||||||||||||||||||||| |||||||||||||||||||||||
tcggatagtagaaccagagacgt <AGAAA
TTTAT>
|||||||||||||||||||||||
<--> AAATATAGCGTACTGAGAAGAAA
agcctatcatcttggtctctgcaTTTATATCGCATGACTCTTCTTT
||||||||||||||||||||||||||||||||||||||||||||||
tcggatagtagaaccagagacgtAAATATAGCGTACTGAGAAGAAA
\\___________________ c ______________________/
In this case only the forward primer of b is fitted with a tail with a part a:
::
agcctatcatcttggtctctgca
|||||||||||||||||||||||
tcggatagtagaaccagagacgt
TTTATATCGCATGACTCTTCTTT
|||||||||||||||||||||||
<AGAAA
tcttggtctctgcaTTTATAT
|||||||||||||||||||||||
AAATATAGCGTACTGAGAAGAAA
PCR products with flanking sequences are formed in the PCR process.
::
agcctatcatcttggtctctgcaTTTATAT
||||||||||||||||||||||||||||||
tcggatagtagaaccagagacgtAAATATA
\\____________/
identical
sequences
____________
/ \\
ctctgcaTTTATATCGCATGACTCTTCTTT
||||||||||||||||||||||||||||||
gagacgtAAATATAGCGTACTGAGAAGAAA
The fragments can be fused by for example Gibson assembly:
::
agcctatcatcttggtctctgcaTTTATAT
||||||||||||||||||||||||||||||
tcggatagtagaacca
TCGCATGACTCTTCTTT
||||||||||||||||||||||||||||||
gagacgtAAATATAGCGTACTGAGAAGAAA
to form c:
::
agcctatcatcttggtctctgcaTTTATATCGCATGACTCTTCTTT
||||||||||||||||||||||||||||||||||||||||||||||
tcggatagtagaaccagagacgtAAATATAGCGTACTGAGAAGAAA
The first argument of this function is a list of sequence objects containing
Amplicons and other similar objects.
The overlap argument controls how many base pairs of overlap required between
adjacent sequence fragments. In the junction between Amplicons, tails with the
length of about half of this value is added to the two primers
closest to the junction.
::
> <
Amplicon1
Amplicon2
> <
⇣
> <-
Amplicon1
Amplicon2
-> <
In the case of an Amplicon adjacent to a Dseqrecord object, the tail will
be twice as long (1*overlap) since the
recombining sequence is present entirely on this primer:
::
Dseqrecd1
Amplicon1
> <
⇣
Dseqrecd1
Amplicon1
--> <
Note that if the sequence of DNA fragments starts or stops with an Amplicon,
the very first and very last prinmer will not be modified i.e. assembles are
always assumed to be linear. There are simple tricks around that for circular
assemblies depicted in the last two examples below.
The maxlink arguments controls the cut off length for sequences that will be
synhtesized by adding them to primers for the adjacent fragment(s). The
argument list may contain short spacers (such as spacers between fusion proteins).
::
Example 1: Linear assembly of PCR products (pydna.amplicon.Amplicon class objects) ------
> < > <
Amplicon1 Amplicon3
Amplicon2 Amplicon4
> < > <
⇣
pydna.design.assembly_fragments
⇣
> <- -> <- pydna.assembly.Assembly
Amplicon1 Amplicon3
Amplicon2 Amplicon4 ➤ Amplicon1Amplicon2Amplicon3Amplicon4
-> <- -> <
Example 2: Linear assembly of alternating Amplicons and other fragments
> < > <
Amplicon1 Amplicon2
Dseqrecd1 Dseqrecd2
⇣
pydna.design.assembly_fragments
⇣
> <-- --> <-- pydna.assembly.Assembly
Amplicon1 Amplicon2
Dseqrecd1 Dseqrecd2 ➤ Amplicon1Dseqrecd1Amplicon2Dseqrecd2
Example 3: Linear assembly of alternating Amplicons and other fragments
Dseqrecd1 Dseqrecd2
Amplicon1 Amplicon2
> < --> <
⇣
pydna.design.assembly_fragments
⇣
pydna.assembly.Assembly
Dseqrecd1 Dseqrecd2
Amplicon1 Amplicon2 ➤ Dseqrecd1Amplicon1Dseqrecd2Amplicon2
--> <-- --> <
Example 4: Circular assembly of alternating Amplicons and other fragments
-> <==
Dseqrecd1 Amplicon2
Amplicon1 Dseqrecd1
--> <-
⇣
pydna.design.assembly_fragments
⇣
pydna.assembly.Assembly
-> <==
Dseqrecd1 Amplicon2 -Dseqrecd1Amplicon1Amplicon2-
Amplicon1 ➤ | |
--> <- -----------------------------
------ Example 5: Circular assembly of Amplicons
> < > <
Amplicon1 Amplicon3
Amplicon2 Amplicon1
> < > <
⇣
pydna.design.assembly_fragments
⇣
> <= -> <-
Amplicon1 Amplicon3
Amplicon2 Amplicon1
-> <- +> <
⇣
make new Amplicon using the Amplicon1.template and
the last fwd primer and the first rev primer.
