pyTax4Fun2cli

Command line interface for pyTax4Fun2

Authors

• Ninda Rachmadani (Department of Biology, Faculty of Matehematics and Natural Sciences,Brawijaya University)
• Maulana Malik Nashrulloh (Division of Biomics Research, Department of Sciences, Generasi Biologi Indonesia Foundation)
• Irfan Mustafa (Department of Biology, Faculty of Matehematics and Natural Sciences,Brawijaya University)
• Brian Rahardi (Department of Bioinformatics, Faculty of Mathematics and Natural Sciences, Brawijaya University)
• Choirul Ainiyati (Division of Biomics Research, Department of Sciences, Generasi Biologi Indonesia Foundation)
• Khalid Hafazallah (Division of Ecology and Conservation, Department of Sciences, Generasi Biologi Indonesia Foundation)
• Reza Raihandhany (Division of Botany, Department of Sciences, Generasi Biologi Indonesia Foundation)
• Muhammad Badrut Tamam (Division of Biomics Research, Department of Sciences, Generasi Biologi Indonesia Foundation)

Quick Start

Dependencies

Make sure that your system have Python >=3.11 installed and these packages/libraries installed:

• pyTax4Fun2==1.2.1
• argparse==1.4.0
• PyYAML==6.0.3
• psutil==7.0.0
• jinja2==3.1.6
• polars[rt64]==1.39.3
• matplotlib==3.10.8
• seaborn==0.13.2

Installation

Currently we only support installation thru pip command only.

pip install pyTax4Fun2cli

We recommend you to install pyTax4Fun2 in an isolated conda environment, e.g. my_pyTax4Fun2. While we use Python>=3.11, we recommend you to use latest Python 3.14 for much better support. Please install these programs

conda create -n my_pyTax4Fun2 python=3.14
conda install anaconda::pyarrow==22.0.0
conda install conda-forge::uproc
conda install bioconda::blast diamond prodigal vsearch
pip install pyTax4Fun2
pip install pyTax4Fun2cli

Acknowledgments

• This program was made as part of research mini-project "PyTax4Fun2: A Python Tool for Functional Profiling and Redundancy Analysis of Bacterial Communities via 16S rRNA Gene Sequences, Featuring Polars for Efficient Processing of Large Genomic Datasets" (Project #BIOMIKA-02), funded internally by Generasi Biologi Indonesia Foundation.
• The collaboration project between Generasi Biologi Indonesia Foundation and Faculty of Mathematics and Natural Sciences Brawijaya University was made possible thru the Cooperation Agreement No. 05.294/Genbinesia/I/2026 and No. 00818/DST/UN10.F0901/B/KS/2026.
• Ninda Rachmadani was supported by Generasi Biologi Indonesia Foundation Undergraduate Thesis Assistance Program thru Contract No. 01.297/Genbinesia/IV/2026.

Citation

A dedicated publication for this program is not yet available. For citation purposes, please refer to the following technical reports and theses:

• Nashrulloh, M.M., Rahardi, B. (2026). pyTax4Fun2: A Python Tool for Functional Profiling and Redundancy Analysis of Bacterial Communities via 16S rRNA Gene Sequences, Featuring Polars for Efficient Processing of Large Genomic Datasets—I: Initial Development (Technical Report No. GBR-TR-BIOMIKA-02/Genbinesia/I/2026). Generasi Biologi Indonesia Foundation. Gresik, Indonesia.

• Rachmadani, N., Nashrulloh, M.M., Mustafa, I., Rahardi, B., Ainiyati, C., Hafazallah, K., Raihandhany, R., Tamam, Mh.B. (2026). pyTax4Fun2: A Python Tool for Functional Profiling and Redundancy Analysis of Bacterial Communities via 16S rRNA Gene Sequences, Featuring Polars for Efficient Processing of Large Genomic Datasets—II: Further Development (On Alpha Diversity and Beta Diversity) (Technical Report No. GBR-TR-BIOMIKA-04/Genbinesia/III/2026). Generasi Biologi Indonesia Foundation. Gresik, Indonesia.

• Rachmadani, N. (2026). Komparasi analisis fungsional komunitas bakteri berbasis sekuen gen 16S rRNA menggunakan pyTax4Fun2 dan Tax4Fun2. Undergraduate Thesis. Departemen Biologi, Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Brawijaya. Malang, Indonesia. [in Indonesian].

If you wish to cite this repository, you may use the following APA-style reference entry:

Rachmadani, N., Nashrulloh, M.M., Mustafa, I., Rahardi, B., Ainiyati, C., Hafazallah, K., Raihandhany, R., Tamam, Mh.B. (2026). pyTax4Fun2cli: Command line interface for pyTax4Fun2 (Version 1.2.1.1) [Computer software]. https://gitlab.com/biomikalab/pytax4fun2cli

License

This project is licensed under the GNU Affero General Public License v3.0 - See the LICENSE file for details.