Data visualization is critical at all steps of genomic data analysis, from QC through final figure preparation. A track hub is way of organizing large numbers of of genomic data “tracks” (data files in a supported format), configured with a set of plain-text files that determine the organization, UI, labels, color, and other details. The files comprising a track hub are uploaded to a server, and a genome browser (e.g., UCSC Genome Browser) is pointed to the served URL for viewing. For example, here is a track hub created by the ENCODE project. It is straightforward to write the configuration files and upload the tracks manually if you have a small number of tracks. For larger data sets however, this becomes tedious and error-prone.
trackhub is a Python package that enables the programmatic construction and
upload of arbitrarily complex track hubs. It has no dependencies besides Python
itself, the common Python package docutils, and the availability of
(a standard Unix command-line tool for remotely transferring files). It is
availabe on PyPI, bioconda, and GitHub; an automated test suite and tested
documentation ensure high-quality code and help.
See the documentation at https://daler.github.io/trackhub for more details.
trackhub validates parameters against UCSC’s documented options, so errors are caught early and less time is spent debugging in the Genome Browser.
The directory structure of an analysis rarely matches the organization you want
for a track hub. trackhub symlinks track files to a staging area so the hub
can be inspected locally before being uploaded, e.g., with
also enables rapid deployment and updating since only files that have changed
will be uploaded on subsequent calls.
Sensible defaults make it easy to build a functioning track hub. However, these defaults can always be overridden for complex configurations or when more precise control is needed. For example, by default a track’s name also becomes the shortLabel, longLabel and filename of the track in the hub unless any of these are overridden by the user.
Easy track documentation¶
Write track hub documentation in ReStructured Text, and it is converted to HTML, connected to the track and uploaded with the rest of the hub. This allows for programmatically including content without the tedium of writing HTML by hand.
The following code demonstrates a track hub built out of all bigWig files found in a directory. It is relatively simple; see these other examples from the documentation for more advanced usage:
- grouping example (load the grouping example hub in UCSC)
- html documentation example (load the HTML documentation example hub in UCSC)
- assembly example (load the assembly example hub in UCSC)
This basis example is run automatically when the documentation is re-generated. You can view the uploaded files in the trackhub-demo GitHub repository, and load the hub directly into UCSC to see what it looks like.
import glob, os import trackhub # First we initialize the components of a track hub hub, genomes_file, genome, trackdb = trackhub.default_hub( hub_name="myhub", short_label='myhub', long_label='myhub', genome="hg38", email="email@example.com") # Next, we add a track for every bigwig found. In practice, you would # point to your own files. In this example we use the path to the data # included with trackhub. for bigwig in glob.glob('../trackhub/test/data/sine-hg38-*.bw'): name = trackhub.helpers.sanitize(os.path.basename(bigwig)) track = trackhub.Track( name=name, # track names can't have any spaces or special chars. source=bigwig, # filename to build this track from visibility='full', # shows the full signal color='128,0,5', # brick red autoScale='on', # allow the track to autoscale tracktype='bigWig', # required when making a track ) # Each track is added to the trackdb trackdb.add_tracks(track) # In this example we "upload" the hub locally. Files are created in the # "example_hub" directory, along with symlinks to the tracks' data files. # This directory can then be pushed to GitHub or rsynced to a server. trackhub.upload.upload_hub(hub=hub, host='localhost', remote_dir='example_hub') # Alternatively, we could upload directly to a web server (not run in this # example): if 0: trackhub.upload.upload_hub( hub=hub, host='example.com', user='username', remote_dir='/var/www/example_hub')
Copyright 2012-2017 Ryan Dale; MIT license.
- Organizing larger track hubs
- Documenting tracks in hubs
- Assembly example
- API documentation