⇣
pydna.assembly.Assembly
+> <= -> <-
Amplicon1 Amplicon3 -Amplicon1Amplicon2Amplicon3-
Amplicon2 ➤ | |
-> <- -----------------------------
Parameters
----------
f : list of :mod:`pydna.amplicon.Amplicon` and other Dseqrecord like objects
list Amplicon and Dseqrecord object for which fusion primers should be constructed.
overlap : int, optional
Length of required overlap between fragments.
maxlink : int, optional
Maximum length of spacer sequences that may be present in f. These will be included in tails for designed primers.
Returns
-------
seqs : list of :mod:`pydna.amplicon.Amplicon` and other Dseqrecord like objects :mod:`pydna.amplicon.Amplicon` objects
::
[Amplicon1,
Amplicon2, ...]
Examples
--------
>>> from pydna.dseqrecord import Dseqrecord
>>> from pydna.design import primer_design
>>> a=primer_design(Dseqrecord("atgactgctaacccttccttggtgttgaacaagatcgacgacatttcgttcgaaacttacgatg"))
>>> b=primer_design(Dseqrecord("ccaaacccaccaggtaccttatgtaagtacttcaagtcgccagaagacttcttggtcaagttgcc"))
>>> c=primer_design(Dseqrecord("tgtactggtgctgaaccttgtatcaagttgggtgttgacgccattgccccaggtggtcgtttcgtt"))
>>> from pydna.design import assembly_fragments
>>> # We would like a circular recombination, so the first sequence has to be repeated
>>> fa1,fb,fc,fa2 = assembly_fragments([a,b,c,a])
>>> # Since all fragments are Amplicons, we need to extract the rp of the 1st and fp of the last fragments.
>>> from pydna.amplify import pcr
>>> fa = pcr(fa2.forward_primer, fa1.reverse_primer, a)
>>> [fa,fb,fc]
[Amplicon(100), Amplicon(101), Amplicon(102)]
>>> from pydna.assembly import Assembly
>>> assemblyobj = Assembly([fa,fb,fc])
>>> assemblyobj
Assembly
fragments....: 100bp 101bp 102bp
limit(bp)....: 25
G.nodes......: 6
algorithm....: common_sub_strings
>>> assemblyobj.assemble_linear()
[Contig(-231), Contig(-166), Contig(-36)]
>>> assemblyobj.assemble_circular()[0].cseguid()
'V3Mi8zilejgyoH833UbjJOtDMbc'
>>> (a+b+c).looped().cseguid()
'V3Mi8zilejgyoH833UbjJOtDMbc'
>>> print(assemblyobj.assemble_circular()[0].figure())
-|100bp_PCR_prod|36
| \\/
| /\\
| 36|101bp_PCR_prod|36
| \\/
| /\\
| 36|102bp_PCR_prod|36
| \\/
| /\\
| 36-
| |
--------------------------------------------------------
>>>
'''
# sanity check for arguments
nf = [item for item in f if len(item)>maxlink]
if not all(hasattr(i[0],"template") or hasattr(i[1],"template") for i in zip(nf,nf[1:])):
raise ValueError("Every second fragment larger than maxlink has to be an Amplicon object")
_module_logger.debug("### assembly fragments ###")
_module_logger.debug("overlap = %s", overlap)
_module_logger.debug("max_link = %s", maxlink)
f = [_copy.copy(f) for f in f]
first_fragment_length = len(f[0])
last_fragment_length = len(f[-1])
if first_fragment_length<=maxlink:
# first fragment should be removed and added to second fragment (new first fragment) forward primer
f[1].forward_primer = f[0].seq._data + f[1].forward_primer
_module_logger.debug("first fragment removed since len(f[0]) = %s", first_fragment_length)
f=f[1:]
else:
_module_logger.debug("first fragment stays since len(f[0]) = %s", first_fragment_length)
if last_fragment_length<=maxlink:
f[-2].reverse_primer = f[-1].seq.reverse_complement()._data + f[-2].reverse_primer
f=f[:-1]
_module_logger.debug("last fragment removed since len(f[%s]) = %s", len(f), last_fragment_length)
else:
_module_logger.debug("last fragment stays since len(f[%s]) = %s", len(f),last_fragment_length)
empty = _Dseqrecord("")
_module_logger.debug(f)
_module_logger.debug("loop through fragments in groups of three:")
tail_length = _math.ceil(overlap/2)
for i in range(len(f)-1):
first = f[i]
secnd = f[i+1]
secnd_len = len(secnd)
_module_logger.debug( "first = %s", str(first.seq))
_module_logger.debug( "secnd = %s", str(secnd.seq))
if secnd_len <= maxlink:
