def looped(self):
"""
Returns a circular version of the Dseqrecord object. The
underlying Dseq object has to have compatible ends.
Examples
--------
>>> from pydna.dseqrecord import Dseqrecord
>>> a=Dseqrecord("aaa")
>>> a
Dseqrecord(-3)
>>> b=a.looped()
>>> b
Dseqrecord(o3)
>>>
See also
--------
pydna.dseq.Dseq.looped
"""
new = _copy.copy(self)
for key, value in list(self.__dict__.items()):
setattr(new, key, value)
new._seq = self.seq.looped()
five_prime = self.seq.five_prime_end()
for fn, fo in zip(new.features, self.features):
if five_prime[0] == "5'":
fn.location = fn.location + self.seq.ovhg
elif five_prime[0] == "3'":
fn.location = fn.location + (-self.seq.ovhg)
if fn.location.start < 0:
loc1 = _FeatureLocation(len(new) + fn.location.start,
len(new),
strand=fn.strand)
loc2 = _FeatureLocation(0, fn.location.end, strand=fn.strand)
fn.location = _CompoundLocation([loc1, loc2])
if fn.location.end > len(new):
loc1 = _FeatureLocation(fn.location.start,
len(new),
strand=fn.strand)
loc2 = _FeatureLocation(0,
fn.location.end - len(new),
strand=fn.strand)
fn.location = _CompoundLocation([loc1, loc2])
fn.qualifiers = fo.qualifiers
return new
def assemble_circular(self):
cps = {} # circular assembly
cpsrc = {}
cpaths = sorted( _nx.simple_cycles(self.G), key=len)
cpaths_sorted=[]
for cpath in cpaths:
order, node = min((self.G.nodes[node]["order"],node) for node in cpath)
i=cpath.index(node)
cpaths_sorted.append((order, cpath[i:]+cpath[:i]))
cpaths_sorted.sort()
for _, cp in cpaths_sorted: # cpaths is a list of nodes representing a circular assembly
edgelol = [] # edgelol is a list of lists of all edges along cp
cp+= cp[0:1]
for u,v in zip(cp, cp[1:]):
e=[]
for d in self.G[u][v].values():
e.append((u,v,d))
edgelol.append(e)
for edges in _itertools.product(*edgelol):
if [True for ((u,v,e),(x,y,z)) in zip(edges, edges[1:]) if (e["seq"],e["piece"].stop) == (z["seq"],z["piece"].start)]:
continue
ct = "".join(e["seq"][e["piece"]] for u,v,e in edges)
key=ct.upper()
if key in cps or key in cpsrc: continue # TODO: cpsrc not needed?
sg=_nx.DiGraph()
sg.add_edges_from(edges)
sg.add_nodes_from( (n,d) for n,d in self.G.nodes(data=True) if n in cp )
edgefeatures=[]
offset=0
for u,v,e in edges:
feats = _deepcopy(e["features"])
for feat in feats:
feat.location+=offset
edgefeatures.extend(feats)
offset+=e["piece"].stop-e["piece"].start
for f in edgefeatures:
if f.location.start>len(ct) and f.location.end>len(ct):
f.location+=(-len(ct))
elif f.location.end>len(ct):
f.location = _CompoundLocation((_FeatureLocation(f.location.start,_ExactPosition(len(ct))),_FeatureLocation(_ExactPosition(0), f.location.end-len(ct))))
cps[key] = cpsrc[_rc(key)] = ct, edgefeatures, sg, {n:self.nodemap[n] for n in cp[:-1]}, cp
return sorted((_Contig.from_string(cp[0],
features = cp[1],
graph = cp[2],
nodemap = cp[3],
linear=False,
circular=True) for cp in cps.values()), key=len, reverse=True)
def __init__(self, primers, template, limit=13, **kwargs):
r"""The Anneal class has to be initiated with at least an iterable of
primers and a template.
Parameters
----------
primers : iterable of :class:`Primer` or Biopython SeqRecord like
objects Primer sequences 5'-3'.
template : Dseqrecord
The template sequence 5'-3'.
limit : int, optional
limit length of the annealing part of the primers.
Attributes
----------
products: list
A list of Amplicon objects, one for each primer pair that may
form a PCR product.
