class TestUpload(object):
def setup(self):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(
name='track1',
tracktype='bam',
local_fn='data/track1.bam'
),
Track(
name='track2',
tracktype='bigWig',
local_fn='data/track2.bigwig',
),
]
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
@unittest.skipUnless(os.path.exists('data/track1.bam'), 'No test data')
def test_upload(self):
self.hub.remote_fn = os.path.join(
'uploaded_version',
self.hub.remote_fn)
self.hub.render()
upload.upload_hub(
'localhost',
None,
self.hub,
symlink=True,
symlink_dir='staging',
run_local=True,)
for t, level in self.hub.leaves(Track):
upload.upload_track(
track=t, host='localhost', user=None, run_local=True)
def test_render(self):
trackdb = str(self.trackdb)
# make sure some of the trackdb rendered correctly
assert 'track track1' in trackdb
assert 'bigDataUrl track1.bam' in trackdb
class TestUpload(object):
def setup(self):
self.hub = Hub(hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(name='track1', tracktype='bam', local_fn='data/track1.bam'),
Track(
name='track2',
tracktype='bigWig',
local_fn='data/track2.bigwig',
),
]
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
@unittest.skipUnless(os.path.exists('data/track1.bam'), 'No test data')
def test_upload(self):
self.hub.remote_fn = os.path.join('uploaded_version',
self.hub.remote_fn)
self.hub.render()
upload.upload_hub(
'localhost',
None,
self.hub,
symlink=True,
symlink_dir='staging',
run_local=True,
)
for t, level in self.hub.leaves(Track):
upload.upload_track(track=t,
host='localhost',
user=None,
run_local=True)
def test_render(self):
trackdb = str(self.trackdb)
# make sure some of the trackdb rendered correctly
assert 'track track1' in trackdb
assert 'bigDataUrl track1.bam' in trackdb
def create_hub(geo,
email=None,
upload=False,
upload_dir=".",
user=None,
host=None):
""" Create an UCSC track hub from a Geo object
"""
hub = Hub(hub=geo.gse,
short_label=geo.gse,
long_label="Hub for {0}".format(geo.gse),
email=email)
genomes_file = GenomesFile()
trackdb = TrackDb()
local_dir = geo.gse
#hub.remote_fn = os.path.join(upload_dir, geo.gse, os.path.basename(hub.local_fn))
all_tracks = {}
for sample in geo.samples.values():
genome = sample['genome']
all_tracks.setdefault(genome, [])
name = re.sub('[^0-9a-zA-Z]+', '_', sample['name'])
track = Track(
name=name,
url=os.path.join(HUB_URLBASE, geo.gse, genome,
"{0}.bw".format(sample['gsm'])),
tracktype='bigWig',
short_label=sample['gsm'],
long_label=name,
color='128,128,0',
maxHeightPixels='30:30:11',
)
basename = os.path.basename(track.url)
track.local_fn = os.path.join(local_dir, basename)
track.remote_fn = os.path.join(upload_dir, geo.gse, genome, basename)
all_tracks[genome].append(track)
for build, tracks in all_tracks.items():
genome = Genome(build)
trackdb.add_tracks(tracks)
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
results = hub.render()
if upload:
for track in trackdb.tracks:
upload_track(track=track, host=host, user=user)
upload_hub(hub=hub, host=host, user=user)
class TestUpload(object):
def setup(self):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(
name='track1',
tracktype='bam',
local_fn='data/track1.bam'
),
Track(
name='track2',
tracktype='bigWig',
local_fn='data/track2.bigwig',
),
]
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
def test_upload(self):
self.hub.remote_fn = os.path.join(
'uploaded_version',
self.hub.remote_fn)
self.hub.render()
upload.upload_hub(
'localhost',
None,
self.hub,
symlink=True,
symlink_dir='staging',
run_local=True,)
for t, level in self.hub.leaves(Track):
upload.upload_track(
track=t, host='localhost', user=None, run_local=True)
def create_hub(geo, email=None, upload=False, upload_dir=".", user=None, host=None):
""" Create an UCSC track hub from a Geo object
"""
hub = Hub(
hub=geo.gse,
short_label=geo.gse,
long_label="Hub for {0}".format(geo.gse),
email=email)
genomes_file = GenomesFile()
trackdb = TrackDb()
local_dir = geo.gse
#hub.remote_fn = os.path.join(upload_dir, geo.gse, os.path.basename(hub.local_fn))
all_tracks = {}
