import pathlib
from typing import Optional
from dae.genomic_resources.gene_models import build_gene_models_from_resource
from dae.genomic_resources.reference_genome import (
build_reference_genome_from_resource,
)
from dae.genomic_resources.repository import GenomicResourceRepo
from dae.genomic_resources.testing import setup_directories
from dae.gpf_instance import GPFInstance
[docs]def setup_gpf_instance(
out_path: pathlib.Path,
reference_genome_id: Optional[str] = None,
gene_models_id: Optional[str] = None,
grr: Optional[GenomicResourceRepo] = None) -> GPFInstance:
"""Set up a GPF instance using prebuild genome, gene models, etc."""
# from dae.gpf_instance import GPFInstance
if not (out_path / "gpf_instance.yaml").exists():
setup_directories(
out_path, {"gpf_instance.yaml": 'instance_id: "test_instance"'},
)
# pylint: disable=import-outside-toplevel
reference_genome = None
if reference_genome_id is not None:
assert grr is not None
res = grr.get_resource(reference_genome_id)
reference_genome = build_reference_genome_from_resource(res)
reference_genome.open()
gene_models = None
if gene_models_id is not None:
assert grr is not None
res = grr.get_resource(gene_models_id)
gene_models = build_gene_models_from_resource(res)
gene_models.load()
return GPFInstance.build(
out_path / "gpf_instance.yaml",
reference_genome=reference_genome, gene_models=gene_models,
grr=grr)