Metadata-Version: 2.4
Name: pyTax4Fun2cli
Version: 1.2.1.1
Summary: Command line interface for pyTax4Fun2
Home-page: https://gitlab.com/biomikalab/pyTax4Fun2cli
Author: Ninda Rachmadani, Maulana Malik Nashrulloh, Irfan Mustafa, Brian Rahardi, Choirul Ainiyati, Khalid Hafazallah, Reza Raihandhany, Muhammad Badrut Tamam
Maintainer: Maulana Malik Nashrulloh
Maintainer-email: maulana@genbinesia.or.id
Project-URL: Documentation, https://gitlab.com/biomikalab/pyTax4Fun2cli
Project-URL: Source Code, https://gitlab.com/biomikalab/pyTax4Fun2cli
Project-URL: Bug Tracker, https://gitlab.com/biomikalab/pyTax4Fun2cli/issues
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: License :: OSI Approved :: GNU Affero General Public License v3
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Development Status :: 5 - Production/Stable
Requires-Python: >=3.11
Description-Content-Type: text/markdown
Requires-Dist: pytest==9.0.2
Requires-Dist: pytest-cov==7.0.0
Requires-Dist: black==26.1.0
Requires-Dist: flake8==7.3.0
Requires-Dist: pyTax4Fun2==1.2.1
Requires-Dist: argparse==1.4.0
Requires-Dist: PyYAML==6.0.3
Requires-Dist: psutil==7.0.0
Requires-Dist: jinja2==3.1.6
Requires-Dist: polars[rt64]==1.39.3
Requires-Dist: matplotlib==3.10.8
Requires-Dist: seaborn==0.13.2
Dynamic: author
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: maintainer
Dynamic: maintainer-email
Dynamic: project-url
Dynamic: requires-dist
Dynamic: requires-python
Dynamic: summary

# pyTax4Fun2cli

![Python Version](https://img.shields.io/badge/python-3.11+-blue.svg)
![License: AGPL v3](https://img.shields.io/badge/License-AGPLv3-blue.svg)
![Version](https://img.shields.io/badge/version-1.2.1.1-green.svg)

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.

```bash
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 

```bash
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.