for sample in geo.samples.values():
genome = sample['genome']
all_tracks.setdefault(genome, [])
name = re.sub('[^0-9a-zA-Z]+', '_',sample['name'])
track = Track(
name=name,
url=os.path.join(HUB_URLBASE, geo.gse, genome, "{0}.bw".format(sample['gsm'])),
tracktype='bigWig',
short_label=sample['gsm'],
long_label=name,
color='128,128,0',
maxHeightPixels='30:30:11',
)
basename = os.path.basename(track.url)
track.local_fn = os.path.join(local_dir, basename)
track.remote_fn = os.path.join(upload_dir, geo.gse, genome, basename)
all_tracks[genome].append(track)
for build,tracks in all_tracks.items():
genome = Genome(build)
trackdb.add_tracks(tracks)
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
results = hub.render()
if upload:
for track in trackdb.tracks:
upload_track(track=track, host=host, user=user)
upload_hub(hub=hub, host=host, user=user)
class TestUpload(object):
def setup(self):
self.hub = Hub(hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(name='track1', tracktype='bam', local_fn='data/track1.bam'),
Track(
name='track2',
tracktype='bigWig',
local_fn='data/track2.bigwig',
),
]
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
def test_upload(self):
self.hub.remote_fn = os.path.join('uploaded_version',
self.hub.remote_fn)
self.hub.render()
upload.upload_hub(
'localhost',
None,
self.hub,
symlink=True,
symlink_dir='staging',
run_local=True,
)
for t, level in self.hub.leaves(Track):
upload.upload_track(track=t,
host='localhost',
user=None,
run_local=True)
if track.endswith(".bb") or track.endswith(".bigBed")
]
for bigBed_file in bigBed_files:
color = "0,100,0" if "pos" in bigBed_file else "100,0,0"
base_track = remove_special_chars(os.path.basename(bigBed_file))
long_name = args.sep.join(base_track.split(
args.sep)[:args.num_sep]) + ".bb"
track = Track(name=long_name,
url=os.path.join(URLBASE, GENOME, base_track),
tracktype="bigBed",
short_label=long_name,
long_label=long_name,
color=color,
local_fn=bigBed_file,
remote_fn=os.path.join(upload_dir, GENOME, base_track),
visibility="dense")
#trackdb.add_tracks(track)
supertrack.add_track(track)
trackdb.add_tracks(supertrack)
result = hub.render()
hub.remote_fn = os.path.join(upload_dir, "hub.txt")
for track in trackdb.tracks:
upload_track(track=track,
host=args.server,
user=args.user,
run_s3=args.no_s3)
upload_hub(hub=hub, host=args.server, user=args.user, run_s3=args.no_s3)
def main():
parser = argparse.ArgumentParser(
description=
'Takes in files to turn into trackhub. This version automatically ')
# tracks files
##############
parser.add_argument('files',
nargs='+',
help='Files to turn into track hub')
# namings
#########
parser.add_argument('--hub', help="hub name (no spaces)", required=True)
parser.add_argument('--genome', help="genome name", required=True)
# upload (in fact run_local=True)
########
#parser.add_argument('--no_s3', default=False, action="store_true", help="upload to defined server instead of s3")
#parser.add_argument('--serverscp', default="tscc-login2.sdsc.edu", help="server to SCP to")
#parser.add_argument('--user', default='adomissy', help="that is uploading files")
# parser.add_argument('--uploaddir', default='yeolab-trackhubs', help="directory to upload files to if not uploading to aws")
# web access
############
# parser.add_argument('--urldomain', default="s3-us-west-2.amazonaws.com", help="url domain for public access to trackhubs")
# parser.add_argument('--urldir', default="yeolab-trackhubs", help="url directory for public access to trackhubs")
# hub labels
############
# parser.add_argument('--hub_short_label', default=None, help="short label for hub")
# parser.add_argument('--hub_long_label', default=None, help="long label for hub")
parser.add_argument('--hub_email',
default='*****@*****.**',
help="email for hub")
# name parts grouping
#####################
parser.add_argument('--sep', default=".", help="Seperator")
parser.add_argument('--num_sep',
default=2,
type=int,
help="Number of seperators deep to group on")
###########################################################################
args = parser.parse_args()
