KEGGaNOG

Motivation

eggNOG-mapper 🤝 KEGG-Decoder

• eggNOG-mapper is a beautiful tool for fast functional annotation of novel sequences. Yet it does not provide any visualization functions.
• KEGG-Decoder is a perfect tool for visualizing KEGG Pathways. But it only takes KEGG-Koala outputs as an input (including blastKOALA, ghostKOALA, KOFAMSCAN).
• KEGG-Koala is a web-tool which can work for more than 24 hours. eggNOG-mapper can be installed locally on your PC / server and work faster.
• This tool KEGGaNOG makes eggNOG-mapper meet KEGG-Decoder! It parses eggNOG-mapper output, make it fit for the input to KEGG-Decoder and then visualize KEGG Pathways as the heatmap!
• Pro-tip: eggNOG-mapper and KEGGaNOG could be wrapped into 🐍 Snakemake pipeline making metabolic profiling a "one-click" process!

Installation

KEGG-Decoder is hardwired into KEGGaNOG
KEGG-Decoder uses python=3.6
That's why KEGGaNOG uses this version too
There are some compatibility issues, yet they are managed (however, installing KEGGaNOG on macOS is a bit not standart)

# Linux / WSL / Intel Macs
conda create -n kegganog python=3.6
conda activate kegganog
pip install kegganog

# ARM Macs (Apple M1-M4 and so on)
CONDA_SUBDIR=osx-64 conda create -n kegganog python=3.6 python.app
conda activate kegganog
pip install kegganog
alias KEGGaNOG="pythonw $(which KEGGaNOG)"

# In case user needs to unalias KEGGaNOG from pythonw
unalias KEGGaNOG
# To check if KEGGaNOG uses python or pythonw
which KEGGaNOG

Usage Guide

usage: KEGGaNOG [-h] [--multi] -i INPUT -o OUTPUT [-dpi DPI] [-c COLOR] [-n NAME] [-g] [--version]

KEGGaNOG: Link eggNOG-mapper and KEGG-Decoder for pathway visualization.

optional arguments:
  -h, --help            show this help message and exit
  --multi               “Multi” mode allows to run KEGGaNOG on multiple
                        eggNOG-mapper annotation files (a text file with file
                        location paths must be passed to the input)
  -i INPUT, --input INPUT
                        Path to eggNOG-mapper annotation file
  -o OUTPUT, --output OUTPUT
                        Output folder to save results
  -dpi DPI, --dpi DPI   DPI for the output image (default: 300)
  -c COLOR, --color COLOR, --colour COLOR
                        Cmap for seaborn heatmap. Recommended options: Greys,
                        Purples, Blues, Greens, Oranges, Reds (default: Blues)
  -n NAME, --name NAME  Sample name for labeling (default: SAMPLE) (not active
                        in `--multi` mode)
  -g, --group           Group the heatmap based on predefined categories
  --version             show program's version number and exit

🔗 Please also visit KEGGaNOG wiki page

Contributing

Contributions are welcome! If you have any ideas, bug fixes, or enhancements, feel free to open an issue or submit a pull request.

Contact

For any inquiries or support, feel free to contact me via email

Happy functional annotation! 💻🧬