Examples
--------
>>> from pydna.readers import read
>>> from pydna.amplify import Anneal
>>> from pydna.dseqrecord import Dseqrecord as Ds
>>> t = Ds("tacactcaccgtctatcattatcta"
... "ctatcgactgtatcatctgatagcac")
>>> from Bio.SeqRecord import SeqRecord
>>> p1 = read(">p1\ntacactcaccgtctatcattatc", ds = False)
>>> p2 = read(">p2\ngtgctatcagatgatacagtcg", ds = False)
>>> ann = Anneal((p1, p2), t)
>>> print(ann.report())
Template name 51 nt linear:
p1 anneals forward (--->) at 23
p2 anneals reverse (<---) at 29
>>> ann.products
[Amplicon(51)]
>>> amplicon_list = ann.products
>>> amplicon = amplicon_list.pop()
>>> amplicon
Amplicon(51)
>>> print(amplicon.figure())
5tacactcaccgtctatcattatc...cgactgtatcatctgatagcac3
||||||||||||||||||||||
3gctgacatagtagactatcgtg5
5tacactcaccgtctatcattatc3
|||||||||||||||||||||||
3atgtgagtggcagatagtaatag...gctgacatagtagactatcgtg5
>>> print(amplicon)
Dseqrecord
circular: False
size: 51
ID: 51bp U96-TO06Y6pFs74SQx8M1IVTBiY
Name: 51bp_PCR_prod
Description: pcr product_p1_p2
Number of features: 2
/molecule_type=DNA
Dseq(-51)
taca..gcac
atgt..cgtg
>>> print(amplicon.program())
<BLANKLINE>
|95°C|95°C | |tmf:59.5
|____|_____ 72°C|72°C|tmr:59.7
|5min|30s \ 47.7°C _____|____|30s/kb
| | \______/ 0: 1|5min|GC 39%
| | 30s | |51bp
>>>
"""
self.primers = primers
self.template = _copy.deepcopy(template)
self.limit = limit
self.kwargs = kwargs
self._products = None
self.forward_primers = []
self.reverse_primers = []
twl = len(self.template.seq.watson)
tcl = len(self.template.seq.crick)
if self.template.linear:
tw = self.template.seq.watson
tc = self.template.seq.crick
else:
tw = self.template.seq.watson + self.template.seq.watson
tc = self.template.seq.crick + self.template.seq.crick
for p in self.primers:
self.forward_primers.extend((
_Primer(
p,
# template = self.template,
position=tcl - pos - min(self.template.seq.ovhg, 0),
footprint=fp,
)
for pos, fp in _annealing_positions(str(p.seq), tc, self.limit)
if pos < tcl))
self.reverse_primers.extend((
_Primer(
p,
# template = self.template,
position=pos + max(0, self.template.seq.ovhg),
footprint=fp,
)
for pos, fp in _annealing_positions(str(p.seq), tw, self.limit)
if pos < twl))
self.forward_primers.sort(key=_operator.attrgetter("position"))
self.reverse_primers.sort(key=_operator.attrgetter("position"),
reverse=True)
for fp in self.forward_primers:
if fp.position - fp._fp >= 0:
start = fp.position - fp._fp
end = fp.position
self.template.features.append(
_SeqFeature(
_FeatureLocation(start, end),
type="primer_bind",
strand=1,
qualifiers={
"label": [fp.name],
"ApEinfo_fwdcolor": ["#baffa3"],
"ApEinfo_revcolor": ["#ffbaba"],
},
))
else:
start = len(self.template) - fp._fp + fp.position
end = start + fp._fp - len(self.template)
sf = _SeqFeature(
_CompoundLocation([
_FeatureLocation(start, len(self.template)),
_FeatureLocation(0, end),
]),
type="primer_bind",
location_operator="join",
qualifiers={
"label": [fp.name],
"ApEinfo_fwdcolor": ["#baffa3"],
"ApEinfo_revcolor": ["#ffbaba"],
},
)
self.template.features.append(sf)
for rp in self.reverse_primers:
if rp.position + rp._fp <= len(self.template):
start = rp.position
