# pylint: disable=W0621,C0114,C0116,W0212,W0613
import pathlib
from gain.genomic_resources.gene_models import GeneModels
from gain.genomic_resources.reference_genome import ReferenceGenome
from gain.genomic_resources.testing import (
setup_gene_models,
setup_genome,
)
# 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
[docs]
def foobar_genes(root_path: pathlib.Path) -> GeneModels:
return setup_gene_models(
root_path / "foobar_genes" / "genes.txt",
GMM_CONTENT, fileformat="refflat")
[docs]
def foobar_genome(root_path: pathlib.Path) -> ReferenceGenome:
return setup_genome(
root_path / "foobar_genome" / "chrAll.fa",
"""
>foo
NNACCCAAAC
GGGCCTTCCN
NNNA
>bar
NNGGGCCTTC
CACGACCCAA
NN
""",
)