def add_parents(args: argparse.Namespace) -> None:
gff = GFF.parse(args.infile)
gff.infer_missing_parents()
for f in gff.select_type("mRNA"):
if len(f.parents) > 0:
continue
if f.attributes is None:
continue
if f.attributes.id is None:
continue
id_ = f.attributes.id
gene_id = f"gene.{id_}"
gene = GFF3Record.infer_from_children([f], id=gene_id, type="gene")
f.add_parent(gene)
gff.add_record(gene)
print("##gff-version 3", file=args.outfile)
for feature in gff.traverse_children(sort=True):
print(feature, file=args.outfile)
return
def deal_with_block(block: List[str], gene_num: int) -> List[GFF3Record]:
parsed: Dict[str, List[GFFRecord[GTFAttributes]]] = dict()
for line in block:
rec = GFFRecord.parse(line, attr=GTFAttributes)
if rec.type in parsed:
parsed[rec.type].append(rec)
else:
parsed[rec.type] = [rec]
assert len(parsed["gene"]) == 1
assert len(parsed["similarity"]) == 1
gene_parsed = parsed["gene"][0]
similarity_parsed = parsed["similarity"][0]
custom: Dict[str, str] = dict()
if similarity_parsed.attributes is not None:
custom["query"] = similarity_parsed.attributes.custom["Query"]
if gene_parsed.attributes is not None:
custom["identity"] = gene_parsed.attributes.custom["identity"]
custom["similarity"] = gene_parsed.attributes.custom["similarity"]
gene = GFF3Record(
parsed["gene"][0].seqid,
"exonerate",
type="gene",
start=parsed["gene"][0].start,
end=parsed["gene"][0].end,
score=parsed["gene"][0].score,
strand=parsed["gene"][0].strand,
phase=parsed["gene"][0].phase,
attributes=GFF3Attributes(
id=f"gene{gene_num}",
custom=custom,
)
)
cdss = [
GFF3Record(
e.seqid,
"exonerate",
"CDS",
e.start,
e.end,
e.score,
e.strand,
e.phase,
attributes=GFF3Attributes(
id=f"CDS{gene_num}",
parent=[f"mRNA{gene_num}"],
custom=(e.attributes.custom
if e.attributes is not None
else None)
)
)
for e
in parsed["exon"]
]
for c in cdss:
if gene.attributes is not None:
# This is safe because we added attributes.
assert c.attributes is not None
c.attributes.custom["query"] = gene.attributes.custom["query"]
mrna = GFF3Record.infer_from_children(
cdss,
id=f"mRNA{gene_num}",
seqid=gene.seqid,
source="exonerate",
type="mRNA",
strand=gene.strand,
score=gene.score,
)
mrna.add_parent(gene)
if gene.attributes is not None:
# This is safe because infer_from_children adds an ID to attributes.
assert mrna.attributes is not None
if gene.attributes.id is not None:
mrna.attributes.parent = [gene.attributes.id]
mrna.attributes.custom["query"] = gene.attributes.custom["query"]
out = [gene, mrna]
out.extend(cdss)
return out