dae.gpf_instance package

Subpackages

• dae.gpf_instance.adjustments package
  • Submodules
  • dae.gpf_instance.adjustments.adjust_command module
    • AdjustmentsCommand
      • AdjustmentsCommand.close()
      • AdjustmentsCommand.execute()
  • dae.gpf_instance.adjustments.adjust_duckdb_storage module
    • AdjustDuckDbStorageCommand
      • AdjustDuckDbStorageCommand.add_arguments()
      • AdjustDuckDbStorageCommand.execute()
  • dae.gpf_instance.adjustments.adjust_impala_storage module
    • AdjustImpalaStorageCommand
      • AdjustImpalaStorageCommand.add_arguments()
      • AdjustImpalaStorageCommand.execute()
  • dae.gpf_instance.adjustments.gpf_instance_adjustments module
    • DefaultGenotypeStorage
      • DefaultGenotypeStorage.adjust_study()
      • DefaultGenotypeStorage.execute()
    • EnableDisableStudies
      • EnableDisableStudies.adjust_dataset()
      • EnableDisableStudies.adjust_study()
      • EnableDisableStudies.execute()
    • InstanceIdCommand
      • InstanceIdCommand.execute()
    • StudyConfigsAdjustmentCommand
      • StudyConfigsAdjustmentCommand.adjust_dataset()
      • StudyConfigsAdjustmentCommand.adjust_study()
    • cli()
  • Module contents

Submodules

dae.gpf_instance.gpf_instance module

Defines GPFInstance class that gives access to different parts of GPF.

class dae.gpf_instance.gpf_instance.GPFInstance(dae_config: Box, dae_dir: str | Path, dae_config_path: Path, **kwargs: dict[str, Any])

Bases: object

Class to access different parts of a GPF instance.

static build(config_filename: str | Path | None = None, **kwargs: Any) → GPFInstance

Construct and return a GPF instance.

If the config_filename is None, tries to discover the GPF instance. First check if a DAE_DB_DIR environment variable is defined and if defined use it as a GPF instance directory.

Otherwise look for a gpf_instance.yaml file in the current directory and its parents. If found use it as a configuration file.

property denovo_gene_sets_db: DenovoGeneSetsDb

property gene_models: GeneModels

Return gene models used in the GPF instance.

property gene_scores_db: Any

Load and return gene scores db.

property gene_sets_db: GeneSetsDb

Return GeneSetsDb populated with gene sets from the GPFInstance.

property genomic_scores: GenomicScoresRegistry

Load and return genomic scores db.

property genotype_storages: Any

Construct and return genotype storage registry.

get_all_common_report_configs() → list[Box]

Return all common report configuration.

get_all_gene_score_descs() → list[ScoreDesc]

get_all_gene_scores() → list[GeneScore]

get_all_genotype_data() → list[GenotypeData]

get_all_phenotype_data() → list[PhenotypeData]

get_annotation_pipeline() → AnnotationPipeline

Return the annotation pipeline configured in the GPF instance.

get_annotation_pipeline_config() → list[dict[str, Any]] | RawFullConfig

Return the annotation pipeline config.

get_cache_path(prefix: str) → Path | None

get_common_report(study_id: str) → CommonReport | None

Load and return common report (dataset statistics) for a study.

get_dataset(dataset_id: str) → GenotypeData

get_enrichment_builder(dataset: GenotypeData) → BaseEnrichmentBuilder

Get enrichment builder for specific dataset.

Will create and register new one if one isn’t found.

get_gene_score(gene_score_id: str) → GeneScore

get_gene_score_desc(score_id: str) → ScoreDesc

get_genotype_data(genotype_data_id: str) → GenotypeData

get_genotype_data_config(genotype_data_id: str) → Box | None

get_genotype_data_ids() → list[str]

get_gp_configuration() → Box

get_gp_statistic(gene_symbol: str) → GPStatistic

get_pheno_cache_path() → Path

get_pheno_tool_adapter(dataset: GenotypeData) → PhenoToolAdapterBase

Get enrichment builder for specific dataset.

Will create and register new one if one isn’t found.

get_phenotype_data(phenotype_data_id: str) → PhenotypeData

get_phenotype_data_config(phenotype_data_id: str) → dict | None

get_phenotype_data_ids() → list[str]

get_transcript_models(gene_symbol: str) → tuple[str | None, list[TranscriptModel] | None]

Get gene model by gene symbol.

property grr: GenomicResourceRepo

Return genomic resource repository configured for GPF instance.

has_gene_score(gene_score_id: str) → bool

has_phenotype_data(phenotype_data_id: str) → bool

list_gp_gene_symbols(page: int, symbol_like: str | None = None) → list[str]

Query AGR statistics and return results.

load() → GPFInstance

Load all GPF instance attributes.

make_enrichment_builder(dataset: GenotypeData) → EnrichmentBuilder

make_pheno_tool_adapter(dataset: GenotypeData) → PhenoToolAdapterBase

Create a pheno tool adapter for dataset.

property phenotype_storages: PhenotypeStorageRegistry

Get phenotype storage registry.

