rcx_tk.__main__

Functions

main()

rcx_tk - Processing tool for metabolomics data and metadata.

sequence(→ None)

Process a sequence metadata file.

alkanes(→ None)

Process an alkane retention index file.

msdial(→ None)

Process an MSDIAL output file to merge duplicate alignments.

Module Contents

rcx_tk.__main__.main()[source]

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.

rcx_tk.__main__.sequence(file_path: str, out_path: str) → None[source]

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.

Parameters:

  • file_path – Path to the input metadata file.

  • out_path – Path where the processed metadata will be saved.

rcx_tk.__main__.alkanes(file_path: str, out_path: str) → None[source]

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.

Parameters:

  • file_path – Path to the input alkane file.

  • out_path – Path where the processed alkane data will be saved.

rcx_tk.__main__.msdial(file_path: str, out_path: str, mz_tol_ppm: int) → None[source]

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

Parameters:

  • file_path – Path to the input MSDIAL output file.

  • out_path – Path where the processed MSDIAL data will be saved.

  • 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.