gnomad_qc.v5.resources.release

Script containing release related resources.

Module Functions

`gnomad_qc.v5.resources.release.release_coverage_path`([...])	Fetch filepath for v5 (AoU + gnomAD v4 genomes) all sites coverage or allele number release Table.
`gnomad_qc.v5.resources.release.release_coverage_tsv_path`([...])	Fetch path to coverage TSV file.
`gnomad_qc.v5.resources.release.release_all_sites_an_tsv_path`([...])	Fetch path to all sites AN TSV file.
`gnomad_qc.v5.resources.release.release_coverage`([...])	Retrieve versioned resource for coverage release Table.
`gnomad_qc.v5.resources.release.release_all_sites_an`([...])	Retrieve versioned resource for all sites allele number release Table.

Script containing release related resources.

gnomad_qc.v5.resources.release.release_coverage_path(release_version='5.0', public=False, test=False, coverage_type='coverage', environment='rwb')[source]

Fetch filepath for v5 (AoU + gnomAD v4 genomes) all sites coverage or allele number release Table.

Parameters:

release_version (str) – Release version.
public (bool) – Determines whether release coverage Table is read from public (True) or private (False) bucket. Default is False.
test (bool) – Whether to use a tmp path for testing. Default is False.
coverage_type (str) – ‘coverage’ or ‘allele_number’. Default is ‘coverage’.
environment (str) – Environment to use. Default is “rwb”.

Return type:

str

Returns:

File path for desired coverage Hail Table.

gnomad_qc.v5.resources.release.release_coverage_tsv_path(release_version='5.0', test=False, environment='rwb')[source]

Fetch path to coverage TSV file.

Parameters:

release_version (str) – Release version. Default is CURRENT_COVERAGE_RELEASE[“genomes”].
test (bool) – Whether to use a tmp path for testing. Default is False.
environment (str) – Environment to use. Default is “rwb”.

Return type:

str

Returns:

Coverage TSV path.

gnomad_qc.v5.resources.release.release_all_sites_an_tsv_path(release_version=None, test=False, environment='rwb')[source]

Fetch path to all sites AN TSV file.

Parameters:

release_version (str) – Release version. Default is None.
test (bool) – Whether to use a tmp path for testing. Default is False.
environment (str) – Environment to use. Default is “rwb”.

Return type:

str

Returns:

All sites AN TSV path.

gnomad_qc.v5.resources.release.release_coverage(public=False, test=False, environment='rwb')[source]

Retrieve versioned resource for coverage release Table.

Parameters:

public (bool) – Determines whether release coverage Table is read from public (True) or private (False) bucket. Default is False.
test (bool) – Whether to use a tmp path for testing. Default is False.
environment (str) – Environment to use. Default is “rwb”.

Return type:

VersionedTableResource

Returns:

Coverage release Table.

gnomad_qc.v5.resources.release.release_all_sites_an(public=False, test=False, environment='rwb')[source]

Retrieve versioned resource for all sites allele number release Table.

Parameters:

public (bool) – Determines whether release allele number Table is read from public or private bucket. Default is private.
test (bool) – Whether to use a tmp path for testing. Default is False.
environment (str) – Environment to use. Default is “rwb”.

Return type:

VersionedTableResource

Returns:

All sites allele number release Table.