LoVis4u (original) (raw)

Description

LoVis4u is a bioinformatics tool for Locus Visualisation.

Supported input: Genbank, gff3 with sequence
Supported output: Static vector graphics (pdf)
Programming language: Python3
OS: MacOS, Linux
Python dependencies: biopython, bcbio-gff, scipy, configs, argparse, pandas, distinctipy, matplotlib, seaborn, reportlab
Python version: >= 3.9
OS-level dependencies: MMseqs2 (included in the package)
License: WTFPL
Version: 0.0.9.3 (October 2024)

Pipeline

Visualisation example

See the gallery page for more examples

Installation

• LoVis4u can be installed directly from pypi:

[](#%5F%5Fcodelineno-0-1)python3 -m pip install lovis4u

• The development version is available at github :

[](#%5F%5Fcodelineno-1-1)git clone https://github.com/art-egorov/lovis4u.git [](#%5F%5Fcodelineno-1-2)cd lovis4u [](#%5F%5Fcodelineno-1-3)python3 -m pip install --upgrade pip [](#%5F%5Fcodelineno-1-4)python3 -m pip install setuptools wheel [](#%5F%5Fcodelineno-1-5)python3 setup.py sdist [](#%5F%5Fcodelineno-1-6)python3 -m pip install .

! If you're a linux user, run lovis4u --linux post-install command once to update paths in the premade config files that set by default for MacOS users.

Reference

If you find LoVis4u useful, please cite:
Artyom. A. Egorov, Gemma C. Atkinson, LoVis4u: Locus Visualisation tool for comparative genomics, bioRxiv 2024.09.11.612399; doi: 10.1101/2024.09.11.612399

Please contact us by e-mail artemdotegorovATmeddotludotse or use Issues to report any technical problems.
You can also use Discussions section for sharing your ideas or feature requests!

LoVis4u is developed by Artyom Egorov at the Atkinson Lab, Department of Experimental Medical Science, Lund University, Sweden. We are open for suggestions to extend and improve LoVis4u functionality. Please don't hesitate to share your ideas or feature requests.