dae.tools package

Submodules

dae.tools.cnv_liftover module

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

Liftover de Novo variants tool main function.

dae.tools.cnv_liftover.parse_cli_arguments(argv: list[str]) → Namespace

Create CLI parser.

dae.tools.dae2vcf module

dae.tools.dae2vcf.main(argv: list[str] | None = None, grr: GenomicResourceRepo | None = None) → None

Convert transmitted DAE variants into VCF file format.

dae.tools.dae2vcf.parse_cli_arguments(argv: list[str]) → Namespace

Create CLI parser.

dae.tools.dae_liftover module

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

Liftover dae variants tool main function.

dae.tools.dae_liftover.parse_cli_arguments() → ArgumentParser

Create CLI parser.

dae.tools.denovo2vcf module

dae.tools.denovo2vcf.main(argv: list[str] | None = None, grr: GenomicResourceRepo | None = None) → None

Liftover de Novo variants tool main function.

dae.tools.denovo2vcf.parse_cli_arguments(argv: list[str]) → Namespace

Create CLI parser.

dae.tools.denovo_liftover module

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

Liftover de Novo variants tool main function.

dae.tools.denovo_liftover.parse_cli_arguments(argv: list[str]) → Namespace

Create CLI parser.

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: Family) → list[Layout]

dae.tools.draw_pedigree.draw_families(families: FamiliesData) → Generator[Figure, None, None]

Draw families.

dae.tools.draw_pedigree.draw_families_report(families: FamiliesData) → Generator[Figure, None, None]

Draw families from families report.

dae.tools.draw_pedigree.draw_pedigree(layout: list[Layout], title: str, *, show_family: bool = True, tags: set[str] | None = None) → Figure

Draw a pedigree layout.

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

Run the CLI for draw_pedigree tool.

dae.tools.generate_common_report module

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

Command line tool to generate dataset statistics.

dae.tools.generate_denovo_gene_sets module

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

Generate denovo gene sets CLI.

dae.tools.gpf_convert_study_config module

dae.tools.gpf_convert_study_config.load_study_config(study_config_filename: str) → dict

Load study config.

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

Convert GPF genotype data configuration to YAML.

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.

counter(status: TestStatus) → int

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.

counter(status: TestStatus) → int

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[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, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

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.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.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.to_gpf_gene_models_format module

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

Convert gene models to default GPF gene models format.

dae.tools.vcf2tsv module

dae.tools.vcf2tsv.main(argv: list[str] | None = None, grr: GenomicResourceRepo | None = None) → None

Liftover de Novo variants tool main function.

dae.tools.vcf2tsv.parse_cli_arguments(argv: list[str]) → Namespace

Create CLI parser.

dae.tools.vcf_liftover module

dae.tools.vcf_liftover.liftover_header(vcffile: str, source_genome: ReferenceGenome, target_genome: ReferenceGenome) → VariantHeader

Create liftover VCF header.

dae.tools.vcf_liftover.main(argv: list[str] | None = None, grr: GenomicResourceRepo | None = None) → None

Liftover dae variants tool main function.

dae.tools.vcf_liftover.parse_cli_arguments() → ArgumentParser

Create CLI parser.

dae.tools.vcf_liftover.report_alleles(alleles: list[tuple[str, int, str, str]]) → str

Report alleles.

dae.tools.vcf_liftover.report_variant(variant: tuple[str, int, str, list[str]] | None) → str

Report variant.

dae.tools.vcf_liftover.report_vcf_variant(vcf_variant: VariantRecord) → str

Report VCF variant.

Module contents