# pylint: disable=W0621,C0114,C0116,W0212,W0613
import pathlib
from typing import Optional
from dae.genomic_resources.gene_models import GeneModels
from dae.genomic_resources.reference_genome import ReferenceGenome
from dae.genomic_resources.repository_factory import (
build_genomic_resource_repository,
)
from dae.genotype_storage.genotype_storage import GenotypeStorage
from dae.gpf_instance.gpf_instance import GPFInstance
from dae.testing import setup_gene_models, setup_genome, setup_gpf_instance
# this content follows the 'refflat' gene model format
GMM_CONTENT = """
#geneName name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds
g1 tx1 foo + 3 17 3 17 2 3,13 6,17
g1 tx2 foo + 3 9 3 6 1 3 6
g2 tx3 bar - 3 20 3 15 1 3 17
""" # noqa
def foobar_genes(root_path: pathlib.Path) -> GeneModels:
genes = setup_gene_models(
root_path / "foobar_genes" / "genes.txt",
GMM_CONTENT, fileformat="refflat")
return genes
def foobar_genome(root_path: pathlib.Path) -> ReferenceGenome:
genome = setup_genome(
root_path / "foobar_genome" / "chrAll.fa",
"""
>foo
NNACCCAAAC
GGGCCTTCCN
NNNA
>bar
NNGGGCCTTC
CACGACCCAA
NN
""",
)
return genome
[docs]def foobar_gpf(
root_path: pathlib.Path,
storage: Optional[GenotypeStorage] = None) -> GPFInstance:
setup_genome(
root_path / "foobar_genome" / "chrAll.fa",
"""
>foo
NNACCCAAAC
GGGCCTTCCN
NNNA
>bar
NNGGGCCTTC
CACGACCCAA
NN
""",
)
setup_gene_models(
root_path / "foobar_genes" / "genes.txt",
GMM_CONTENT, fileformat="refflat")
local_repo = build_genomic_resource_repository({
"id": "foobar_local",
"type": "directory",
"directory": str(root_path),
})
gpf_instance = setup_gpf_instance(
root_path / "gpf_instance",
reference_genome_id="foobar_genome",
gene_models_id="foobar_genes",
grr=local_repo)
if storage:
gpf_instance\
.genotype_storages\
.register_default_storage(storage)
return gpf_instance