# TODO: unhack this, but let's keep all trackhubs here for now.
urldomain = "s3-us-west-2.amazonaws.com"
urldir = "yeolab-trackhubs"
uploaddir = "yeolab-trackhubs"
hub_name = args.hub
hub_email = args.hub_email
# default label settings
########################
hub_short_label = hub_name
hub_long_label = hub_name
# hard coding serverscp, in variable HOST
HOST = "localhost"
# hard coding user, in variable USER
USER = "******"
GENOME = args.genome
# hack for tutorial dataset so it is easy to view in ucsd genome browser
if GENOME == 'hg19chr19kbp255':
GENOME == 'hg19'
uploaddir = os.path.join(uploaddir, hub_name)
URLBASE = os.path.join("http://" + urldomain + "/" + urldir + "/",
hub_name)
# create data structures
########################
hub = Hub(
hub=hub_name,
short_label=hub_short_label,
long_label=hub_long_label,
email=hub_email,
)
hub.upload_fn = uploaddir
genomes_file = GenomesFile()
hub.add_genomes_file(genomes_file)
genome = Genome(GENOME)
genomes_file.add_genome(genome)
trackdb = TrackDb()
genome.add_trackdb(trackdb)
supertrack = SuperTrack(name=hub_name,
short_label=hub_short_label,
long_label=hub_long_label)
# separate bigwigs, bigbeds and others for different processing methods
#######################################################################
bigwig_files = [
file for file in args.files
if file.endswith(".posbw") or file.endswith(".negbw") or file.endswith(
".bw") or file.endswith(".bigWig") or file.endswith(".bigwig")
]
bigbed_files = [
file for file in args.files if file.endswith(".bb")
or file.endswith(".bigBed") or file.endswith(".bigbed")
]
# not used
#other_files = [file for file in args.files if (file not in bigwig_files and file not in bigbed_files )]
# process bigwig files , re-grouped by third 2 dot-sepatarated name-parts, as multitracks
##########################################################################################
key_func = lambda x: x.split(args.sep)[:args.num_sep]
for group_key, group_bigwig_files in groupby(
sorted(bigwig_files, key=key_func), key_func):
group_bigwig_files_list = list(group_bigwig_files)
print("args sep: {}".format(args.sep))
print("args num sep: {}".format(args.num_sep))
print("split filename: {}".format(bigwig_files[0].split(
args.sep)[:args.num_sep]))
print "-----------------------------------------"
print "processing bigwig files group with key :", group_key
print "comprised of following files:", group_bigwig_files_list
print "-----------------------------------------"
long_name = remove_plus_and_pct(
os.path.basename(args.sep.join(group_key[:args.num_sep])))
aggregate = AggregateTrack(name=long_name,
tracktype='bigWig',
short_label=long_name,
long_label=long_name,
aggregate='transparentOverlay',
showSubtrackColorOnUi='on',
autoScale='on',
priority='1.4',
alwaysZero='on',
visibility="full")
for bigwigfile in group_bigwig_files_list:
print "--------------------------"
print "bigwigfile", bigwigfile
print "--------------------------"
base_track = remove_plus_and_pct(os.path.basename(bigwigfile))
split_track = base_track.split(args.sep)
long_name = args.sep.join(split_track[:args.num_sep] +
split_track[-3:])
color = "0,100,0" if "pos" in bigwigfile else "100,0,0"
track = Track(name=long_name,
url=os.path.join(URLBASE, GENOME, base_track),
tracktype="bigWig",
short_label=long_name,
long_label=long_name,
color=color,
local_fn=bigwigfile,
remote_fn=os.path.join(uploaddir, GENOME,
base_track))
#print "aggregate.add_subtrack", track.name
aggregate.add_subtrack(track)
#print "supertrack.add_track", aggregate
supertrack.add_track(aggregate)
#print "trackdb.add_tracks", aggregate
#trackdb.add_tracks(aggregate)
# process bigbed files as single track
######################################
