trann

A simple Python command-line tool for working with tabs (.csv, .xlsx) and phylogenetic tree in newick format files (like PhyML and FastTree outputs).
It automatically detects file types, reads their contents using the csv and openpyxl library, and provides clear error messages with colored console output.

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Project structure

trann/
├── src/
│   ├── trann.py        # main CLI logic (entry point)
│   ├── scripts.py       # helper functions
│   └── __init__.py
├── pyproject.toml       # project configuration
└── README.md

Dependencies

• python>=3.10
• biopython>=1.86
• numpy>=2.3.4
• openpyxl>=3.1.5

Installation

It is recommended to use virtual environment (conda or venv)

Clone the repository and install the package:

git clone https://github.com/pour221/trann.git
cd trann
uv pip install -e .

or without uv:

pip install -e .

Usage

trann -i info_table.csv -t newik.tree -o res_tree.tree

If no paths are provided (. as default), the tool automatically searches the current directory for:

the first .csv file (for --info)

the first .tree file (for --tree)

For instance:

trann

will use the first .csv file and the first .tree file.