dae.variants_loaders.parquet package

Subpackages

• dae.variants_loaders.parquet.tests package
  • Submodules
  • dae.variants_loaders.parquet.tests.conftest module
  • dae.variants_loaders.parquet.tests.test_filepaths module
  • dae.variants_loaders.parquet.tests.test_full_variants module
  • dae.variants_loaders.parquet.tests.test_loader module
  • dae.variants_loaders.parquet.tests.test_readers module
  • dae.variants_loaders.parquet.tests.test_summary_variants module
  • Module contents

Submodules

dae.variants_loaders.parquet.loader module

class dae.variants_loaders.parquet.loader.MultiReader(dirs: Iterable[str], columns: Iterable[str])

Bases: object

Incrementally fetch variants from multiple files.

This class assumes variants are ordered by their bucket and summary index!

close() → None

property current_idx: tuple[int, int]

class dae.variants_loaders.parquet.loader.ParquetLoader(layout: Schema2DatasetLayout)

Bases: object

Variants loader implementation for the Parquet format.

FAMILY_COLUMNS: ClassVar[list[str]] = ['bucket_index', 'summary_index', 'family_id', 'family_variant_data']

SUMMARY_COLUMNS: ClassVar[list[str]] = ['bucket_index', 'summary_index', 'allele_index', 'summary_variant_data', 'chromosome', 'position', 'end_position']

fetch_family_variants(region: Region | None = None) → Generator[FamilyVariant, None, None]

Iterate over family variants.

fetch_summary_variants(region: Region | None = None) → Generator[SummaryVariant, None, None]

Iterate over summary variants.

fetch_variants(region: Region | None = None) → Generator[tuple[SummaryVariant, list[FamilyVariant]], None, None]

Iterate over summary and family variants.

get_family_pq_filepaths(summary_path: str) → list[str]

Get all family parquet files for given summary parquet file.

get_summary_pq_filepaths(region: Region | None = None) → Generator[list[str], None, None]

Produce paths to available Parquet files grouped by region.

Can filter by region if region bins are configured.

static load_from_dir(input_dir: str) → ParquetLoader

exception dae.variants_loaders.parquet.loader.ParquetLoaderException

Bases: Exception

class dae.variants_loaders.parquet.loader.Reader(path: str, columns: Iterable[str])

Bases: object

Helper class to incrementally fetch variants.

This class assumes variants are ordered by their bucket and summary index!

BATCH_SIZE = 5000

close() → None

property current_idx: tuple[int, int]

Module contents