ezTracks

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 without rebuilding indexes. It's smart enough to detect all beds inside folders, and also to omit tracks when they are not overlapping the queried region. Additionally, it generates annotations in BED and CSV format as well as an XML IGV session for further local inspection.

The core of this tool is pyGenomeTracks.

One advantage of ezTracks is the minimal effort to generate feature-oriented annotations and plots. For example, with a 17 line ezTracks configuration file one can automatically generate 150 lines of pyGenomeTracks' configuration and the corresponding annotation files. Additionally, one is not limited by the number of tracks/annotation BEDs plotted, as it usually occurs with genome browsers.

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Setup

The program it's just the file eztracks.py and the helper script reverseBed. It have been tested in Linux and Windows (Ubuntu WSL1).

I suggest to setup a conda environment (Python 3.7+) for installing ezTracks dependencies:

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

conda create -n eztracks -c bioconda -c conda-forge -c anaconda nomkl pygenometracks bedtools freetype python=3.7

Make sure you activate the environment (conda activate eztracks) before running the script. If you are having problems activating the environment, adjust to your local anaconda installation:

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

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Showcase

Data in test_config/test_tracks were obtained from the following references:

• Annotation: Frankish, Adam, et al. "GENCODE reference annotation for the human and mouse genomes." Nucleic acids research 47.D1 (2019): D766-D773.
• CRS: Seemann, Stefan E., et al. "The identification and functional annotation of RNA structures conserved in vertebrates." Genome research 27.8 (2017): 1371-1383.
• phastCons: Siepel, Adam, et al. "Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes." Genome research 15.8 (2005): 1034-1050.
• repeats: Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0. 2013-2015 <http://www.repeatmasker.org>. and Karolchik, Donna, et al. "The UCSC genome browser database." Nucleic acids research 31.1 (2003): 51-54..

With ezTracks you can generate three different views:

Plot genomic region

Look for annotations overlapping genomic coordinates. This is specified in the field region in the [default] section of the configuration file.

Example at test_config/config.region.ini

Query individual transcripts

ezTracks will look for a transcript ID in your GTF file. This is specified in the field transcript in the [default] section of the configuration file.

(Note: if region is also specified in the configuration, this mode won't work.)

Example at test_config/config.trans.ini

Transcript-relative annotation

One advantage of ezTracks over a regular genome browser is that you can easily get plots of the exonic regions of your transcript of interest. This is particularly usefull for long transcripts with low exonic content, such as lncRNAs. ezTracks will force the view to forward direction regardless of the transcript strand. ezTracks will look for a transcript ID in your GTF file. This is specified in the field transcript in the [default] section of the configuration file. Also, the option no_introns should be set to yes.

(Note: if region is also specified in the configuration, this mode won't work.)

Example at Check test_config/config.trans_relative.ini

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Micro tutorial

Introduction

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

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

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Output files

Output image

Output image as specified in the field output_img in the [plot] section of the configuration file.

config.ini

Configuration file for PyGenomeTracks. This is the file to modify if you want to fine tune your plot without rerunning the whole annotation. After modifying, you need to run the script cmd_draw.sh.

output.annotation.bed

Annotation in BED6 format. name field (column 4) is coded as DATASET</SUBDATASET>:FEATURE_NAME, and strand field (column 6) has a . if the dataset didn't include strand information. For the transcript-relative mode, the strand is indicated as relative to the strand direction, not the forward strand.

output.annotation.csv

Same information as output.annotation.bed but with DATASET and FEATURE_NAME split into two distinct columns.

output.igv.session.xml

The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. You can load this file into your IGV local installation.

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TODO

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

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About

Developed by Hugo Guillen, 2021.