rcx_tk.__main__
===============

.. py:module:: rcx_tk.__main__


Functions
---------

.. autoapisummary::

   rcx_tk.__main__.main
   rcx_tk.__main__.sequence
   rcx_tk.__main__.alkanes
   rcx_tk.__main__.msdial


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

.. py:function:: main()

   rcx_tk - Processing tool for metabolomics data and metadata.

   This tool provides subcommands for processing different types of metabolomics
   files: sequence metadata files, alkane retention index files, and MSDIAL
   output files.


.. py:function:: sequence(file_path: str, out_path: str) -> None

   Process a sequence metadata file.

   Processes a sequence metadata file to perform the following operations:
   - Validate and rearrange columns
   - Validate file names
   - Ensure 'injectionOrder' column is of integer type
   - Derive new metadata columns: sampleName, sequenceIdentifier,
     subjectIdentifier, and localOrder

   The processed metadata is exported as a TSV file.

   :param file_path: Path to the input metadata file.
   :param out_path: Path where the processed metadata will be saved.


.. py:function:: alkanes(file_path: str, out_path: str) -> None

   Process an alkane retention index file.

   Extracts and processes alkane retention index data from the input file,
   producing a structured output containing carbon numbers and retention times.
   The processed data is exported as a TSV file.

   :param file_path: Path to the input alkane file.
   :param out_path: Path where the processed alkane data will be saved.


.. py:function:: msdial(file_path: str, out_path: str, mz_tol_ppm: int) -> None

   Process an MSDIAL output file to merge duplicate alignments.

   Features with identical peak abundances across samples are identified
   as duplicates and merged using aggregation:
   - Mean aggregation for RT, m/z, and other numeric metadata
   - Concatenation for text metadata
   - Maximum values for abundance data

   :param file_path: Path to the input MSDIAL output file.
   :param out_path: Path where the processed MSDIAL data will be saved.
   :param mz_tol_ppm: Mass-to-charge tolerance in parts per million (PPM) used
                      to distinguish between duplicate alignments. Lower values create
                      finer groupings. Default is 5 PPM.