Will load if not cached.

query_gp_statistics(page: int, symbol_like: str | None = None, sort_by: str | None = None, order: str | None = None) → list[GPStatistic]

Query AGR statistics and return results.

property reference_genome: ReferenceGenome

Return reference genome defined in the GPFInstance config.

register_enrichment_builder(dataset_id: str, builder: BaseEnrichmentBuilder) → None

Register a new enrichment builder to a given dataset ID.

register_pheno_tool_adapter(dataset_id: str, adapter: PhenoToolAdapterBase) → None

Register a new enrichment builder to a given dataset ID.

reload() → None

Reload GPF instance studies, de Novo gene sets, etc.

Module contents

class dae.gpf_instance.GPFInstance(dae_config: Box, dae_dir: str | Path, dae_config_path: Path, **kwargs: dict[str, Any])

Bases: object

Class to access different parts of a GPF instance.

static build(config_filename: str | Path | None = None, **kwargs: Any) → GPFInstance

Construct and return a GPF instance.

If the config_filename is None, tries to discover the GPF instance. First check if a DAE_DB_DIR environment variable is defined and if defined use it as a GPF instance directory.

Otherwise look for a gpf_instance.yaml file in the current directory and its parents. If found use it as a configuration file.

property denovo_gene_sets_db: DenovoGeneSetsDb

property gene_models: GeneModels

Return gene models used in the GPF instance.

property gene_scores_db: Any

Load and return gene scores db.

property gene_sets_db: GeneSetsDb

Return GeneSetsDb populated with gene sets from the GPFInstance.

property genomic_scores: GenomicScoresRegistry

Load and return genomic scores db.

property genotype_storages: Any

Construct and return genotype storage registry.

get_all_common_report_configs() → list[Box]

Return all common report configuration.

get_all_gene_score_descs() → list[ScoreDesc]

get_all_gene_scores() → list[GeneScore]

get_all_genotype_data() → list[GenotypeData]

get_all_phenotype_data() → list[PhenotypeData]

get_annotation_pipeline() → AnnotationPipeline

Return the annotation pipeline configured in the GPF instance.

get_annotation_pipeline_config() → list[dict[str, Any]] | RawFullConfig

Return the annotation pipeline config.

get_cache_path(prefix: str) → Path | None

get_common_report(study_id: str) → CommonReport | None

Load and return common report (dataset statistics) for a study.

get_dataset(dataset_id: str) → GenotypeData

get_enrichment_builder(dataset: GenotypeData) → BaseEnrichmentBuilder

Get enrichment builder for specific dataset.

Will create and register new one if one isn’t found.

get_gene_score(gene_score_id: str) → GeneScore

get_gene_score_desc(score_id: str) → ScoreDesc

get_genotype_data(genotype_data_id: str) → GenotypeData

get_genotype_data_config(genotype_data_id: str) → Box | None

get_genotype_data_ids() → list[str]

get_gp_configuration() → Box

get_gp_statistic(gene_symbol: str) → GPStatistic

get_pheno_cache_path() → Path

get_pheno_tool_adapter(dataset: GenotypeData) → PhenoToolAdapterBase

Get enrichment builder for specific dataset.

Will create and register new one if one isn’t found.

get_phenotype_data(phenotype_data_id: str) → PhenotypeData

get_phenotype_data_config(phenotype_data_id: str) → dict | None

get_phenotype_data_ids() → list[str]

get_transcript_models(gene_symbol: str) → tuple[str | None, list[TranscriptModel] | None]

Get gene model by gene symbol.

property grr: GenomicResourceRepo

Return genomic resource repository configured for GPF instance.

has_gene_score(gene_score_id: str) → bool

has_phenotype_data(phenotype_data_id: str) → bool

list_gp_gene_symbols(page: int, symbol_like: str | None = None) → list[str]

Query AGR statistics and return results.

load() → GPFInstance

Load all GPF instance attributes.

make_enrichment_builder(dataset: GenotypeData) → EnrichmentBuilder

make_pheno_tool_adapter(dataset: GenotypeData) → PhenoToolAdapterBase

Create a pheno tool adapter for dataset.

property phenotype_storages: PhenotypeStorageRegistry

Get phenotype storage registry.

Will load if not cached.

query_gp_statistics(page: int, symbol_like: str | None = None, sort_by: str | None = None, order: str | None = None) → list[GPStatistic]

Query AGR statistics and return results.

property reference_genome: ReferenceGenome

Return reference genome defined in the GPFInstance config.

register_enrichment_builder(dataset_id: str, builder: BaseEnrichmentBuilder) → None

Register a new enrichment builder to a given dataset ID.

register_pheno_tool_adapter(dataset_id: str, adapter: PhenoToolAdapterBase) → None

Register a new enrichment builder to a given dataset ID.

reload() → None

Reload GPF instance studies, de Novo gene sets, etc.