# pylint: disable=W0621,C0114,C0116,W0212,W0613
import pathlib
from typing import Optional
from dae.genomic_resources.repository_factory import (
build_genomic_resource_repository,
)
from dae.genotype_storage.genotype_storage import GenotypeStorage
from dae.gpf_instance import GPFInstance
from dae.testing import (
setup_empty_gene_models,
setup_genome,
setup_gpf_instance,
)
[docs]def acgt_gpf(
root_path: pathlib.Path,
storage: Optional[GenotypeStorage] = None) -> GPFInstance:
setup_genome(
root_path / "acgt_gpf" / "genome" / "allChr.fa",
f"""
>chr1
{25 * "ACGT"}
>chr2
{25 * "ACGT"}
>chr3
{25 * "ACGT"}
""",
)
setup_empty_gene_models(
root_path / "acgt_gpf" / "empty_gene_models" / "empty_genes.txt")
local_repo = build_genomic_resource_repository({
"id": "acgt_local",
"type": "directory",
"directory": str(root_path / "acgt_gpf"),
})
gpf_instance = setup_gpf_instance(
root_path / "gpf_instance",
reference_genome_id="genome",
gene_models_id="empty_gene_models",
grr=local_repo)
if storage:
gpf_instance\
.genotype_storages\
.register_default_storage(storage)
return gpf_instance