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python module to plot beautiful and highly customizable genome browser tracks

License: GNU General Public License v3.0

Python 100.00%

pygenometracks's Introduction

PyPI Version bioconda-badge

pyGenomeTracks

Standalone program and library to plot beautiful genome browser tracks

pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:

  • bigwig
  • bed (many options)
  • bedgraph
  • links (represented as arcs)

pyGenomeTracks example

The configuration file for this image is here

Installation

pyGenomeTracks works with python 2.7 and python 3.6.

Currently, the best way to install pyGenomeTracks is with anaconda

$ conda install -c bioconda pygenometracks 

Also, pyGenomeTracks can be installed using pip

$ pip install pyGenomeTracks

If the latest version wants to be installed use:

$ pip install  git+https://github.com/maxplanck-ie/pyGenomeTracks.git

Usage

To run pyGenomeTracks a configuration file describing the tracks is required. The easiest way to create this file is using make_tracks_file which setups up a file with defaults that can be easily changed. The format is:

$ make_tracks_file --trackFiles <file1.bed> <file2.bw> ... -o tracks.ini

make_tracks_file uses the file ending to guess the file type.

Then, a region can be plotted using:

$ pyGenomeTracks --tracks tracks.ini --region chr2:10,000,000-11,000,000 -o nice_image.pdf

pyGenomeTracks is used by HiCExporer and HiCBrowser (See e.g. Chorogenome navigator which is made with HiCBrowser)

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