Skip to main content

Set of programs to process, analyze and visualize Hi-C data

Project description

[![PyPI Version](https://img.shields.io/pypi/v/pyGenomeTracks.svg?style=plastic)](https://pypi.org/project/deepTools/) [![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=plastic)](https://anaconda.org/bioconda/pygenometracks)

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](https://github.com/maxplanck-ie/pyGenomeTracks/raw/master/pygenometracks/tests/test_data/master_plot.png)

The configuration file for this image is [here](https://github.com/maxplanck-ie/pyGenomeTracks/blob/master/pygenometracks/tests/test_data/browser_tracks.ini)

Installation

pyGenomeTracks works with python 2.7 and python 3.6.

Currently, the best way to install pyGenomeTracks is

`bash $ pip install pyGenomeTracks `

If the latest version wants to be installed use:

`bash $ 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:

`bash $ 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:

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

pyGenomeTracks is used by [HiCExporer](https://hicexplorer.readthedocs.io/) and [HiCBrowser](https://github.com/maxplanck-ie/HiCBrowser) (See e.g. [Chorogenome navigator](http://chorogenome.ie-freiburg.mpg.de/) which is made with HiCBrowser)

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

pyGenomeTracks-1.0.tar.gz (25.4 kB view hashes)

Uploaded Source

Built Distribution

pyGenomeTracks-1.0-py2.py3-none-any.whl (29.1 kB view hashes)

Uploaded Python 2 Python 3

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