seismicrna.pool package

Submodules

class seismicrna.pool.data.PoolDataset(sample: str, datasets: Iterable[Dataset])

Bases: TallMutsDataset

Load pooled batches of relation vectors.

classmethod get_dataset_load_func()

Function to load one constituent dataset.

classmethod get_report_type()

Type of report.

seismicrna.pool.main.pool_samples(out_dir: Path, name: str, ref: str, samples: Iterable[str], *, force: bool)

Combine one or more samples into a pooled sample.

Parameters:

  • out_dir (pathlib.Path) – Output directory.

  • name (str) – Name of the pool.

  • ref (str) – Name of the reference

  • samples (Iterable[str]) – Names of the samples in the pool.

  • force (bool) – Force the report to be written, even if it exists.

Returns:

Path of the Pool report file.

Return type:

pathlib.Path

seismicrna.pool.main.run(input_path: tuple[str, ...], *, pool: str = '', max_procs: int = 16, parallel: bool = True, force: bool = False) → list[Path]

Merge samples (vertically) from the Relate step.

Parameters:

  • pool (str) – Pooled sample name [keyword-only, default: ‘’]

  • max_procs (int) – Run up to this many processes simultaneously [keyword-only, default: 16]

  • parallel (bool) – Run tasks in parallel or in series [keyword-only, default: True]

  • force (bool) – Force all tasks to run, overwriting any existing output files [keyword-only, default: False]

class seismicrna.pool.report.PoolReport(**kwargs: Any | Callable[[Report], Any])

Bases: Report, RefIO

classmethod auto_fields()

Names and automatic values of selected fields.

classmethod fields()

All fields of the report.

classmethod file_seg_type()

Type of the last segment in the path.

classmethod path_segs()