def result_vec_to_motif(query: CDSFeature, result: Lassopeptide) -> Prepeptide:
""" Converts a Lassopeptide to a Prepeptide """
core = result.core
tail = result.c_cut
if tail:
core = result.core[:-len(tail)]
weight = result.molecular_weight
cut_mass = result.cut_mass
cut_weight = result.cut_weight
feature = Prepeptide(query.location,
"lassopeptide",
core,
query.get_name(),
"lassopeptides",
peptide_subclass=result.lasso_class,
score=result.score,
monoisotopic_mass=result.monoisotopic_mass,
molecular_weight=weight,
leader=result.leader,
tail=tail)
feature.detailed_information = LassoQualifier(result.rodeo_score,
result.number_bridges,
result.macrolactam, cut_mass,
cut_weight)
return feature
def result_vec_to_feature(orig_feature: CDSFeature, res_vec: Lanthipeptide) -> Prepeptide:
""" Generates a Prepeptide feature from a CDSFeature and a Lanthipeptide
Arguments:
orig_feature: the CDSFeature the lanthipeptide was found in
res_vec: the Lanthipeptide instance that was calculated
Returns:
a Prepeptide instance
"""
assert res_vec.leader is not None
feature = Prepeptide(orig_feature.location, "lanthipeptide", res_vec.core,
orig_feature.get_name(), "lanthipeptides", res_vec.lantype, res_vec.score,
res_vec.monoisotopic_mass, res_vec.molecular_weight,
res_vec.alternative_weights, res_vec.leader)
qual = LanthiQualifier(res_vec.number_of_lan_bridges,
res_vec.rodeo_score, res_vec.aminovinyl_group,
res_vec.chlorinated, res_vec.oxygenated, res_vec.lactonated)
feature.detailed_information = qual
return feature
def from_json(json: Dict[str, Any], record: Record) -> Optional["LanthiResults"]:
if json.get("schema_version") != LanthiResults.schema_version:
logging.warning("Discarding Lanthipeptide results, schema version mismatch")
return None
results = LanthiResults(json["record_id"])
for locus, motifs in json["motifs"].items():
for motif in motifs:
results.motifs_by_locus[locus].append(Prepeptide.from_json(motif))
results.clusters = {int(key): set(val) for key, val in json["protoclusters"].items()}
for location, name in json["new_cds_features"]:
cds = all_orfs.create_feature_from_location(record, location_from_string(location), label=name)
results.new_cds_features.add(cds)
return results
def test_compound_location(self):
old = Prepeptide(CompoundLocation(
[FeatureLocation(10, 50, 1),
FeatureLocation(130, 180, 1)],
operator="join"),
peptide_class="test_class",
core="coreseq...",
locus_tag="loc",
tool="test tool",
leader="10chleader",
tail="10chartail")
leader, core, tail = old.to_biopython()
assert leader.location.start == 10
assert leader.location.end == 40
assert isinstance(core.location, CompoundLocation)
assert core.location.start == 40
assert core.location.end == 150
assert tail.location.start == 150
assert tail.location.end == 180
new = Prepeptide.from_biopython(core)
assert str(new.location) == str(old.location)
def test_basic_conversion(self):
old = Prepeptide(FeatureLocation(5, 95),
peptide_class="test_class",
core="coreseq...",
locus_tag="loc",
tool="test tool",
peptide_subclass="test_subclass",
score=20.4,
monoisotopic_mass=6.7,
molecular_weight=0.5,
alternative_weights=[5.2, 6.7, 20.5],
leader="leaderseq.",
tail="tailseq...")
leader, core, tail = old.to_biopython()
assert leader.location.start == 5
assert leader.location.end == 35
assert leader.qualifiers["prepeptide"] == ["leader"]
assert core.location.start == 35
assert core.location.end == 65
assert core.qualifiers["prepeptide"] == ["core"]
assert tail.location.start == 65
assert tail.location.end == 95
assert tail.qualifiers["prepeptide"] == ["tail"]
with self.assertRaisesRegex(
ValueError, "can only be reconstructed from core feature"):
Prepeptide.from_biopython(leader)
with self.assertRaisesRegex(
ValueError, "can only be reconstructed from core feature"):
Prepeptide.from_biopython(tail)
new = Prepeptide.from_biopython(core)
assert isinstance(new, Prepeptide)
assert str(new.location) == str(old.location)
assert new.peptide_class == old.peptide_class
assert new.core == old.core
assert new.locus_tag == old.locus_tag
assert new.peptide_subclass == old.peptide_subclass
assert new.score == old.score
assert new.monoisotopic_mass == old.monoisotopic_mass
assert new.molecular_weight == old.molecular_weight
assert new.alternative_weights == old.alternative_weights
assert new.leader == old.leader
assert new.tail == old.tail