dae.tools package

Submodules

dae.tools.annotate_variants module

dae.tools.annotate_variants.cli(argv: list[str] | None = None) → None

Annotate variants main function.

dae.tools.annotate_variants.cli_genome_options(parser: ArgumentParser) → ArgumentParser

Create parser options for reference genome and gene models.

dae.tools.annotate_variants.cli_variants_options(parser: ArgumentParser) → None

Configure parser for variant specifying options.

dae.tools.annotate_variants.cli_vcf(argv: list[str] | None = None) → None

Annotate variants main function for annotating VCF file.

dae.tools.annotate_variants.parse_cli_genome_options(args: Namespace) → tuple[Optional[dae.genomic_resources.reference_genome.ReferenceGenome], Optional[dae.genomic_resources.gene_models.GeneModels]]

Parse reference genome and gene models options.

dae.tools.annotate_variants.parse_cli_variants_options(args: Namespace) → dict[str, Any]

Parse variant definition options.

dae.tools.cnv2parquet module

dae.tools.create_sqlite_gene_set module

dae.tools.create_sqlite_gene_set.main(argv)

Entry point for the tool.

dae.tools.cshl2vcf module

dae.tools.dae2parquet module

dae.tools.denovo2parquet module

dae.tools.denovo2ped module

dae.tools.denovo2vcf module

dae.tools.draw_pedigree module

Tool to draw pedigrees defined in a file.

dae.tools.draw_pedigree.build_families_report(families: FamiliesData) → FamiliesReport

Build a family report based on affected status.

dae.tools.draw_pedigree.build_family_layout(family)

dae.tools.draw_pedigree.draw_families(families)

Draw families.

dae.tools.draw_pedigree.draw_families_report(families)

Draw families from families report.

dae.tools.draw_pedigree.draw_pedigree(layout, title, show_family=True, tags=None)

dae.tools.draw_pedigree.main(argv=None)

Run the CLI for draw_pedigree tool.

dae.tools.extract_family_variants module

dae.tools.family_pedigree_generator module

dae.tools.generate_autism_gene_profile module

dae.tools.generate_common_report module

dae.tools.generate_denovo_gene_sets module

dae.tools.generate_denovo_gene_sets.main(gpf_instance: GPFInstance | None = None, argv: list[str] | None = None) → None

Generate denovo gene sets CLI.

dae.tools.genotype_data_tool module

dae.tools.gpf_instance_adjustments module

class dae.tools.gpf_instance_adjustments.AdjustDuckDbStorageCommand(instance_dir: str, storage_id: str, read_only: str)

Bases: AdjustmentsCommand

Adjusts impala storage.

execute() → None

Execute adjustment command.

class dae.tools.gpf_instance_adjustments.AdjustImpalaStorageCommand(instance_dir: str, storage_id: str, read_only: bool, hdfs_host: str, impala_hosts: list[str])

Bases: AdjustmentsCommand

Adjusts impala storage.

execute() → None

Execute adjustment command.

class dae.tools.gpf_instance_adjustments.AdjustmentsCommand(instance_dir: str)

Bases: ABC

Abstract class for adjusting an GPF instance config.

close() → None

Save adjusted config.

abstract execute() → None

Execute adjustment command.

class dae.tools.gpf_instance_adjustments.DefaultGenotypeStorage(instance_dir: str, storage_id: str)

Bases: StudyConfigsAdjustmentCommand

Adjust default genotype storage.

adjust_study(_study_id: str, study_config: dict[str, Any]) → dict[str, Any]

execute() → None

Execute adjustment command.

class dae.tools.gpf_instance_adjustments.EnableDisableStudies(instance_dir: str, study_ids: Iterable[str], enabled: bool = False)

Bases: StudyConfigsAdjustmentCommand

Enable or disable collection of studies.

adjust_dataset(dataset_id: str, dataset_config: dict[str, Any]) → dict[str, Any]

adjust_study(study_id: str, study_config: dict[str, Any]) → dict[str, Any]

execute() → None

Execute adjustment command.

class dae.tools.gpf_instance_adjustments.InstanceIdCommand(instance_dir: str, instance_id: str)

Bases: AdjustmentsCommand

Adjusts GPF instance ID.

execute() → None

Execute adjustment command.

class dae.tools.gpf_instance_adjustments.StudyConfigsAdjustmentCommand(instance_dir: str)

Bases: AdjustmentsCommand

Command to adjust study configs.

adjust_dataset(_dataset_id: str, dataset_config: dict[str, Any]) → dict[str, Any]

adjust_study(_study_id: str, study_config: dict[str, Any]) → dict[str, Any]

dae.tools.gpf_instance_adjustments.cli(argv: list[str] | None = None) → None

Handle cli invocation.

dae.tools.gpf_validation_runner module

class dae.tools.gpf_validation_runner.AbstractRunner(expectations: dict[str, Any], gpf_instance: GPFInstance)

Bases: object

The base class for test runners.

property error_case_count: int

property failed_case_count: int

property passed_case_count: int

class dae.tools.gpf_validation_runner.BaseGenotypeBrowserRunner(expectations: dict[str, Any], gpf_instance: GPFInstance)

Bases: AbstractRunner

Base class for Genotype Browser Runners.

