def rnammer2gff(args: argparse.Namespace) -> None:
records: List[GFF3Record] = []
for line in args.infile:
if line.startswith("#"):
continue
sline = line.strip().split("\t")
rrna_type = sline[8]
new_type = TYPE_MAP[args.kingdom][rrna_type.lower()]
sline[1] = args.source
sline[2] = new_type
sline[8] = "."
rna_record = cast(GFF3Record, GFF3Record.parse("\t".join(sline)))
gene_record = deepcopy(rna_record)
gene_record.type = "rRNA_gene"
gene_record.add_child(rna_record)
records.append(gene_record)
records.append(rna_record)
num = 0
for record in GFF(records).traverse_children(sort=True):
if record.attributes is None:
attr = GFF3Attributes()
record.attributes = attr
else:
attr = record.attributes
if record.type == "rRNA_gene":
num += 1
attr.id = f"rRNA_gene{num}"
else:
attr.id = f"rRNA{num}"
attr.parent = [
p.attributes.id for p in record.parents
if (p.attributes is not None and p.attributes.id is not None)
]
print(record, file=args.outfile)
return
def add_antifam(args: argparse.Namespace) -> None:
antifam_records: Dict[str, List[DomTbl]] = defaultdict(list)
for rec in DomTbl.from_file(args.antifam):
antifam_records[rec.target_name].append(rec)
for line in args.infile:
sline = line.strip()
if sline.startswith("#") or sline == "":
args.outfile.write(line)
continue
record = GFF3Record.parse(sline)
if record.attributes is None:
print(record, file=args.outfile)
continue
field = record.attributes.get(args.field, None)
if field is None:
print(record, file=args.outfile)
continue
if str(field) not in antifam_records:
print(record, file=args.outfile)
continue
dbxrefs = []
matches = []
for antifam_record in antifam_records[str(field)]:
dbxrefs.append(f"AntiFam:{antifam_record.query_acc}")
matches.append(
f"{antifam_record.query_acc} {antifam_record.full_evalue} "
f"{antifam_record.full_score} {antifam_record.domain_score} "
f"{antifam_record.hmm_from} {antifam_record.hmm_to} "
f"{antifam_record.ali_from} {antifam_record.ali_to}")
record.attributes.dbxref.extend(dbxrefs)
record.attributes.custom["antifam_match"] = ",".join(matches)
print(record, file=args.outfile)
return