end = rp.position + rp._fp
self.template.features.append(
_SeqFeature(
_FeatureLocation(start, end),
type="primer_bind",
strand=-1,
qualifiers={
"label": [rp.name],
"ApEinfo_fwdcolor": ["#baffa3"],
"ApEinfo_revcolor": ["#ffbaba"],
},
))
else:
start = rp.position
end = rp.position + rp._fp - len(self.template)
self.template.features.append(
_SeqFeature(
_CompoundLocation([
_FeatureLocation(0, end),
_FeatureLocation(start, len(self.template)),
]),
type="primer_bind",
location_operator="join",
strand=-1,
qualifiers={"label": [rp.name]},
))
def map_trace_files(self, pth, limit=25): # TODO allow path-like objects
import glob
traces = []
for name in glob.glob(pth):
trace = SeqIO.read(name, "abi").lower()
trace.annotations["filename"] = trace.fname = name
traces.append(trace)
if not traces:
raise ValueError("No trace files found in {}".format(pth))
if hasattr(self.map_target, "step"):
area = self.map_target
elif hasattr(self.map_target, "extract"):
area = slice(self.map_target.location.start,
self.map_target.location.end)
else:
area = None # TODO allow other objects as well and do some checks on map target
if area:
self.matching_reads = []
self.not_matching_reads = []
target = str(self[area].seq).lower()
target_rc = str(self[area].seq.rc()).lower()
for trace in traces:
if target in str(trace.seq) or target_rc in str(trace.seq):
self.matching_reads.append(trace)
else:
self.not_matching_reads.append(trace)
reads = self.matching_reads
else:
self.matching_reads = None
self.not_matching_reads = None
reads = traces
matching_reads = []
for read_ in reads:
matches = _common_sub_strings(
str(self.seq).lower(), str(read_.seq), limit)
if not matches:
continue
if len(matches) > 1:
newmatches = [
matches[0],
]
for i, x in enumerate(matches[1:]):
g, f, h = matches[i]
if g + h < x[0] and f + h < x[1]:
newmatches.append(x)
else: # len(matches)==1
newmatches = matches
matching_reads.append(read_)
if len(newmatches) > 1:
ms = []
for m in newmatches:
ms.append(_FeatureLocation(m[0], m[0] + m[2]))
loc = _CompoundLocation(ms)
else:
a, b, c = newmatches[0]
loc = _FeatureLocation(a, a + c)
self.features.append(
_SeqFeature(
loc,
qualifiers={"label": [read_.annotations["filename"]]},
type="trace",
))
return [x.annotations["filename"] for x in matching_reads]
def __init__(
self,
primers,
template,
limit=13,
primerc=1000.0, # nM
saltc=50, # mM
**kwargs):
r'''The Anneal class has to be initiated with at least an iterable of primers and a template.
Parameters
----------
primers : iterable of :class:`Primer` or Biopython SeqRecord like objects
Primer sequences 5'-3'.
template : Dseqrecord
The template sequence 5'-3'.
limit : int, optional
limit length of the annealing part of the primers.
fprimerc : float, optional
Concentration of forward primer in nM, set to 1000.0 nM by default
rprimerc : float, optional
Concentration of reverse primer in nM, set to 1000.0 nM by default
saltc : float, optional
Salt concentration (monovalet cations) :mod:`tmbresluc` set to 50.0 mM by default
Attributes
----------
products: list
A list of Amplicon objects, one for each primer pair that may form a PCR product.