for bigbed_file in bigbed_files:
# print "--------------------------"
# print "bigbedfile", bigbedfile
# print "--------------------------"
color = "0,100,0" if "pos" in bigbed_file else "100,0,0"
base_track = remove_plus_and_pct(os.path.basename(bigbed_file))
long_name = args.sep.join(base_track.split(
args.sep)[:args.num_sep]) + ".bb"
track = Track(name=long_name,
url=os.path.join(URLBASE, GENOME, base_track),
tracktype="bigBed",
short_label=long_name,
long_label=long_name,
color=color,
local_fn=bigbed_file,
remote_fn=os.path.join(uploaddir, GENOME, base_track),
visibility="full")
#trackdb.add_tracks(track)
supertrack.add_track(track)
trackdb.add_tracks(supertrack)
result = hub.render()
hub.remote_fn = os.path.join(uploaddir, "hub.txt")
# process bigbed files (bam?)
######################
## UNUSED
# if bigwigfile.endswith(".bw") or bigwigfile.endswith('.bigWig'): tracktype = "bigWig"
# if bigwigfile.endswith(".bb") or bigwigfile.endswith('.bigBed'): tracktype = "bigBed"
# if bigwigfile.endswith(".bam"): tracktype = "bam"
# 'upolading' (locally)
########################
for track in trackdb.tracks:
#print("upload_track(track=" + track.__repr__() + ", host=" + args.serverscp + ", user="******"run_local=True")
#upload_track(track=track, host=args.serverscp, user=args.user)
# upload_track(track=track, host=args.serverscp, user=args.user, run_s3=args.no_s3)
upload_track(track=track, host=HOST, user=USER, run_local=True)
#print("upload_hub(hub=" + hub.__repr__() + ", host=" + args.serverscp + ", user="******"run_local=True")
#upload_hub(hub=hub, host=args.serverscp, user=args.user)
# upload_hub(hub=hub, host=args.serverscp, user=args.user, run_s3=args.no_s3)
pass
upload_hub(hub=hub, host=HOST, user=USER, run_local=True)
#
print("UPLOADDIR: {}".format(uploaddir))
print("BUCKET: {}".format(uploaddir))
copy_dir_to_aws(
src=uploaddir,
dest=uploaddir,
)
print("FINAL URL: {}/hub.txt".format(URLBASE))
if track.endswith(".bw") or track.endswith('.bigWig'):
tracktype = "bigWig"
if track.endswith(".bb") or track.endswith('.bigBed'):
tracktype = "bigBed"
if track.endswith(".bam"):
tracktype = "bam"
print base_track
track = Track(
name= base_track,
url = os.path.join(URLBASE, GENOME, base_track),
tracktype = tracktype,
short_label=base_track,
long_label=base_track,
color = color,
local_fn = track,
remote_fn = os.path.join(upload_dir, GENOME, base_track)
)
aggregate.add_subtrack(track)
trackdb.add_tracks(aggregate)
result = hub.render()
hub.remote_fn = os.path.join(upload_dir, "hub.txt")
for track in trackdb.tracks:
upload_track(track=track, host=args.server, user=args.user)
upload_hub(hub=hub, host=args.server, user=args.user)
def files2viz(files_to_visualize):
if DEBUG:
print "Visualizing"
print files_to_visualize
from trackhub import Hub, GenomesFile, Genome, TrackDb, Track
from trackhub.upload import upload_hub
HUBHOST = 'http://cherry-vm45.stanford.edu'
HUBDIR = 'trackhubs'
USER = '******'
URLBASE = os.path.join(HUBHOST, HUBDIR)
EDWBASE = 'http://encodedcc.sdsc.edu/warehouse'
GENOME = 'hg19'
hub = Hub(hub='Selected_ENCODE_Tracks',
short_label='Selected_ENCODE_Tracks_short',
long_label='Selected_ENCODE_Tracks_long',
email='*****@*****.**')
genomes_file = GenomesFile()
genome = Genome(GENOME)
trackdb = TrackDb()
for accession in files_to_visualize:
file_obj = get_ENCODE(accession)
if DEBUG:
print file_obj
if file_obj['file_format'] == 'bigWig':
track = Track(name=accession,
url=os.path.join(EDWBASE,
str(file_obj['download_path'])),
tracktype='bigWig',
short_label=accession,
long_label=accession,
color='128,0,0',
visibility='full')
trackdb.add_tracks([track])
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
results = hub.render()
if DEBUG:
print hub
print '...'
