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Report

Report helper functions.

make_all_reports(pairs)

Make reports for all status levels into the output_folder specified in the config.

Parameters:

Name Type Description Default
pairs list[ProteinPair]

list of all protein pairs.

 required
Source code in src/xlranker/report.py 
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def make_all_reports(pairs: list[ProteinPair]) -> None:
    """Make reports for all status levels into the output_folder specified in the config.

    Args:
        pairs (list[ProteinPair]): list of all protein pairs.

    """
    output_folder = Path(config.output).joinpath("reports")
    output_folder.mkdir(exist_ok=True)
    make_report(pairs, ReportStatus.CONSERVATIVE, output_folder / "conservative.tsv")
    make_report(pairs, ReportStatus.MINIMAL, output_folder / "minimal.tsv")
    make_report(pairs, ReportStatus.EXPANDED, output_folder / "expanded.tsv")
    make_report(pairs, ReportStatus.ALL, output_folder / "all.tsv")

make_report(pairs, status, output_path)

Write network of protein pairs that have the level of the inputted status or higher.

Status order (highest on top): 1. Conservative 2. Minimal 3. Expanded 4. All

Parameters:

Name Type Description Default
pairs list[ProteinPair]

list of all protein pairs

 required
status ReportStatus

Minimum status to accept.

 required
output_path Path

output path to save pair to

 required
Source code in src/xlranker/report.py 
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def make_report(
    pairs: list[ProteinPair], status: ReportStatus, output_path: Path
) -> None:
    """Write network of protein pairs that have the level of the inputted status or higher.

    Status order (highest on top):
        1. Conservative
        2. Minimal
        3. Expanded
        4. All

    Args:
        pairs (list[ProteinPair]): list of all protein pairs
        status (ReportStatus): Minimum status to accept.
        output_path (Path): output path to save pair to

    """
    valid_pairs = [pair for pair in pairs if pair.report_status <= status]
    write_pair_to_network(valid_pairs, str(output_path))