def from_json(data: Dict, _record: secmet.Record) -> "ThiopeptideMotif":
""" Builds a ThiopeptideMotif from a JSON object"""
args = []
args.append(serialiser.location_from_json(data["location"]))
for arg_name in ["core", "leader", "locus_tag", "monoisotopic_mass",
"molecular_weight", "alternative_weights",
"peptide_subclass", "score", "rodeo_score", "macrocycle",
"tail", "core_features", "mature_weights",
"amidation"]:
args.append(data[arg_name])
# pylint doesn't do well with the splat op, so don't report errors
return ThiopeptideMotif(*args) # pylint: disable=no-value-for-parameter
def convert(self, location, expected_type=FeatureLocation):
assert isinstance(location, expected_type)
before_string = str(location)
print(before_string) # just for help when debugging a failing test
after_string = serialiser.location_to_json(location)
assert isinstance(after_string, str)
assert before_string == after_string
new_location = serialiser.location_from_json(after_string)
assert isinstance(new_location, expected_type)
return new_location
def from_json(data: Dict[str, Any]) -> "LassopeptideMotif":
""" Converts a JSON representation of the motif back into an instance
of LassopeptideMotif
"""
args = []
args.append(serialiser.location_from_json(data["location"]))
for arg_name in [
"leader", "core", "tail", "locus_tag", "monoisotopic_mass",
"molecular_weight", "cut_mass", "cut_weight", "num_bridges",
"peptide_subclass", "score", "rodeo_score", "macrolactam"
]:
args.append(data[arg_name])
# pylint doesn't do well with the splat op, so don't report errors
return LassopeptideMotif(*args) # pylint: disable=no-value-for-parameter
def from_json(json: Dict[str, Any], record: secmet.Record) -> "SactiResults":
if json.get("schema_version") != SactiResults.schema_version:
logging.warning("Discarding Sactipeptide results, schema version mismatch")
return None
results = SactiResults(json["record_id"])
for locus, motifs in json["motifs"].items():
for motif in motifs:
results.motifs_by_locus[locus].append(SactipeptideMotif.from_json(motif))
results.clusters = {int(key): set(val) for key, val in json["clusters"].items()}
for location, name in json["new_cds_features"]:
loc = serialiser.location_from_json(location)
cds = all_orfs.create_feature_from_location(record, loc, label=name)
results.new_cds_features.add(cds)
return results
def from_json(data: Dict[str, Any]) -> "LanthipeptideMotif":
""" Converts a JSON representation of the motif back into an instance
of LanthipeptideMotif
"""
args = []
args.append(serialiser.location_from_json(data["location"]))
args.append(data["core"])
for arg_name in [
"leader", "locus_tag", "monoisotopic_mass", "molecular_weight",
"alternative_weights", "lan_bridges", "peptide_subclass",
"score", "rodeo_score", "aminovinyl_group", "chlorinated",
"oxygenated", "lactonated"
]:
args.append(data[arg_name])
# pylint doesn't do well with the splat op, so don't report errors
return LanthipeptideMotif(*args) # pylint: disable=no-value-for-parameter
def add_to_record(self, record: Record) -> None:
db_version = pfamdb.get_db_version_from_path(self.database)
for i, hit in enumerate(self.hits):
pfam_feature = PFAMDomain(serialiser.location_from_json(
hit["location"]),
description=hit["description"],
protein_start=hit["protein_start"],
protein_end=hit["protein_end"])
for key in [
"label", "locus_tag", "domain", "evalue", "score",
"translation", "db_xref"
]:
setattr(pfam_feature, key, hit[key])
pfam_feature.tool = self.tool
pfam_feature.database = db_version
pfam_feature.detection = "hmmscan"
pfam_feature.domain_id = "{}_{}_{:04d}".format(
self.tool, pfam_feature.locus_tag, i + 1)
record.add_pfam_domain(pfam_feature)
def from_json(json: Dict[str, Any]) -> "SactipeptideMotif":
""" Regenerate an instance of the class from a JSON representation """
location = serialiser.location_from_json(json["location"])
return SactipeptideMotif(location, json["name"], json["score"],
json["leader"], json["core"])