print genomes_file
print '...'
print genome
print '...'
print trackdb
#upload_hub(hub=hub, host=HUBHOST, user=USER) #doesn't seem to work
import subprocess
subprocess.call(
"cd .. && rsync -r trackhub [email protected]:/www/html/trackhubs",
shell=True)
import webbrowser
hubfile = str(hub.hub) + '.hub.txt'
UCSC_url = 'http://genome.ucsc.edu/cgi-bin/hgTracks?udcTimeout=1&db=hg19' + \
'&hubUrl=' + os.path.join(HUBHOST,HUBDIR,'trackhub',hubfile) # + \
#'&hsS_doLoadUrl=submit' + '&hgS_loadUrlName=' + os.path.join(HUBHOST,HUBDIR,'trackhub','session.txt')
print UCSC_url
webbrowser.open(UCSC_url)
bed_view.add_tracks(track)
# Make the bigWig tracks
def make_bigWig_tracks(signal_view, url_base):
for bw in glob.glob('*.bw'):
label = bw.replace('.bw', '')
basename = os.path.basename(bw)
track = Track(name='signal_%s' % label,
tracktype='bigWig',
url=url_base + basename,
local_fn=bw,
shortLabel='signal %s' % label,
longLabel='signal %s' % label)
# add this track to the signal view
signal_view.add_tracks(track)
make_bigBed_tracks(bed_view, args.base_url)
make_bigWig_tracks(signal_view, args.base_url)
trackdb.add_tracks(composite)
print trackdb
os.chdir('%s' % args.output_dir)
results = hub.render()
# add this track to the bed view
bed_view.add_tracks(track)
# Make the bigWig tracks
def make_bigWig_tracks(signal_view, url_base):
for bw in glob.glob('*.bw'):
label = bw.replace('.bw', '')
basename = os.path.basename(bw)
track = Track(
name='signal_%s' % label,
tracktype='bigWig',
url=url_base + basename,
local_fn=bw,
shortLabel='signal %s' % label,
longLabel='signal %s' % label)
# add this track to the signal view
signal_view.add_tracks(track)
make_bigBed_tracks(bed_view, args.base_url)
make_bigWig_tracks(signal_view, args.base_url)
trackdb.add_tracks(composite)
print trackdb
os.chdir('%s' % args.output_dir)
results = hub.render()
def files2viz(files_to_visualize):
if DEBUG:
print "Visualizing"
print files_to_visualize
from trackhub import Hub, GenomesFile, Genome, TrackDb, Track
from trackhub.upload import upload_hub
HUBHOST = 'http://cherry-vm45.stanford.edu'
HUBDIR = 'trackhubs'
USER = '******'
URLBASE = os.path.join(HUBHOST, HUBDIR)
EDWBASE = 'http://encodedcc.sdsc.edu/warehouse'
GENOME = 'hg19'
hub = Hub(
hub='Selected_ENCODE_Tracks',
short_label='Selected_ENCODE_Tracks_short',
long_label='Selected_ENCODE_Tracks_long',
email='*****@*****.**')
genomes_file = GenomesFile()
genome = Genome(GENOME)
trackdb = TrackDb()
for accession in files_to_visualize:
file_obj = get_ENCODE(accession)
if DEBUG:
print file_obj
if file_obj['file_format'] == 'bigWig':
track = Track(
name=accession,
url=os.path.join(EDWBASE, str(file_obj['download_path'])),
tracktype='bigWig',
short_label=accession,
long_label=accession,
color='128,0,0',
visibility='full')
trackdb.add_tracks([track])
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
results=hub.render()
if DEBUG:
print hub
print '...'
