"""Useful functions built on top of the DnaCauldron classes to simplify the
most common operations."""
import os
from Bio import Restriction
from ..AssemblyMix import (
RestrictionLigationMix,
generate_type2s_restriction_mix
)
from ..Filter import FragmentSetContainsPartsFilter, NoRestrictionSiteFilter
from ..Fragment.StickyEndFragment import StickyEnd
from ..biotools import (
sequence_to_biopython_record,
annotate_record,
load_record,
autoselect_enzyme,
)
[docs]def list_overhangs_from_record_annotations(rec, with_locations=False):
"""Return a least of the (probable) overhangs used building the construct
"""
def is_overhang(h):
return (len(h) == 4) and (set(h) <= set("ATGC"))
if isinstance(rec, str):
rec = load_record(rec)
rec.seq = rec.seq.upper()
overhangs = [
(f.location.start, "".join(f.qualifiers.get("label", "")))
for f in sorted(
rec.features,
key=lambda f: 0 if (f.location is None) else f.location.start,
)
if f.type == "homology"
]
overhangs = [(start, o) for start, o in overhangs if is_overhang(o)]
if overhangs == []:
# try to identify overhangs another way
part_locs = []
for f in rec.features:
if f.type == "misc_feature":
note = "".join(f.qualifiers.get("note", ""))
if note.startswith("From "):
part_locs.append(
(int(f.location.start), int(f.location.end))
)
part_locs = [(0, 0)] + sorted(part_locs) + [(len(rec), len(rec))]
seq = str(rec.seq)
inter_parts = [
(f1[1], seq[f1[1] : f2[0]])
for f1, f2 in zip(part_locs, part_locs[1:])
]
overhangs = [(start, o) for start, o in inter_parts if is_overhang(o)]
if with_locations:
return overhangs
else:
return [o for start, o in overhangs]
[docs]def substitute_overhangs(
record, substitutions, enzyme="auto", return_linear_parts=False
):
"""Replace the record's subsequence that corresponds to overhangs.
This is practical to change the position of a part in a Type-2S
assembly standard
Examples
----------
>>> new_record = replace_overhangs(record, {'ATGC': 'CTCG'})
Parameters
----------
record
A Biopython record whose internal sequence needs to be replaced
substitutions
A dict {overhang: new_overhang} of which overhangs must be replaced
enzyme
Either 'BsmBI', 'BsaI', etc. or just "auto" for automatic selection.
"""
if enzyme == "auto":
enzyme = autoselect_enzyme([record])
mix = generate_type2s_restriction_mix(parts=[record], enzyme=enzyme)
fragments = [f for f in mix.fragments if not f.is_reversed]
for fragment in fragments:
left = fragment.seq.left_end
if str(left).upper() in substitutions:
end = StickyEnd(substitutions[str(left).upper()], left.strand)
fragment.seq.left_end = end
right = fragment.seq.right_end
if str(right).upper() in substitutions:
end = StickyEnd(substitutions[str(right).upper()], right.strand)
fragment.seq.right_end = end
new_mix = RestrictionLigationMix(
fragments=fragments, enzymes=[enzyme], fragment_filters=()
)
if return_linear_parts:
fragment = [f for f in new_mix.filtered_fragments if not f.is_reversed][
0
]
site = sequence_to_biopython_record(mix.enzymes[0].site)
annotate_record(site, label="%s" % enzyme)
rev_site = site.reverse_complement()
annotate_record(site, label="%s" % enzyme)
left_end = sequence_to_biopython_record(str(fragment.seq.left_end))
right_end = sequence_to_biopython_record(str(fragment.seq.right_end))
for end in left_end, right_end:
annotate_record(end, (0, len(end), 0), label="overhang")
return site + "A" + left_end + fragment + right_end + "A" + rev_site
else:
return list(new_mix.compute_circular_assemblies())[0]
[docs]def list_digestion_overhangs(records, enzyme="auto", parts_only=True):
"""List all overhangs created by restriction in the provided records.
Warning: only overhangs on non-reversed fragments are returned, not
their reverse-complement.
Parameters
----------
records
List of records
enzyme
Either 'BsmBI', 'BsaI', etc. or just "auto" for automatic selection.
parts_only
If true, overhangs created by restriction which are not on a part
(so for instance inside a backbone) will be ignored.
"""
if enzyme == "auto":
enzyme = autoselect_enzyme(records)
mix = generate_type2s_restriction_mix(parts=records, enzyme=enzyme)
return mix.list_overhangs(filtered_fragments_only=parts_only)
