pgfinder.find_pg
================

.. py:module:: pgfinder.find_pg

.. autoapi-nested-parse::

   Run pgfinder at the command line.

   ..
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Attributes
----------

.. autoapisummary::

   pgfinder.find_pg.LOGGER
   pgfinder.find_pg.LOGGER


Functions
---------

.. autoapisummary::

   pgfinder.find_pg.create_parser
   pgfinder.find_pg.process_file
   pgfinder.find_pg.main


Module Contents
---------------

.. py:data:: LOGGER

.. py:data:: LOGGER

.. py:function:: create_parser() -> argparse.ArgumentParser

   
   Create a parser for reading options.
















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.. py:function:: 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)

   
   Process files

   :param input_file: Mass Spectrometry input file to process.
   :type input_file: str | Path
   :param masses_file: Input file of known masses.
   :type masses_file: str | Path
   :param mod_list: Modifications to include.
   :type mod_list: list
   :param ppm_tolerance: Parts Per Million tolerance for matching.
   :type ppm_tolerance: float
   :param time_delta: Time difference.
   :type time_delta: int
   :param output_dir: Output directory where results are written to.
   :type output_dir: str | Path
   :param float_format: Decimal places to use in CSV files.
   :type float_format: int
   :param to_csv: Dictionary of options to pass to pd.to_csv(), primarly used to overwrite existing files.
   :type to_csv: dict















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.. py:function:: main()

   
   Run processing.
















   ..
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