Examples
--------
>>> from pydna.readers import read
>>> from pydna.amplify import Anneal
>>> from pydna.dseqrecord import Dseqrecord
>>> template = Dseqrecord("tacactcaccgtctatcattatctactatcgactgtatcatctgatagcac")
>>> from Bio.SeqRecord import SeqRecord
>>> p1 = read(">p1\ntacactcaccgtctatcattatc", ds = False)
>>> p2 = read(">p2\ngtgctatcagatgatacagtcg", ds = False)
>>> ann = Anneal((p1, p2), template)
>>> print(ann.report())
Template name 51 nt linear:
Primer p1 anneals forward at position 23
<BLANKLINE>
Primer p2 anneals reverse at position 29
>>> ann.products
[Amplicon(51)]
>>> amplicon_list = ann.products
>>> amplicon = amplicon_list.pop()
>>> amplicon
Amplicon(51)
>>> print(amplicon.figure())
5tacactcaccgtctatcattatc...cgactgtatcatctgatagcac3
|||||||||||||||||||||| tm 55.9 (dbd) 60.5
3gctgacatagtagactatcgtg5
5tacactcaccgtctatcattatc3
||||||||||||||||||||||| tm 54.6 (dbd) 58.8
3atgtgagtggcagatagtaatag...gctgacatagtagactatcgtg5
>>> amplicon.annotations['date'] = '02-FEB-2013' # Set the date for this example to pass the doctest
>>> print(amplicon)
Dseqrecord
circular: False
size: 51
ID: 51bp U96-TO06Y6pFs74SQx8M1IVTBiY
Name: 51bp_PCR_prod
Description: pcr product_p1_p2
Number of features: 2
/date=02-FEB-2013
Dseq(-51)
taca..gcac
atgt..cgtg
>>> print(amplicon.program())
<BLANKLINE>
Taq (rate 30 nt/s) 35 cycles |51bp
95.0°C |95.0°C | |Tm formula: Biopython Tm_NN
|_________|_____ 72.0°C |72.0°C|SaltC 50mM
| 03min00s|30s \ ________|______|Primer1C 1.0µM
| | \ 45.4°C/ 0min 2s| 5min |Primer2C 1.0µM
| | \_____/ | |GC 39%
| | 30s | |4-12°C
>>>
'''
self.primers = primers
self.primerc = primerc
self.saltc = saltc
self.template = _copy.deepcopy(template)
self.limit = limit
self.kwargs = defaultdict(str, kwargs)
self._products = None
self.forward_primers = []
self.reverse_primers = []
twl = len(self.template.seq.watson)
tcl = len(self.template.seq.crick)
if self.template.linear:
tw = self.template.seq.watson
tc = self.template.seq.crick
else:
tw = self.template.seq.watson + self.template.seq.watson
tc = self.template.seq.crick + self.template.seq.crick
for p in self.primers:
self.forward_primers.extend((
_Primer(p,
position=tcl - pos - min(self.template.seq.ovhg, 0),
footprint=fp)
for pos, fp in _annealing_positions(str(p.seq), tc, self.limit)
if pos < tcl))
self.reverse_primers.extend((
_Primer(p,
position=pos + max(0, self.template.seq.ovhg),
footprint=fp)
for pos, fp in _annealing_positions(str(p.seq), tw, self.limit)
if pos < twl))
self.forward_primers.sort(key=_operator.attrgetter('position'))
self.reverse_primers.sort(key=_operator.attrgetter('position'),
reverse=True)
for fp in self.forward_primers:
if fp.position - fp._fp >= 0:
start = fp.position - fp._fp
end = fp.position
self.template.features.append(
_SeqFeature(_FeatureLocation(start, end),
type="primer_bind",
strand=1,
qualifiers={
"label": [fp.name],
"ApEinfo_fwdcolor": ["#baffa3"],
"ApEinfo_revcolor": ["#ffbaba"]
}))
else:
start = len(self.template) - fp._fp + fp.position
end = start + fp._fp - len(self.template)
sf = _SeqFeature(_CompoundLocation([
_FeatureLocation(start, len(self.template)),
_FeatureLocation(0, end)
]),
type="primer_bind",
location_operator="join",
qualifiers={
"label": [fp.name],
"ApEinfo_fwdcolor": ["#baffa3"],
"ApEinfo_revcolor": ["#ffbaba"]
})
self.template.features.append(sf)
for rp in self.reverse_primers:
if rp.position + rp._fp <= len(self.template):
start = rp.position
end = rp.position + rp._fp
self.template.features.append(
_SeqFeature(_FeatureLocation(start, end),
type="primer_bind",
strand=-1,
qualifiers={
"label": [rp.name],
"ApEinfo_fwdcolor": ["#baffa3"],
"ApEinfo_revcolor": ["#ffbaba"]
}))
else:
start = rp.position
end = rp.position + rp._fp - len(self.template)
self.template.features.append(
_SeqFeature(_CompoundLocation([
_FeatureLocation(0, end),
_FeatureLocation(start, len(self.template))
]),
type="primer_bind",
location_operator="join",
strand=-1,
qualifiers={"label": [rp.name]}))
