Skip to main content

A tool for generating KEGG heatmaps from eggnog-mapper outputs.

Project description

KEGGaNOG

Python3 Pandas Seaborn Matplotlib Numpy KEGG-Decoder License

Linux macOS

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

# 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] [-M] -i INPUT -o OUTPUT [-dpi DPI] [-c COLOR] [-n NAME]
                [-g] [-V]

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

optional arguments:
  -h, --help            show this help message and exit
  -M, --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
  -V, --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! 💻🧬

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

KEGGaNOG-0.5.6.tar.gz (13.9 kB view details)

Uploaded Source

Built Distribution

KEGGaNOG-0.5.6-py3-none-any.whl (18.6 kB view details)

Uploaded Python 3

File details

Details for the file KEGGaNOG-0.5.6.tar.gz.

File metadata

  • Download URL: KEGGaNOG-0.5.6.tar.gz
  • Upload date:
  • Size: 13.9 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.8.0 pkginfo/1.10.0 readme-renderer/34.0 requests/2.27.1 requests-toolbelt/1.0.0 urllib3/1.26.20 tqdm/4.64.1 importlib-metadata/4.8.3 keyring/23.4.1 rfc3986/1.5.0 colorama/0.4.5 CPython/3.6.13

File hashes

Hashes for KEGGaNOG-0.5.6.tar.gz
Algorithm Hash digest
SHA256 7b86e822d99b3ce340d4a97ce24c9a57434c3ae9ce8207bb9cf61fc91b474612
MD5 63343df7d0d7e1f574afdc734ad3cee8
BLAKE2b-256 5b94bf1e571858fddf4805c19fdb52ac0f7702f2ac0ed977de5d3de9c612435f

See more details on using hashes here.

File details

Details for the file KEGGaNOG-0.5.6-py3-none-any.whl.

File metadata

  • Download URL: KEGGaNOG-0.5.6-py3-none-any.whl
  • Upload date:
  • Size: 18.6 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.8.0 pkginfo/1.10.0 readme-renderer/34.0 requests/2.27.1 requests-toolbelt/1.0.0 urllib3/1.26.20 tqdm/4.64.1 importlib-metadata/4.8.3 keyring/23.4.1 rfc3986/1.5.0 colorama/0.4.5 CPython/3.6.13

File hashes

Hashes for KEGGaNOG-0.5.6-py3-none-any.whl
Algorithm Hash digest
SHA256 9739e127d72c30af07b250e7879849616553118e318aa696f01fda7f622b47df
MD5 7bf1b0a4d27ad114350c9f896b5ea0b4
BLAKE2b-256 763c0423b13e9124e947715e4acbf008bd0a6d2e642b80b7ceb7a55261c2f63e

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page