dae.testing package

Submodules

dae.testing.import_helpers module

class dae.testing.import_helpers.StudyInputLayout(study_id: 'str', pedigree: 'pathlib.Path', vcf: 'list[pathlib.Path]', denovo: 'list[pathlib.Path]', dae: 'list[pathlib.Path]', cnv: 'list[pathlib.Path]')

Bases: object

cnv: list[pathlib.Path]

dae: list[pathlib.Path]

denovo: list[pathlib.Path]

pedigree: Path

study_id: str

vcf: list[pathlib.Path]

dae.testing.import_helpers.cnv_import(root_path: Path, study_id: str, ped_path: Path, cnv_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None) → ImportProject

Import a de Novo study and return the import project.

dae.testing.import_helpers.cnv_study(root_path: Path, study_id: str, ped_path: Path, cnv_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, study_config_update: dict[str, Any] | None = None) → GenotypeData

Import a de Novo study and return the imported study.

dae.testing.import_helpers.denovo_import(root_path: Path, study_id: str, ped_path: Path, denovo_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None) → ImportProject

Import a de Novo study and return the import project.

dae.testing.import_helpers.denovo_study(root_path: Path, study_id: str, ped_path: Path, denovo_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, study_config_update: dict[str, Any] | None = None) → GenotypeData

Import a de Novo study and return the imported study.

dae.testing.import_helpers.pedigree_import(root_path: Path, study_id: str, ped_path: Path, gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, project_config_replace: dict[str, Any] | None = None) → ImportProject

Import a VCF study and return the import project.

dae.testing.import_helpers.setup_dataset(dataset_id: str, gpf_instance: GPFInstance, *studies: GenotypeData, dataset_config_update: str = '') → GenotypeDataGroup

Create and register a dataset dataset_id with studies.

dae.testing.import_helpers.setup_import_project(root_path: Path, study: StudyInputLayout, gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, project_config_replace: dict[str, Any] | None = None) → ImportProject

Set up an import project for a study and imports it.

dae.testing.import_helpers.setup_import_project_config(root_path: Path, study: StudyInputLayout, gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, project_config_replace: dict[str, Any] | None = None) → Path

Set up import project config.

dae.testing.import_helpers.study_update(gpf_instance: GPFInstance, study: GenotypeData, study_config_update: dict[str, Any]) → GenotypeData

dae.testing.import_helpers.update_study_config(gpf_instance: GPFInstance, study_id: str, study_config_update: dict[str, Any]) → None

Update study configuration.

dae.testing.import_helpers.vcf_import(root_path: Path, study_id: str, ped_path: Path, vcf_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, project_config_replace: dict[str, Any] | None = None) → ImportProject

Import a VCF study and return the import project.

dae.testing.import_helpers.vcf_study(root_path: Path, study_id: str, ped_path: Path, vcf_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, study_config_update: dict[str, Any] | None = None) → GenotypeData

Import a VCF study and return the imported study.

dae.testing.setup_helpers module

dae.testing.setup_helpers.setup_gpf_instance(out_path: Path, reference_genome_id: str | None = None, gene_models_id: str | None = None, grr: GenomicResourceRepo | None = None) → GPFInstance

Set up a GPF instance using prebuild genome, gene models, etc.

Module contents

class dae.testing.StudyInputLayout(study_id: 'str', pedigree: 'pathlib.Path', vcf: 'list[pathlib.Path]', denovo: 'list[pathlib.Path]', dae: 'list[pathlib.Path]', cnv: 'list[pathlib.Path]')

Bases: object

cnv: list[pathlib.Path]

dae: list[pathlib.Path]

denovo: list[pathlib.Path]

pedigree: Path

study_id: str

vcf: list[pathlib.Path]

dae.testing.acgt_gpf(root_path: Path, storage: GenotypeStorage | None = None) → GPFInstance

dae.testing.alla_gpf(root_path: Path, storage: GenotypeStorage | None = None) → GPFInstance

dae.testing.cnv_import(root_path: Path, study_id: str, ped_path: Path, cnv_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None) → ImportProject

Import a de Novo study and return the import project.

dae.testing.cnv_study(root_path: Path, study_id: str, ped_path: Path, cnv_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, study_config_update: dict[str, Any] | None = None) → GenotypeData

Import a de Novo study and return the imported study.

dae.testing.convert_to_tab_separated(content: str) → str

Convert a string into tab separated file content.

Useful for testing purposes. If you need to have a space in the file content use ‘||’.

dae.testing.denovo_import(root_path: Path, study_id: str, ped_path: Path, denovo_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None) → ImportProject

Import a de Novo study and return the import project.

dae.testing.denovo_study(root_path: Path, study_id: str, ped_path: Path, denovo_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, study_config_update: dict[str, Any] | None = None) → GenotypeData

Import a de Novo study and return the imported study.

dae.testing.foobar_gpf(root_path: Path, storage: GenotypeStorage | None = None) → GPFInstance

dae.testing.setup_dae_transmitted(root_path: Path, summary_content: str, toomany_content: str) → tuple[str, str]

Set up a DAE transmitted variants file using passed content.

dae.testing.setup_dataset(dataset_id: str, gpf_instance: GPFInstance, *studies: GenotypeData, dataset_config_update: str = '') → GenotypeDataGroup

Create and register a dataset dataset_id with studies.

dae.testing.setup_denovo(denovo_path: Path, content: str) → Path

dae.testing.setup_directories(root_dir: Path, content: str | dict[str, Any]) → None

Set up directory and subdirectory structures using the content.

dae.testing.setup_empty_gene_models(out_path: Path) → GeneModels

Set up empty gene models.

dae.testing.setup_gene_models(out_path: Path, content: str, fileformat: str | None = None) → GeneModels

Set up gene models in refflat format using the passed content.

dae.testing.setup_genome(out_path: Path, content: str) → ReferenceGenome

Set up reference genome using the content.

dae.testing.setup_gpf_instance(out_path: Path, reference_genome_id: str | None = None, gene_models_id: str | None = None, grr: GenomicResourceRepo | None = None) → GPFInstance

Set up a GPF instance using prebuild genome, gene models, etc.

dae.testing.setup_import_project(root_path: Path, study: StudyInputLayout, gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, project_config_replace: dict[str, Any] | None = None) → ImportProject

Set up an import project for a study and imports it.

dae.testing.setup_pedigree(ped_path: Path, content: str) → Path

dae.testing.setup_vcf(out_path: Path, content: str, csi: bool = False) → Path

Set up a VCF file using the content.

dae.testing.study_update(gpf_instance: GPFInstance, study: GenotypeData, study_config_update: dict[str, Any]) → GenotypeData

dae.testing.t4c8_gpf(root_path: Path, storage: GenotypeStorage | None = None) → GPFInstance

dae.testing.vcf_import(root_path: Path, study_id: str, ped_path: Path, vcf_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, project_config_replace: dict[str, Any] | None = None) → ImportProject

Import a VCF study and return the import project.

dae.testing.vcf_study(root_path: Path, study_id: str, ped_path: Path, vcf_paths: list[pathlib.Path], gpf_instance: GPFInstance, project_config_update: dict[str, Any] | None = None, project_config_overwrite: dict[str, Any] | None = None, study_config_update: dict[str, Any] | None = None) → GenotypeData

Import a VCF study and return the imported study.