UCSC-custom-track-generator

Script to automatically generate custom tracks to load in the UCSC Genome Browser.

Usage

Simply pass the script a list of your input files, and the base URL for UCSC to access the files from.

./make-tracks.py test1.bw test2.bw -url http://myserver.edu.external/

UCSC Tracks output to file:
UCSC_custom_tracks-2017-04-04-16-45-46.txt

Output will look like this:

track type=bigWig name="test1.bw" bigDataUrl=http://myserver.edu.external/test1.bw
track type=bigWig name="test2.bw" bigDataUrl=http://myserver.edu.external/test2.bw

You can pass a mixed list of files, and the script will create a track tailored for each file's type. An output file can also be specified, instead of the default timestamped file (warning: output file will be overwritten).

find sample-data/mixed/ -type f ! -name "*.bai" | xargs ./make-tracks.py -url http://myserver.edu.external/ -o my_custom_tracks.txt

UCSC Tracks output to file:
my_custom_tracks.txt

In this case, our output file my_custom_tracks.txt looks like this:

track type=BAM name="test.bam" bigDataUrl=http://myserver.edu.external/test.bam
track type=bigWig name="test.bw" bigDataUrl=http://myserver.edu.external/test.bw

Params file

Extra params to be included in each track can be placed in a separate params file. This file should contain items to be included in every track, with one item per line. The params file argument can be invoked like this:

./make-tracks.py sample-data/bigwigs/test1.bw sample-data/bigwigs/test2.bw -url http://myserver.edu.external/ -p bigwig_params.txt

Where bigwig_params.txt is our params file, and contains:

visibility=full
autoScale=off
alwaysZero=on
maxHeightPixels=50
graphType=bar
viewLimits=0:0.3

Resulting in tracks that looks like this:

track type=bigWig name="test1.bw" bigDataUrl=http://myserver.edu.external/test1.bw visibility=full autoScale=off alwaysZero=on maxHeightPixels=50 graphType=bar viewLimits=0:0.3
track type=bigWig name="test2.bw" bigDataUrl=http://myserver.edu.external/test2.bw visibility=full autoScale=off alwaysZero=on maxHeightPixels=50 graphType=bar viewLimits=0:0.3

Notes

URL

The URL supplied must be reachable by UCSC. If the URL requires a user-login, it will not work. If you are not sure, you should test the URL for one or more tracks by trying to navigate to them from your web browser; login screens and network restrictions may prevent them from working for UCSC.

The basename of the provided file is simply added to the end of the supplied URL. For example, file external/path/to/my/peaks.bigbed and URL http://server.edu/external/path/to will combine as http://server.edu/external/path/to/peaks.bigbed; be sure to provide the full path to the file in the base URL. More complex relative path matching between the provided file path & URL path is not yet implemented.

Supported Types

Currently, only the following file formats are supported by the script:

• bigWig: .bw, .bigwig
• bigBed: .bb, .bigbed, bigBed
• VCF: .vcf
• BAM: .bam

More types may be added later (or you can add them yourself in the script).

Unsupported Customizations

This script is designed to apply attributes to tracks for all given files; it is currently not set up to include browser customizations such as:

browser position chr22:10000000-10020000
browser hide all

These options are easy enough to copy/paste into your tracks text file as-is.

More information

Information on track customization can be found here:

• https://genome.ucsc.edu/goldenpath/help/hgTracksHelp.html
• https://genome.ucsc.edu/goldenpath/help/customTrack.html

You can load your custom tracks here:

• https://genome.ucsc.edu/cgi-bin/hgCustom

Software Requirements

• Python 2.7+ (tested on 2.7.3 and 3.4.3)