class dae.tools.gpf_validation_runner.GenotypeBrowserRunner(expectations: dict[str, Any], gpf_instance: GPFInstance, detailed_reporting: bool, skip_columns: set)

Bases: BaseGenotypeBrowserRunner

Run Genotype Browser tests.

run() → None

Run tests.

store_results(dirname: str) → None

Store results.

class dae.tools.gpf_validation_runner.MainRunner(gpf_instance: GPFInstance, outfilename: str, detailed_reporting: bool, skip_columns: list[Any])

Bases: object

Main runner.

static collect_expectations(expectations: str) → Iterator[dict[str, Any]]

Collect expectations.

property errors_case_count: int

property failed_case_count: int

main(expectations_iterator: Iterator[Any]) → None

Entry point for this runner.

make_validation_runner(expectations: dict[str, Any]) → GenotypeBrowserRunner

Create a validation runner.

property passed_case_count: int

static store_junit_results(runners: list[dae.tools.gpf_validation_runner.AbstractRunner], outfilename: str) → None

Store junit results.

store_results(expectations_iterator: Iterator[dict[str, Any]], dirname: str) → None

summary() → None

Print a summary of the test results.

class dae.tools.gpf_validation_runner.TestResult(expectation: dict[str, Any] | None = None, case: dict[str, Any] | None = None, test_for: str | None = None, params: dict[str, Any] | None = None, result: str | None = None)

Bases: object

Encapsulate the result of a test.

to_xml_element() → Element

Convert to an XML element.

class dae.tools.gpf_validation_runner.TestStatus(value)

Bases: Enum

An enumeration.

ERROR = 4

FAIL = 2

NOTSET = 0

PASSED = 1

class dae.tools.gpf_validation_runner.TestSuite(study: str, target: str, name: str)

Bases: object

A collection of tests.

append(case: TestResult) → None

to_xml_element() → Element

Convert to an XML element.

dae.tools.gpf_validation_runner.main(argv: list[str] | None = None) → None

Entry point for the runner script.

dae.tools.grr_cache_repo module

Provides CLI tools for caching genomic resources.

dae.tools.grr_cache_repo.cli_cache_repo(argv: list[str] | None = None) → None

CLI for caching genomic resources.

dae.tools.grr_cache_repo.extract_resource_ids_from_annotation(annotation: str, repository: GenomicResourceRepo) → set[str]

Collect resources and resource files used by annotation.

dae.tools.hdfs_parquet_loader module

dae.tools.impala_batch_import module

dae.tools.impala_parquet_loader module

dae.tools.impala_tables_loader module

dae.tools.impala_tables_stats module

dae.tools.impala_tables_summary_variants module

dae.tools.ped2parquet module

dae.tools.ped2ped module

Tool to convert pedigree file into cannonical GPF pedigree file.

dae.tools.ped2ped.main(argv: list[str] | None = None) → None

Transform a pedigree file into cannonical GPF pedigree.

It should be called from the command line.

dae.tools.phase module

dae.tools.phase.checkConsistency(inp)

Check consistency.

dae.tools.phase.getDims(inp)

dae.tools.phase.phase(inp)

Calculate phase.

dae.tools.phase.possiblePersonPhasing(inp, L, P, nCpies, p)

dae.tools.phase.possiblePersonPhasingR(inp, L, P, p, ll, cPh, posPhs, seenHet)

Is person phasing R possible.

dae.tools.pheno2browser module

pheno2browser – prepares a DAE pheno browser data.

exception dae.tools.pheno2browser.CLIError(msg: str)

Bases: Exception

Generic exception to raise and log different fatal errors.

dae.tools.pheno2browser.build_pheno_browser(dbfile, pheno_name, output_dir, pheno_regressions=None)

dae.tools.pheno2browser.calc_dbfile_hashsum(dbfilename)

dae.tools.pheno2browser.main(argv=None)

Command line options.

dae.tools.pheno2dae module

dae.tools.remote_instance_mirror module

dae.tools.simple_family2pedigree module

dae.tools.simple_family2pedigree.main(argv)

dae.tools.simple_family2pedigree.parse_cli_arguments(argv=['-b', 'html', '-d', '_build/doctrees', '.', '_build/html'])

dae.tools.simple_pheno_import module

dae.tools.simple_study_import module

dae.tools.simple_study_import.build_import_project(args: Namespace, gpf_instance: GPFInstance) → ImportProject

Build an import project based on the CLI arguments.

dae.tools.simple_study_import.cli_arguments(dae_config: Box, argv: list[str] | None = None) → Namespace

Create and return CLI arguments parser.

dae.tools.simple_study_import.main(argv: list[str] | None = None, gpf_instance: GPFInstance | None = None) → None

Run the simple study import procedure.

dae.tools.toGATKformat module

dae.tools.vcf2parquet module

dae.tools.vcfinfo_extractor module

dae.tools.vcfinfo_extractor.info_get(info, column=None)

dae.tools.vcfinfo_extractor.info_get_allele(info, column=None)

dae.tools.vcfinfo_extractor.info_get_allele_percent(info, column=None)

dae.tools.vcfinfo_extractor.main(argv, gpf_instance=None)

Module contents