print genomes_file
print '...'
print genome
print '...'
print trackdb
#upload_hub(hub=hub, host=HUBHOST, user=USER) #doesn't seem to work
import subprocess
subprocess.call("cd .. && rsync -r trackhub [email protected]:/www/html/trackhubs", shell=True)
import webbrowser
hubfile = str(hub.hub) + '.hub.txt'
UCSC_url = 'http://genome.ucsc.edu/cgi-bin/hgTracks?udcTimeout=1&db=hg19' + \
'&hubUrl=' + os.path.join(HUBHOST,HUBDIR,'trackhub',hubfile) # + \
#'&hsS_doLoadUrl=submit' + '&hgS_loadUrlName=' + os.path.join(HUBHOST,HUBDIR,'trackhub','session.txt')
print UCSC_url
webbrowser.open(UCSC_url)
def ENCSR2viz(experiments_to_visualize):
if DEBUG:
print "Visualizing"
print experiments_to_visualize
from trackhub import Hub, GenomesFile, Genome, TrackDb, Track
from trackhub.upload import upload_hub
HUBHOST = 'http://cherry-vm45.stanford.edu'
HUBDIR = 'jseth/trackhubs'
USER = '******'
URLBASE = os.path.join(HUBHOST, HUBDIR)
EDWBASE = 'http://encodedcc.sdsc.edu/warehouse'
GENOME = 'hg19'
hub = Hub(
hub='ENCODE',
short_label='ENCODE',
long_label='ENCODE',
email='*****@*****.**')
genomes_file = GenomesFile()
genome = Genome(GENOME)
trackdb = TrackDb()
for accession in experiments_to_visualize:
experiment_obj = get_ENCODE(accession)
if DEBUG:
print experiment_obj
for file_id in experiment_obj['files']:
file_obj = get_ENCODE(file_id)
if file_obj['file_format'] in ['bigWig', 'bigBed', 'broadPeak', 'narrowPeak']:
if file_obj['file_format'] in ['bigWig']:
track_type = 'bigWig'
elif file_obj['file_format'] in ['bigBed', 'broadPeak', 'narrowPeak']:
track_type = 'bigBed'
track = Track(
name=str(file_obj['accession']),
url=os.path.join(EDWBASE, str(file_obj['download_path'])),
tracktype=track_type,
long_label=str(file_obj['accession']),
short_label=str(file_obj['output_type']),
color='128,0,0',
visibility='dense',
metadata='cell_type=primary')
print file_obj['accession']
trackdb.add_tracks([track])
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
results=hub.render()
if DEBUG:
print hub
print '...'
print genomes_file
print '...'
print genome
print '...'
print trackdb
#upload_hub(hub=hub, host=HUBHOST, user=USER) #doesn't seem to work
import subprocess
subprocess.call("cd .. && rsync -r trackhub [email protected]:/www/html/jseth/trackhubs", shell=True)
import webbrowser
hubfile = str(hub.hub) + '.hub.txt'
UCSC_url = 'http://genome.ucsc.edu/cgi-bin/hgTracks?udcTimeout=1&db=hg19' + \
'&hubUrl=' + os.path.join(HUBHOST,HUBDIR,'trackhub',hubfile) # + \
#'&hsS_doLoadUrl=submit&hgS_loadUrlName=' + os.path.join(HUBHOST,HUBDIR,'trackhub','session.txt')
print UCSC_url
webbrowser.open(UCSC_url)
