import pathlib
import textwrap
from dae.genomic_resources.gene_models.gene_models_factory 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,
grr: GenomicResourceRepo | None = None,
reference_genome_id: str | None = None,
gene_models_id: str | None = None,
) -> GPFInstance:
"""Set up a GPF instance using prebuild genome, gene models, etc."""
if not (out_path / "gpf_instance.yaml").exists():
content = textwrap.dedent(f"""
instance_id: "test_instance"
reference_genome:
resource_id: {reference_genome_id}
gene_models:
resource_id: {gene_models_id}
""")
if grr is not None and grr.definition is not None:
grr_definition = grr.definition
assert grr_definition is not None
content += textwrap.dedent(f"""
grr:
type: {grr.definition['type']}
id: {grr.definition['id']}
directory: {grr.definition['directory']}
""")
setup_directories(
out_path, {
"gpf_instance.yaml": content,
},
)
# 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)