seismicrna.collate package

Submodules

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

Collate HTML graph files (and SVG drawings) into one HTML file.

Parameters:

  • input_graphs (Iterable[Path]) – Paths to the HTML and/or SVG files to collate.

  • out_path (Path) – Path to write the output collated HTML file.

  • group (str) – Field by which to group graphs in the output (e.g. “sample”, “ref”, “reg”, “branches”, or “all”).

  • portable (bool) – If True, embed all resources so the HTML file is self-contained.

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

Determine the output path for the collated HTML file.

Parameters:

  • name (str) – Base name for the output collated file.

  • verbose_name (bool) – If True, include sample, reference, region, and graph type information in the output file name.

  • input_files (list[Path]) – List of input graph/SVG files to be collated.

  • collate_out_dir (str | Path | None) – Directory for the output file; if None, use the common ancestor directory of the input files.

seismicrna.collate.main.run(input_path: Iterable[str | Path] = Sentinel.UNSET, 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]