karyoplot: annotations along the genome
Project description
karyoplot
What is karyoplot ?
karyoplot
is a python package developed to draw simple karyoplot/ideogram with a simple configuration file like Circos [1], without any lines of code like karyoploteR [2].
karyoplot
deals with conventional bioinformatics formats (.bed, .fasta, .gff, .gtf, .vcf, ...) to avoid file manipulations before drawing.
How does it work ?
karyoplot
takes as an argument a configuration file with different sections which will have a sequence Fasta file as reference for ideograms. Every plot to draw on reference sequences is described in a track section with link to associated data and drawing options.
karyoplot
is mainly based on matplotlib
for graph rendering and pysam for bioinformatics file format parsing.
karyoplot
is under developpement, currently supported format are:
- fasta
- bed
available soon:
- gff
- vcf
- bam
- wig/bigWig
Install
create your virtual env in a dedicated directory
python3 -m venv $HOME/myvenvs/karyoplot
set up the new env
source $HOME/myvenvs/karyoplot/bin/activate
install karyoplot
pip install karyoplot
enjoy
karyoplot -h
to leave the env
deactivate
Usage
Simple usage
karyoplot config.ini -o genome_karyo.png -v 2
The config.ini
file is a configuration file in Microsoft Windows INI style, readable by the configparser Python module.
Some sections are expected with defined options to customize your plot. See the associated documentation here for full options and required sections/options.
Support
For any request please contact nicolas.lapalu[at]inrae.fr or adeline.simon[at]inrae.fr
Authors and acknowledgment
- Rosanne Phebe
- Nicolas Lapalu
- Adeline Simon
License
licensed under GNU General Public License v3.0
References
- [1] Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645
- [2] Bernat Gel & Eduard Serra. (2017). karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics, 31–33. doi:10.1093/bioinformatics/btx346
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for karyoplot-0.0.2-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 9b84a52142778251ed219a99e48bd30fc936a5008a14bb7952bf6e646c8721a9 |
|
MD5 | c1e59fd27e2a000e9bfa4ef7aadbaa6e |
|
BLAKE2b-256 | 038349b5fd09d03a66595e18e8589ed4e5f366744709946e520a1333b408fcea |