def write_gff(
gff: GFF,
outfile: TextIO,
) -> None:
print("#gff-version 3", file=outfile)
for feature in gff.traverse_children(sort=True, breadth=True):
print(feature, file=outfile)
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 shift_gff(gff: GFF, seqid: str, start: int) -> GFF:
out = list()
for feature in gff.traverse_children(sort=True):
f = deepcopy(feature)
f.start -= start
f.end -= start
f.seqid = seqid
if f.attributes is not None:
if f.attributes.id is not None:
f.attributes.id = seqid + "_" + f.attributes.id
new_parents = []
for parent in f.attributes.parent:
new_parent = seqid + "_" + parent
new_parents.append(new_parent)
f.attributes.parent = new_parents
out.append(f)
return GFF(out)