pgfinder.find_pg

Run pgfinder at the command line.

Module Contents

Functions

create_parser(→ argparse.ArgumentParser)

Create a parser for reading options.

process_file(input_file, masses_file, mod_list[, ...])

Process files

main()

Run processing.

Attributes

LOGGER

LOGGER

pgfinder.find_pg.LOGGER
pgfinder.find_pg.LOGGER
pgfinder.find_pg.create_parser() → argparse.ArgumentParser[source]

Create a parser for reading options.

pgfinder.find_pg.process_file(input_file: str | pathlib.Path, masses_file: str | pathlib.Path, mod_list: list, ppm_tolerance: float = 10, consolidation_ppm: float = 1, time_delta: int = 0.5, output_dir: str | pathlib.Path = './', float_format: int = 4, to_csv: dict = None)[source]

Process files

Parameters:

  • input_file (str | Path) – Mass Spectrometry input file to process.

  • masses_file (str | Path) – Input file of known masses.

  • mod_list (list) – Modifications to include.

  • ppm_tolerance (float) – Parts Per Million tolerance for matching.

  • time_delta (int) – Time difference.

  • output_dir (str | Path) – Output directory where results are written to.

  • float_format (int) – Decimal places to use in CSV files.

  • to_csv (dict) – Dictionary of options to pass to pd.to_csv(), primarly used to overwrite existing files.

pgfinder.find_pg.main()[source]

Run processing.