seismicrna.lists package

Submodules

seismicrna.lists.listpos.find_pos(table: PosTable, max_fmut_pos: float, complement: bool)
seismicrna.lists.listpos.list_pos(table_file: Path, force: bool, **kwargs)

List positions meeting specific criteria from the table.

seismicrna.lists.listpos.run(input_path: tuple[str, ...], *, max_fmut_pos=1.0, complement: bool = False, force: bool = False, max_procs: int = 16, parallel: bool = True) → list[Path]

List positions meeting specific criteria from each table.

Parameters:

  • max_fmut_pos – Mask positions with more than this fraction of mutated base calls [keyword-only, default: 1.0]

  • complement (bool) – List the complement [keyword-only, default: False]

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

  • 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]

seismicrna.lists.lists.get_list_path(table: Table)

Get the path to a list file corresponding to a table.