MetaPhlAnTaxaProcessor

MetaPhlAnTaxaProcessor is a Python-based utility designed to streamline the downstream analysis of MetaPhlAn output. It processes MetaPhlAn's taxonomic profiling data, converting it into structured CSV files for each taxonomic rank (e.g., Kingdom, Phyla, Class, etc.). Additionally, it offers the option to consolidate these CSV files into a single Excel workbook, with each sheet named after the corresponding taxonomic rank. This tool enhances the accessibility and interpretability of metagenomic data, facilitating further statistical analysis and visualization.

Table of Contents

• Installation
• Usage
• License

Installation

You can install the latest version of MetaPhlAnTaxaProcessor using pip:

pip install metaphlantaxaprocessor

Usage

Once installed, you can use MetaPhlAnTaxaProcessor via the command line to process your MetaPhlAn output files.

Basic Command

metaphlan-taxaprocessor.main INPUT_TSV_FILE

Where INPUT_TSV_FILE is the path to your MetaPhlAn-generated TSV file.

Available Options

• --outdir: Specify the output directory for the generated CSV files (default is <prefix>-taxa).
• --combine: Optionally combine the generated CSV files into a single Excel workbook.

Example usage with options:

metaphlan-taxaprocessor.main tests/test_data/Galaxy-res.tsv --outdir ./output --combine

This command will process the Galaxy-res.tsv file and store the CSVs in the ./output directory, then combine them into a single Excel workbook.

License

metaphlantaxaprocessor is distributed under the terms of the MIT license.