trackhub

trackhub is a Python package for handling the creation and uploading of track hubs for the UCSC Genome Browser (see http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html for more info)

Some reasons for using trackhub to manage your track hubs:

• filename handling: automatic (yet still completely configurable, if needed) handling of filenames and directory structure
• uploading: upload a full hub -- hub/genomes/trackdb files, plus all data files (bam/bigWig/bigBed) -- via rsync over ssh
• validation: mechanisms for handling validation of parameters so errors are [hopefully] caught prior to uploading
• rapid deployment: mapping local filenames to remote filenames on the host enables rapid updating of the hub with new or updated data (e.g., when analysis parameters change)
• flexibility: support for simple hubs up through complex composite hubs with views and subtracks
• extensible: provides a framework for working with hub components, allowing new functionality to be easily added

Full documentation, including a full in-depth tutorial, can be found at http://packages.python.org/trackhub.

Here's an example of creating a hub, and uploading the hub and files to a remote server. This hub will show all the bigWig files in the current directory, and any of them that have "control" in the filename will be colored gray in the hub

from trackhub imoprt Track, default_hub
from trackhub.upload import upload_hub, upload_track

hub, genomes_file, genome, trackdb = default_hub(
    hub_name="myhub",
    genome="hg19",
    short_label="example hub",
    long_label="My example hub",
    email="[email protected]")

# publicly accessible hub URL
hub.url = "http://example.com/hubs/my_example_hub.txt"

# hub's location on remote host, for use with rsync
hub.remote_fn = "/var/www/data/hubs/my_example_hub.txt"

# Make tracks for all bigWigs in current dir
import glob, os
for fn in glob.glob('*.bigwig'):
    label = fn.replace('.bigwig', '')

    # Parameters are checked for valid values, see
    # http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html
    # for what's available
    track = Track(
        name=label,
        short_label=label,
        long_label=label,
        autoScale='off',
        local_fn=fn,
        tracktype='bigWig',
        )
    trackdb.add_tracks(track)

# Demonstrate some post-creation adjustments...here, just make control
# samples gray
for track in trackdb.tracks:
    if 'control' in track.name:
        track.add_params(color="100,100,100")

# Render the hub to text files
hub.render()

# Upload the hub files and all the bigwig files using rsync.
kwargs = dict(host='www.example.com', user='me')
upload_hub(hub=hub, **kwargs)
for track, level in hub.leaves(Track):
    upload_track(track=track, **kwargs)

Note: trackhub is still under active development and should be considered an alpha version. Please open an issue on github (https://github.com/daler/trackhub/issues) if you run into problems.

Copyright 2012 Ryan Dale; BSD 2-clause license.