def hints(args: argparse.Namespace) -> None:
gff_to_hints = get_hints_map(args)
type_to_trim = get_trim_map(args)
type_to_priority = get_priority_map(args)
gff = GFF.parse(args.infile)
for parent in gff.select_type(args.group_level):
group_name = fmap(lambda a: getattr(a, "id"), parent.attributes)
if group_name is None:
raise GPMissingID(
"One of the selected records doesn't have an ID. "
f"The offending line is {parent}.")
for feature in gff.traverse_children([parent]):
hint_feature = transform_child(
feature,
group_name,
gff_to_hints,
type_to_trim,
type_to_priority,
args.source,
args.priority,
)
if hint_feature is not None:
print(hint_feature, file=args.outfile)
return
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 main():
args = cli(sys.argv[0], sys.argv[1:])
gff = GFF.parse(args.infile)
itree = gff_to_itree(gff.select_type(args.group_level))
for mrna in gff.select_type(args.group_level):
if mrna.attributes is None:
mrna.attributes = GFF3Attributes()
failed_antifam = "antifam_match" in mrna.attributes.custom
if failed_antifam:
mrna.attributes.custom["is_unreliable"] = "true"
mrna.attributes.custom["should_exclude"] = "true"
length, aligned = deal_with_kids(
gff.traverse_children([mrna]),
args.type,
0,
defaultdict(int)
)
coverages = find_coverages(aligned, length)
supported = [k for k, v in coverages.items() if v > args.min_cov]
not_supported = ((len(supported) == 0) or
(all(s in args.exclude for s in supported)))
is_novel = is_novel_locus(mrna, itree, args.threshold)
if not_supported:
mrna.attributes.custom["is_unreliable"] = "true"
if not is_novel:
mrna.attributes.custom["should_exclude"] = "true"
if args.stats:
line = coverages
line["id"] = mrna.attributes.id
line["length"] = length
line["is_supported"] = not not_supported
line["is_novel_locus"] = is_novel
line["antifam_match"] = failed_antifam
line["excluded"] = (failed_antifam
or (not_supported and not is_novel))
print(json.dumps(line), file=args.stats)
kept, dropped = split_gffs(gff, args.group_level)
write_gff(kept, args.outfile)
if args.filtered is not None:
write_gff(dropped, args.filtered)
return
def ncbi(args: argparse.Namespace) -> None:
gff = GFF.parse(args.infile).break_bubbles()
so = Ontology.from_obo_library(args.so)
name_to_so = {term.name: term for term in so.values()}
add_so_as_ontologies(gff, name_to_so)
add_ncrna_types(gff, name_to_so, so, NCRNA_TYPES)
add_pseudogene_types(gff, name_to_so, so, PSEUDOGENE_TYPES)
return
def expandcds(args: argparse.Namespace) -> None:
gff = GFF.parse(args.infile)
if args.infasta is None:
seqs = None
else:
seqs = SeqIO.to_dict(SeqIO.parse(args.infasta, format="fasta"))
codon_table = CodonTable.unambiguous_dna_by_id[args.gencode]
cds_parents: Set[GFF3Record] = set()
for record in gff.select_type(args.cds_type):
cds_parents.update((cast(GFF3Record, p) for p in record.parents))
for parent in cds_parents:
cdss = sorted([
cast(GFF3Record, f)
for f in parent.children if f.type == args.cds_type
],
key=lambda f: (f.start, f.end))
strand = find_strand(cdss, parent)
if args.start:
bump_start(cdss, strand)
if args.stop:
bump_end(cdss, strand)
if seqs is not None and parent.seqid in seqs:
start_codon = check_start(cdss, parent, strand, seqs, codon_table)
if start_codon is not None:
print(start_codon, file=args.warnings)
stop_codon = check_stop(cdss, parent, strand, seqs, codon_table)
if stop_codon is not None:
print(stop_codon, file=args.warnings)
child_cdss: Sequence[GFF3Record] = list(gff.select_type(args.cds_type))
for parent in gff.traverse_parents(child_cdss):
parent.expand_to_children()
print("##gff-version 3", file=args.outfile)
for feature in gff.traverse_children(sort=True):
print(feature, file=args.outfile)
return
def run_extract(args) -> None:
if args.good is not None:
good_ids: Optional[Set[str]] = get_good_ids(args.good)
else:
good_ids = None
in_gff = GFF.parse(args.gff)
in_fasta = SeqIO.to_dict(SeqIO.parse(args.fasta, format="fasta"))
if args.hints is not None:
in_hints = GFF.parse(args.hints)
else:
in_hints = None
block_iter = get_blocks(in_fasta, in_gff, in_hints, args.pad, args.merge,
good_ids)
print("##gff-version 3", file=args.outgff)
if args.outhints is not None:
print("##gff-version 3", file=args.outhints)
for name, seq, genes, hints in block_iter:
SeqIO.write(seq, args.outfasta, format="fasta")
sr = f"##sequence-region {name} 1 {len(seq)}"
print(sr, file=args.outgff)
print(genes, file=args.outgff)
if (args.outhints is not None and hints is not None
and len(hints.inner) > 0):
print(sr, file=args.outhints)
print(hints, file=args.outhints)
return
def select(args: argparse.Namespace) -> None:
gff = GFF.parse(args.infile)
ids = {l.strip() for l in args.ids}
to_keep: Set[GFF3Record] = set()
for record in gff:
if record.attributes is not None and record.attributes.id in ids:
to_keep.update(
cast(Iterator[GFF3Record], record.traverse_parents()))
to_keep.update(
cast(Iterator[GFF3Record], record.traverse_children()))
pruned = prune_gff(to_keep)
print("#gff-version 3", file=args.outfile)
for feature in pruned.traverse_children(sort=True):
print(feature, file=args.outfile)
def main():
args = cli(sys.argv[0], sys.argv[1:])
gff = GFF.parse(args.ingff)
seqs = SeqIO.to_dict(SeqIO.parse(args.infasta, format="fasta"))
counter = 1
for region in gff:
region.type = args.type
region.source = args.source
region.strand = Strand.UNSTRANDED
region.attributes.id = f"{args.type}{counter}"
sf = gff_to_seqfeature(region)
seq = sf.extract(seqs[region.seqid])
base_counts = count_frequencies(seq)
region.attributes.custom = base_counts
counter += 1
print(region, file=args.outfile)
return
