def __getitem__(self, sl):
answer = Dseqrecord(_copy.copy(self))
answer.seq = self.seq.__getitem__(sl)
# answer.seq.alphabet = self.seq.alphabet
sl_start = sl.start or 0 # 6
sl_stop = sl.stop or len(answer.seq) # 1
if self.linear or sl_start < sl_stop:
answer.features = super().__getitem__(sl).features
elif self.circular and sl_start > sl_stop:
answer.features = self.shifted(sl_start).features
answer.features = [
f for f in answer.features
if f.location.parts[-1].end.position <= answer.seq.length
]
else:
x = len(answer.seq)
answer.features = self.shifted(sl_start)[:x].features
# answer.features = [f for f in answer.features if f.location.parts == sorted(f.location.parts)]
identifier = "part_{id}".format(id=self.id)
if answer.features:
sf = max(answer.features, key=len) # default
if "label" in sf.qualifiers:
identifier = " ".join(sf.qualifiers["label"])
elif "note" in sf.qualifiers:
identifier = " ".join(sf.qualifiers["note"])
answer.id = _identifier_from_string(identifier)[:16]
answer.name = _identifier_from_string(
"part_{name}".format(name=self.name))[:16]
return answer
def __getitem__(self, sl):
answer = Dseqrecord(_copy.copy(self))
answer.seq = self.seq.__getitem__(sl)
answer.seq.alphabet = self.seq.alphabet
sl_start = sl.start or 0
sl_stop = sl.stop or len(answer.seq)
if self.linear or sl_start < sl_stop:
answer.features = super().__getitem__(sl).features
else:
answer.features = self.shifted(sl_stop).features
answer.features = [
f for f in answer.features
if f.location.parts == sorted(f.location.parts)
]
identifier = "part_{id}".format(id=self.id)
if answer.features:
sf = max(answer.features, key=len) # default
if "label" in sf.qualifiers:
identifier = " ".join(sf.qualifiers["label"])
elif "note" in sf.qualifiers:
identifier = " ".join(sf.qualifiers["note"])
answer.id = _identifier_from_string(identifier)[:16]
answer.name = answer.id
return answer
def extract(self, parent_sequence):
answer = super().extract(parent_sequence)
identifier = "feat_{}".format(parent_sequence.id)
if "label" in self.qualifiers:
identifier = " ".join(self.qualifiers["label"])
elif "note" in self.qualifiers:
identifier = " ".join(self.qualifiers["note"])
answer.name = answer.id = _identifier_from_string(identifier)[:16]
return answer
def __getitem__(self, index):
from pydna.utils import (
identifier_from_string as _identifier_from_string,
) # TODO: clean this up
answer = super().__getitem__(index)
if len(answer) < 2:
return answer
identifier = "part_{id}".format(id=self.id)
if answer.features:
sf = max(answer.features, key=len) # default
if "label" in sf.qualifiers:
identifier = " ".join(sf.qualifiers["label"])
elif "note" in sf.qualifiers:
identifier = " ".join(sf.qualifiers["note"])
answer.id = _identifier_from_string(identifier)[:16]
answer.name = _identifier_from_string(f"part_{self.name}")[:16]
return answer
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