from copy import deepcopy
from Bio.SeqRecord import SeqRecord
from ..Fragment import Fragment
try:
# Biopython <1.78
from Bio.Alphabet import DNAAlphabet
has_dna_alphabet = True
except ImportError:
# Biopython >=1.78
has_dna_alphabet = False
from ...biotools import set_record_topology, crop_record_with_saddling_features
[docs]class HomologousFragment(Fragment):
[docs] @staticmethod
def from_biopython_record(biopython_record):
"""Convert a Biopython record into a HomologousFragment (class change).
"""
new_record = deepcopy(biopython_record)
new_record.original_part = biopython_record
new_record.__class__ = HomologousFragment
return new_record
[docs] def circularized(
self, homology_checker, annotate_homology=False, annotation_type="homology",
):
"""Return the Biopython record obtained by cirularizing the result.
Only works if the left and right sticky ends are compatible. The
return is a simple Biopython record where the sticky end has been
integrated in the sequence.
"""
double_self = self.assemble_with(
self,
homology_checker=homology_checker,
annotate_homology=True,
annotation_type="homology",
)
def only_parts_indicators(feature):
return feature.qualifiers.get("indicates_part", False)
result = crop_record_with_saddling_features(
record=double_self,
start=len(self),
end=len(double_self),
filters=(only_parts_indicators,),
)
result.__class__ = SeqRecord
set_record_topology(result, "circular")
return result
def _push_source_features(self, homology_size, side="left"):
"""Relocate one end of a feature so it won't be cut out when the
fragment is cropped."""
if side == "left":
maximum = len(self) - homology_size
for f in self.features:
if f.qualifiers.get("is_source", False):
f.location.start = min(f.location.start, maximum)
f.location.end = min(f.location.end, maximum)
if side == "right":
for f in self.features:
if f.qualifiers.get("is_source", False):
f.location.start = max(f.location.start, homology_size)
f.location.end = max(f.location.end, homology_size)
[docs] def will_clip_in_this_order_with(self, other_fragment, homology_checker):
"""Return whether the fragment will assemble with anoter via homology
recombination.
homology_checker should be an HomologyChecker instance definining the
homology conditions.
"""
homology_size = homology_checker.find_end_homologies(self, other_fragment)
return homology_size > 0
[docs] def assemble_with(
self,
fragment,
homology_checker,
annotate_homology=True,
annotation_type="homology",
):
"""Return the fragment resulting from the assembly of this fragment
with another, in that order.
Parameters
----------
fragment
The other parameter to assemble with.
homology_checker
An HomologyChecker instance definining the homology conditions.
annotate_homology
If true, homologies will have an annotation in the final, predicted
construct records.
"""
homology_size = homology_checker.find_end_homologies(self, fragment)
if homology_size == 0:
raise ValueError(
"Only fragments with end homologies ends can be assembled."
)
new_self = deepcopy(self)
new_fragment = deepcopy(fragment)
new_self._push_source_features(homology_size, side="left")
new_fragment._push_source_features(homology_size, side="right")
if annotate_homology:
feature = self.create_homology_annotation(
start=0,
end=homology_size,
annotation_type=annotation_type,
label="homology",
)
new_fragment.features.append(feature)
def only_parts_indicators(feature):
return feature.qualifiers.get("indicates_part", False)
self_subrecord = crop_record_with_saddling_features(
record=self,
start=0,
end=len(self) - homology_size,
filters=(only_parts_indicators,),
)
assert len(self_subrecord) == len(self[:-homology_size])
result = self_subrecord + new_fragment
result.__class__ = HomologousFragment
return result
[docs] @staticmethod
def assemble(
fragments, homology_checker, circularize=False, annotate_homologies=False,
):
"""Return the record obtained by assembling the fragments.
Parameters
----------
fragments
List of HomologousFragments to assemble.
homology_checker
An HomologyChecker instance definining the homology conditions.
circularize
True to also assemble the end flanks of the final construct.
annotate_homologies
If true, homologies will have an annotation in the final, predicted
construct records.
"""
result = fragments[0]
for fragment in fragments[1:]:
result = result.assemble_with(
fragment=fragment,
homology_checker=homology_checker,
annotate_homology=annotate_homologies,
)
if circularize:
result = result.circularized(
annotate_homology=annotate_homologies,
homology_checker=homology_checker,
)
if has_dna_alphabet: # Biopython <1.78
result.seq.alphabet = DNAAlphabet()
result.annotations["molecule_type"] = "DNA"
return result