_module_logger.debug("secnd is smaller or equal to maxlink; should be added to primer(s)")
third = f[i+2]
_module_logger.debug( "third = %s", str(third.seq))
if hasattr(f[i], "template") and hasattr(third, "template"):
_module_logger.debug("secnd is is flanked by amplicons, so half of secnd should be added each flanking primers")
first.reverse_primer = secnd.seq.reverse_complement()._data[secnd_len//2:] + first.reverse_primer
third.forward_primer = secnd.seq._data[secnd_len//2:] + third.forward_primer
lnk = (third.seq.reverse_complement()._data+secnd.reverse_complement().seq._data[:secnd_len//2])[-tail_length:]
_module_logger.debug("1 %s", lnk)
first.reverse_primer = lnk + first.reverse_primer
lnk = (first.seq._data + secnd.seq._data[:secnd_len//2])[-tail_length:]
_module_logger.debug("2 %s", lnk)
third.forward_primer = lnk + third.forward_primer
elif hasattr(first , "template"):
first.reverse_primer = secnd.seq.reverse_complement()._data + first.reverse_primer
lnk = str(third.seq[:overlap].reverse_complement())
first.reverse_primer = lnk + first.reverse_primer
elif hasattr(third , "template"):
third.forward_primer = secnd.seq._data + third.forward_primer
lnk = str(first.seq[-overlap:])
third.forward_primer = lnk + third.forward_primer
secnd=empty
f[i+2] = third
else: # secnd is larger than maxlink
if hasattr(first, "template") and hasattr(secnd, "template"):
lnk = str(first.seq[-tail_length:])
#_module_logger.debug("4 %s", lnk)
secnd.forward_primer = lnk + secnd.forward_primer
lnk = str(secnd.seq[:tail_length].reverse_complement())
#_module_logger.debug("5 %s", lnk)
first.reverse_primer = lnk + first.reverse_primer
elif hasattr(first , "template"):
lnk = str(secnd.seq[:overlap].reverse_complement())
#_module_logger.debug("6 %s", lnk)
first.reverse_primer = lnk + first.reverse_primer
elif hasattr(secnd , "template"):
lnk = str(first.seq[-overlap:])
#_module_logger.debug("7 %s", lnk)
secnd.forward_primer = lnk + secnd.forward_primer
f[i] = first
f[i+1] = secnd
_module_logger.debug("loop ended")
f = [item for item in f if len(item)]
return [_pcr(p.forward_primer, p.reverse_primer, p.template) if hasattr(p, "template") else p for p in f]
circular=True) for cp in cps.values()), key=len, reverse=True)
def __repr__(self):
# https://pyformat.info
return _pretty_str( "Assembly\n"
"fragments..: {sequences}\n"
"limit(bp)..: {limit}\n"
"G.nodes....: {nodes}\n"
"algorithm..: {al}".format(sequences = " ".join("{}bp".format(len(x["mixed"])) for x in self.fragments),
limit = self.limit,
nodes = self.G.order(),
al = self.algorithm.__name__))
example_fragments = ( _Dseqrecord("AacgatCAtgctcc", name ="a"),
_Dseqrecord("TtgctccTAAattctgc", name ="b"),
_Dseqrecord("CattctgcGAGGacgatG",name ="c") )
linear_results = ( _Dseqrecord("AacgatCAtgctccTAAattctgcGAGGacgatG", name ="abc"),
_Dseqrecord("ggagcaTGatcgtCCTCgcagaatG", name ="ac_rc"),
_Dseqrecord("AacgatG", name ="ac") )
circular_results = ( _Dseqrecord("acgatCAtgctccTAAattctgcGAGG", name ="abc", circular=True),
_Dseqrecord("ggagcaTGatcgtCCTCgcagaatTTA", name ="abc_rc", circular=True))
if __name__=="__main__":
# !!!!!!!!!!!![]!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!![]!!!!!!!!!!!!!
# ^^^^^^^^^^^^[]^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^[]^^^^^^^^^^^^^
# [] []
# [] []
# [] []
# ~~^-~^_~^~/ \~^-~^~_~^-~_^~-^~_^~~-^~_~^~-~_~-^~_^/ \~^-~_~^-~~-
# ~ _~~- ~^-^~-^~~- ^~_^-^~~_ -~^_ -~_-~~^- _~~_~-^_ ~^-^~~-_^-~ ~^
"""Assembly of sequences by GoldenGate ligation assebmly."""
from pydna.dseqrecord import Dseqrecord as _Dseqrecord
from copy import deepcopy as _deepcopy
import logging as _logging
_module_logger = _logging.getLogger("pydna." + __name__)
from Bio.Restriction import BsaI, BsmBI, BbsI, FokI
DNA = _Dseqrecord("gatcGAAGACtagagtctgattcg")
a,b = DNA.cut(BbsI)
assert a+b == DNA
# MoClo