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
def trnascan2gff(args: argparse.Namespace) -> None:
genes: List[GFF3Record] = []
matches = TRNAScanRecord.from_file(args.txt)
sses = TRNAScanSS.from_file(args.ss)
num_to_ss = {f"{r.seqid}.{r.num}": r for r in sses}
for match in matches:
ss = num_to_ss[f"{match.seqid}.{match.num}"]
if match.note is not None and "pseudo" in match.note:
type_ = "pseudogene"
else:
type_ = "tRNA_gene"
gene = match_to_gene(match, args.source, type=type_)
genes.append(gene)
trna = match_to_trna(
match,
ss,
args.source,
type_map=TYPE_MAP,
parents=[gene]
)
genes.append(trna)
introns = match_to_introns(
match,
args.source,
type="tRNA_intron",
parents=[trna]
)
genes.extend(introns)
anticodon = match_to_anticodon(
match,
ss,
args.source,
type="anticodon",
parents=[trna]
)
genes.append(anticodon)
for record in GFF(genes).traverse_children(sort=True):
print(record, file=args.outfile)
return
def prune_gff(records: Set[GFF3Record]) -> GFF:
new_records: Dict[GFF3Record, GFF3Record] = dict()
# Create a mapping from old to new objects
# to preserve hashing/lookup capability
for record in records:
new_record = deepcopy(record)
new_record.children = []
new_record.parents = []
new_records[record] = new_record
for record in records:
new_record = new_records[record]
for parent in record.parents:
# Don't add parents that shouldn't be in this set
if parent not in records:
continue
new_parent = new_records[cast(GFF3Record, parent)]
new_record.add_parent(new_parent)
for child in record.children:
# Don't add children that shouldn't be in this set
if child not in records:
continue
new_child = new_records[cast(GFF3Record, child)]
new_record.add_child(new_child)
# Update the record parent IDS to reflect the new split set.
if new_record.attributes is not None:
new_record.attributes.parent = []
for parent in new_record.parents:
# This should always be true, as the ID is necessary
assert parent.attributes is not None
assert parent.attributes.id is not None
new_record.attributes.parent.append(parent.attributes.id)
else:
# This necessarily should be true, since attributes define parent
# child relationships.
assert len(new_record.children) == 0
assert len(new_record.parents) == 0
return GFF(list(new_records.values()))
def rnammer2gff(args: argparse.Namespace) -> None:
records: List[GFFRecord] = []
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 = GFFRecord.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 = GFFAttributes()
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 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)
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
