A tool for generating KEGG heatmaps from eggnog-mapper outputs.
Project description
KEGGaNOG
Motivation
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 takesKEGG-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
makeseggNOG-mapper
meetKEGG-Decoder
! It parseseggNOG-mapper
output, make it fit for the input toKEGG-Decoder
and then visualize KEGG Pathways as the heatmap! - Pro-tip:
eggNOG-mapper
andKEGGaNOG
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
# Linux / WSL / Intel Macs
conda create -n kegganog python=3.6
# ARM Macs (Apple M1-M4 and so on)
CONDA_SUBDIR=osx-64 conda create -n kegganog python=3.6
conda activate kegganog
pip install kegganog
Usage Guide
usage: KEGGaNOG [-h] -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
-i INPUT, --input INPUT
Path to eggnog-mapper output 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)
-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! 💻🧬
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