def make_new_subsequence(
seqid: str, start: int, end: int, gene_itree: IntervalTree,
hint_itree: Optional[IntervalTree], gene_features: Sequence[GFFRecord],
hint_features: Optional[Sequence[GFFRecord]],
seq: SeqRecord) -> Tuple[str, SeqRecord, GFF, Optional[GFF]]:
gene_intervals = gene_itree[start:end]
min_gene_start = min(f.begin for f in gene_intervals) - 10
max_gene_end = max(f.end for f in gene_intervals) + 10
start = min([start, min_gene_start])
if start < 0:
start = 0
end = max([end, max_gene_end])
if end > len(seq):
end = len(seq)
if hint_itree is None:
hint_intervals = None
else:
hint_intervals = [
i for i in hint_itree[start:end]
if i.begin >= start and i.end <= end
]
name = f"{seqid}:{start}-{end}"
subseq = FeatureLocation(start, end, 1).extract(seq)
subseq.id = name
subseq.name = name
subseq.description = name
subgenes = GFF([gene_features[i.data] for i in gene_intervals])
subgenes_shifted = shift_gff(subgenes, name, start)
if hint_intervals is None or hint_features is None:
subhints_shifted = None
else:
subhints = GFF([hint_features[i.data] for i in hint_intervals])
subhints_shifted = shift_gff(subhints, name, start)
return name, subseq, subgenes_shifted, subhints_shifted
