ezTracks (easy tracks) plots a single GTF annotation followed by grouped bed files. ezTracks preprocesses the input tracks, allowing to change and render the plot faster. It's smart enough to detect all beds inside folders, and also to omit tracks when they result empty in the queried region.

The core of this tool is pyGenomeTracks.

With ezTracks you can generate three different views:

Check test/config.region.ini

Check test/config.trans.ini

Check test/config.trans_ni_ff.ini

The program it's just the file eztracks.py. It works on Linux and Windows (Ubuntu WSL1) (I have not checked on Mac but it should work too).

I suggest to setup a conda environment (Python 3.6+) for installing ezTracks dependencies:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

conda create -n eztracks --yes python=3
conda activate eztracks
conda install -c anaconda freetype
conda install -c bioconda bedtools
pip install git+https://github.com/deeptools/HiCMatrix.git
pip install git+https://github.com/deeptools/pyGenomeTracks.git

Note: if you are having problems activating the environment, probably you can replace the line

conda activate eztracks

with

source ~/anaconda3/etc/profile.d/conda.sh && conda activate eztracks

ezTracks only needs a configuration file to work. The options implemented are the same as the sample file test/config.*.ini. To generate the first image shown above you just need to enter the test folder and run:

conda activate eztracks
python eztracks.py check test/config.region.ini
python eztracks.py prepare test/config.region.ini
python eztracks.py draw test/config.region.ini

The complete tutorial is located here. However, just keep in mind that the different modes are accessed via the configuration file in the [default] section:

• Update tutorial to cover all modes and explain parameters.
• Accept arguments via command line and override configuration file.
• Global configuration for PYGT template.