def get_blocks(
seqs: Dict[str, SeqRecord], genes: GFF, hints: Optional[GFF], pad: int,
merge: bool, target_ids: Optional[Set[str]]
) -> Iterator[Tuple[str, SeqRecord, GFF, Optional[GFF]]]:
hints_by_seqid = fmap(groupby_seqid, hints)
for seqid, gene_features in groupby_seqid(
genes.select_type("gene")).items():
if seqid not in seqs:
continue
gene_itree = IntervalTree(gffrecords_to_intervals(gene_features))
try:
hint_itree = fmap(
IntervalTree,
fmap(gffrecords_to_intervals,
fmap(lambda h: h.get(seqid, []), hints_by_seqid)))
except ValueError as e:
if hints_by_seqid is not None:
print(seqid, hints_by_seqid.get(seqid, []))
raise e
if target_ids is None:
target_features: List[GFFRecord] = gene_features
else:
target_features = subset_features_by_id(gene_features, target_ids)
if merge:
block_iter = merge_overlapping(target_features, pad)
else:
block_iter = pad_features(target_features, pad)
seen: Set[Tuple[int, int]] = set()
for start, end in block_iter:
if (start, end) in seen:
continue
else:
seen.add((start, end))
yield make_new_subsequence(
seqid,
start,
end,
gene_itree,
hint_itree,
gene_features,
fmap(lambda h: h.get(seqid, []), hints_by_seqid),
seqs[seqid],
)
return
def split_gffs(gff: GFF, group_level: str) -> Tuple[GFF, GFF]:
keep: Set[GFF3Record] = set()
drop: Set[GFF3Record] = set()
for mrna in gff.select_type(group_level):
if mrna.attributes is None:
should_keep = True
elif "should_exclude" in mrna.attributes.custom:
should_keep = False
else:
should_keep = True
if should_keep:
keep.update(gff.traverse_children([mrna]))
keep.update(gff.traverse_parents([mrna]))
else:
drop.update(gff.traverse_children([mrna]))
drop.update(gff.traverse_parents([mrna]))
kept = prune_gff(keep)
dropped = prune_gff(drop)
return kept, dropped
def main():
args = cli(sys.argv[0], sys.argv[1:])
rows = list()
for line in args.infile:
if line.startswith("#"):
continue
record = GFFRecord.parse(line)
record.attributes.id = record.attributes.name
record.attributes.name = None
record.attributes.custom = {}
rows.append(record)
gff = GFF(rows)
gff.infer_missing_parents()
counter = 1
for mrna in gff.select_type("mRNA"):
if len(mrna.children) < 2:
continue
region = deepcopy(mrna)
region.type = "repeat_region"
region.attributes.id = f"repeat_region{counter}"
region.attributes.ontology_term = ["SO:0000657"],
mrna.type = "helitron"
mrna.parents = [region]
mrna.attributes.parent = [region.attributes.id]
mrna.attributes.id = f"helitron{counter}"
mrna.attributes.ontology_term = ["SO:0000544", "SO:helitron"]
mrna.attributes.custom = {}
flank3 = [c for c in mrna.children
if c.attributes.id.endswith(".3")][0]
flank5 = [c for c in mrna.children
if c.attributes.id.endswith(".5.1")][0]
flank3.type = "three_prime_flanking_region"
flank3.attributes.ontology_term = [
"SO:0001417",
"SO:three_prime_flanking_region",
"SO:0000364",
"SO:transposable_element_flanking_region"
]
flank3.attributes.id = None
flank3.attributes.parent = [mrna.attributes.id]
flank5.type = "five_prime_flanking_region"
flank5.attributes.ontology_term = [
"SO:0001416",
"SO:five_prime_flanking_region",
"SO:0000364",
"SO:transposable_element_flanking_region"
]
flank5.attributes.id = None
flank5.attributes.parent = [mrna.attributes.id]
mrna.source = flank5.source
print(region, file=args.outfile)
print(mrna, file=args.outfile)
if mrna.strand == Strand.MINUS:
print(flank3, file=args.outfile)
print(flank5, file=args.outfile)
else:
print(flank5, file=args.outfile)
print(flank3, file=args.outfile)
counter += 1
return