def annotate_domains(self, record: Record, cds: CDSFeature) -> None:
""" Adds domain annotations to CDSFeatures and creates ModularDomain
features for all domains found
"""
if not self.domain_hmms:
return
cds.nrps_pks.type = self.type
# generate domain features
self.domain_features = generate_domain_features(cds, self.domain_hmms)
ks_sub = iter(self.ks_subtypes)
for domain, domain_feature in self.domain_features.items():
if domain.hit_id == "PKS_KS":
sub = next(ks_sub)
else:
sub = ""
record.add_antismash_domain(domain_feature)
# update the CDS' NRPS_PKS qualifier
cds.nrps_pks.add_domain(domain, domain_feature.get_name(), sub)
# construct CDSMotif features
if not self.motif_hmms:
return
motif_features = generate_motif_features(cds, self.motif_hmms)
for motif in motif_features:
record.add_cds_motif(motif)
cds.motifs.extend(motif_features)
def annotate_domains(self, record: Record, cds: CDSFeature) -> None:
""" Adds domain annotations to CDSFeatures and creates AntismashDomain
features for all domains found
"""
if not self.domain_hmms:
return
cds.nrps_pks.type = self.type
# generate AntismashDomain features
domain_features = generate_domain_features(record, cds,
self.domain_hmms)
for domain, domain_feature in domain_features.items():
record.add_antismash_domain(domain_feature)
# update the CDS' NRPS_PKS qualifier
cds.nrps_pks.add_domain(domain, domain_feature.get_name())
# construct CDSMotif features
if not self.motif_hmms:
return
motif_features = generate_motif_features(record, cds, self.motif_hmms)
for motif in motif_features:
record.add_cds_motif(motif)
cds.motifs.extend(motif_features)
