def add_to_record(self, record: Record) -> None:
# track multi-CDS modules to avoid duplication
added_modules = set()
for cds, result in self.cds_results.items():
for module in result.modules:
if module in added_modules:
continue
added_modules.add(module)
domains: List[AntismashDomain] = []
for component in module:
if component.locus == cds.get_name():
domain = result.domain_features[component.domain]
else:
other_cds_results = self.cds_results[
record.get_cds_by_name(component.locus)]
domain = other_cds_results.domain_features[
component.domain]
domains.append(domain)
mod_type = ModuleFeature.types.UNKNOWN
if module.is_nrps():
mod_type = ModuleFeature.types.NRPS
elif module.is_pks():
mod_type = ModuleFeature.types.PKS
feature = ModuleFeature(domains,
mod_type,
complete=module.is_complete(),
starter=module.is_starter_module(),
final=module.is_termination_module(),
iterative=module.is_iterative())
record.add_module(feature)
def from_json(json: Dict[str, Any], record: Record) -> Optional["NRPSPKSDomains"]:
if NRPSPKSDomains.schema_version != json.get("schema_version"):
logging.warning("Schema version mismatch, discarding NRPS PKS domain results")
return None
if record.id != json.get("record_id"):
logging.warning("Record identifier mismatch, discarding NRPS PKS domain results")
return None
cds_results = {}
for cds_name, cds_result in json["cds_results"].items():
cds = record.get_cds_by_name(cds_name)
cds_result = CDSResult.from_json(cds_result)
cds_result.annotate_domains(record, cds)
cds_results[cds] = cds_result
return NRPSPKSDomains(record.id, cds_results)
