seismicrna.collate package

Submodules

seismicrna.collate.collate.collate_graphs(input_graphs: Iterable[Path], out_path: Path, group: str, portable: bool, **kwargs) → Path

seismicrna.collate.main.get_out_path(name: str, verbose_name: bool, input_files: list[Path], collate_out_dir: str | Path | None)

seismicrna.collate.main.run(input_path: Iterable[str | Path], name: str = 'collated', verbose_name: bool = False, include_svg: bool = True, include_graph: bool = True, *, group: str = 'sample', portable: bool = False, collate_out_dir: str | Path | None = None, force: bool = False, **kwargs) → list[Path]

Collate HTML graphs into one HTML file.

Parameters:

• name (str) – Prefix the HTML report with this name. [positional or keyword, default: ‘collated’]

• verbose_name (bool) – Add collated file information to report name. [positional or keyword, default: False]

• include_svg (bool) – Include RNA structure drawings from the draw module. [positional or keyword, default: True]

• include_graph (bool) – Include graphs from the graph module. [positional or keyword, default: True]

• group (str) – Group collated graphs by one of ‘sample’, ‘graph’, ‘branches’, ‘region’, or ‘all’. [keyword-only, default: ‘sample’]

• portable (bool) – Embed collated graphs into the output HTML file for portability at the expense of live updates and file size. [keyword-only, default: False]

• collate_out_dir (str | pathlib._local.Path | None) – Write collated report to this directory. By default, write to the lowest level directory common to all input graphs. [keyword-only, default: None]

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