def add_to_record(self, record: Record) -> None:
for feature in self.new_cds_features:
record.add_cds_feature(feature)
for motifs in self.motifs_by_locus.values():
for motif in motifs:
record.add_cds_motif(motif)
def add_to_record(self, record: secmet.Record) -> None:
""" Adds any relevant result constructions to the record """
for features in self.cds_features.values():
for cds in features:
record.add_cds_feature(cds)
for motif in self.motifs:
record.add_cds_motif(motif)
def add_to_record(self, record: Record) -> None:
for feature in self.new_cds_features:
record.add_cds_feature(feature)
motifs_added: Set[str] = set()
for motifs in self.motifs_by_locus.values():
for motif in motifs:
if motif.get_name() not in motifs_added:
record.add_cds_motif(motif)
motifs_added.add(motif.get_name())
def annotate_domains(record: Record) -> None:
""" Annotates NRPS/PKS domains on CDS features. The `nrps_pks` member of
each feature will be updated, along with creating CDSMotif features
when relevant.
Arguments:
record: the secmet.Record of which to annotate CDS features
Returns:
None
"""
cds_within_clusters = record.get_cds_features_within_clusters()
assert cds_within_clusters # because every cluster should have genes
fasta = get_fasta_from_features(cds_within_clusters)
cds_domains = find_domains(fasta, record)
cds_motifs = find_ab_motifs(fasta)
for cds in cds_within_clusters:
cds_name = cds.get_name()
# gather domains and classify
domains = cds_domains.get(cds_name)
if not domains:
continue
domain_type = classify_feature([domain.hit_id for domain in domains])
cds.nrps_pks.type = domain_type
for domain in domains:
cds.nrps_pks.add_domain(domain)
# construct motif features
motifs = cds_motifs.get(cds_name)
if not motifs:
continue
motif_features = generate_motif_features(record, cds, motifs)
for motif in motif_features:
record.add_cds_motif(motif)
cds.motifs.extend(motif_features)
def strip_record(record: Record) -> None:
""" Discard antismash specific features and feature qualifiers """
logging.debug(
"Stripping antiSMASH features and annotations from record: %s",
record.id)
record.clear_clusters()
record.clear_superclusters()
record.clear_subregions()
record.clear_regions()
record.clear_antismash_domains()
record.clear_pfam_domains()
# clean up antiSMASH-created CDSMotifs, but leave the rest
motifs = list(record.get_cds_motifs())
record.clear_cds_motifs()
for motif in motifs:
if not motif.created_by_antismash:
record.add_cds_motif(motif)
# clean up antiSMASH annotations in CDS features
for feature in record.get_cds_features():
feature.sec_met = SecMetQualifier()
feature.gene_functions.clear()
