Welcome to karyoplot documentation!
======================================

:Author: Rosanne Phebe, Nicolas Lapalu and Adeline Simon - BioinfoBioger team
:Date: |today|
:Version: |version|


.. toctree::
   :hidden:

   install.rst
   options.rst
   use_cases.rst


What is karyoplot ?
-------------------

``karyoplot`` is a python package developed to draw simple karyoplot/ideogram with a simple coniguration file like Circos [#f1]_, without any lines of code like karyoploteR [#f2]_. 
The goal of ``karyoplot`` is use to deal with conventional bioinformatics formats (.bed, .fasta, .gff, .gtf, .vcf, ...) to avoid file manipulations before drawing. 

How does it work ?
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``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.

To start off, a well-formatted configuration file is required, you can learn how to set yours :ref:`options <config_file>`. The `config.ini` file is a configuration file in Microsoft Windows INI style, readable by the ``configparser`` Python module.

``karyoplot`` is under developpement, currently supported format are:

* fasta
* bed

available soon:

* gff
* vcf
* bam
* wig/bigWig
   
License
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licensed under GNU General Public License v3.0 

Support
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For any request please contact nicolas.lapalu[at]inrae.fr or adeline.simon[at]inrae.fr

References
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.. [#f1] Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645
.. [#f2] 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