casanovoutils

casanovoutils — utilities for working with de novo peptide sequencing data.

Provides MGF file processing, precision/coverage evaluation, sequence alignment, and residue mass vocabulary management. Exposes configure_logging for consistent log setup across submodules.

Submodules

• casanovoutils.align
• casanovoutils.constants
• casanovoutils.datasets
• casanovoutils.denovoutils
• casanovoutils.graphloss
• casanovoutils.main
• casanovoutils.mgfutils
• casanovoutils.mzmlutils
• casanovoutils.preccov
• casanovoutils.residues
• casanovoutils.summarize_mgf
• casanovoutils.types

Functions

configure_logging(→ None)

Configure logging to stdout, optionally also writing to a file.

Package Contents

casanovoutils.configure_logging(log_file: os.PathLike | None = None, level: int | None = None) → None

Configure logging to stdout, optionally also writing to a file.

This function is a no-op if it’s already been called.

Parameters:

• log_file (PathLike, optional) – If provided, log output is written to this file in addition to stdout. The file is opened in append mode. If None (default), only stdout is used.

• level (int, optional) – Logging level. If None (default), reads from the LOG_LEVEL environment variable. If that is not set, defaults to logging.INFO.