from obnb.data.annotated_ontology.base import BaseAnnotatedOntologyData
from obnb.data.annotation import HumanPhenotypeOntologyAnnotation
from obnb.data.ontology import MondoDiseaseOntology
from obnb.label.filters import Compose, LabelsetNonRedFilter, LabelsetRangeFilterSize
from obnb.typing import List, Mapping, Optional, Union
[docs]class HPO(BaseAnnotatedOntologyData):
"""The HPO disease and triat gene set collection."""
def __init__(
self,
root: str,
min_size: int = 10,
max_size: int = 600,
overlap: float = 0.7,
jaccard: float = 0.5,
data_sources: Optional[List[str]] = None,
gene_id_converter: Optional[Union[Mapping[str, str], str]] = None,
**kwargs,
):
"""Initialize the HPO data object."""
self.min_size = min_size
self.max_size = max_size
self.jaccard = jaccard
self.overlap = overlap
super().__init__(
root,
annotation_factory=HumanPhenotypeOntologyAnnotation,
ontology_factory=MondoDiseaseOntology,
annotation_kwargs={
"data_sources": data_sources,
"gene_id_converter": gene_id_converter,
},
ontology_kwargs={"xref_prefix": "HP"},
**kwargs,
)
@property
def default_pre_transform(self):
return Compose(
LabelsetRangeFilterSize(max_val=self.max_size),
LabelsetNonRedFilter(self.jaccard, self.overlap),
LabelsetRangeFilterSize(min_val=self.min_size),
log_level=self.log_level,
)