def add_record(self, record: GFF3Record) -> None:
""" """
# Attributes can be None
id_: Optional[str] = fmap(lambda a: getattr(a, "id"),
record.attributes)
if id_ is not None:
self.index[id_].append(record)
children = self.missing_parents.pop(id_, [])
record.add_children(children)
parent_ids: List[str] = or_else([],
fmap(lambda a: getattr(a, "parent"),
record.attributes))
for parent_id in parent_ids:
parents = self.index.get(parent_id, [])
if len(parents) == 0:
self.missing_parents[parent_id].append(record)
else:
record.add_parents(parents)
self.inner.append(record)
return
def parse(
cls,
string: str,
strip_quote: bool = False,
unescape: bool = False,
) -> "GFF3Attributes":
if string.strip() in (".", ""):
return cls()
fields = (f.split("=", maxsplit=1)
for f in string.strip(" ;").split(";"))
if strip_quote:
kvpairs: Dict[str, str] = {
k.strip(): v.strip(" '\"")
for k, v in fields
}
else:
kvpairs = {k.strip(): v.strip() for k, v in fields}
id = kvpairs.pop("ID", None)
name = kvpairs.pop("Name", None)
alias = cls._parse_list_of_strings(kvpairs.pop("Alias", ""),
strip_quote, unescape)
parent = cls._parse_list_of_strings(kvpairs.pop("Parent", ""),
strip_quote, unescape)
target: Optional[Target] = fmap(
Target.parse,
fmap(lambda x: cls._attr_unescape(x) if unescape else x,
kvpairs.pop("Target", None)))
gap = fmap(
Gap.parse,
fmap(lambda x: cls._attr_unescape(x) if unescape else x,
kvpairs.pop("Gap", None)))
derives_from = cls._parse_list_of_strings(
kvpairs.pop("Derives_from", ""), strip_quote, unescape)
note = cls._parse_list_of_strings(kvpairs.pop("Note", ""), strip_quote,
unescape)
dbxref = cls._parse_list_of_strings(kvpairs.pop("Dbxref", ""),
strip_quote, unescape)
ontology_term = cls._parse_list_of_strings(
kvpairs.pop("Ontology_term", ""), strip_quote, unescape)
is_circular = fmap(parse_bool, kvpairs.pop("Is_circular", None))
return cls(id, name, alias, parent, target, gap, derives_from, note,
dbxref, ontology_term, is_circular, kvpairs)
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