from trackhub import 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)