def upload(self, hub_only=False, host=None, user=None, rsync_options=None,
hub_remote=None):
self.process()
if 'server' in self.group:
host = host or self.group['server'].get('host')
user = user or self.group['server'].get('user')
rsync_options = rsync_options or self.group['server'].get('rsync_options')
hub_remote = hub_remote or self.group['server'].get('hub_remote')
self.hub.remote_fn = hub_remote
self.hub.remote_dir = os.path.dirname(hub_remote)
self.hub.render()
if user == '$USER':
user = os.environ.get('USER')
kwargs = dict(host=host, user=user, rsync_options=rsync_options)
upload_hub(hub=self.hub, **kwargs)
if not hub_only:
for track, level in self.hub.leaves(Track):
upload_track(track=track, **kwargs)
log("Hub can now be accessed via {0}"
.format(self.hub.url), style=Fore.BLUE)
def upload(self,
hub_only=False,
host=None,
user=None,
rsync_options=None,
hub_remote=None):
self.process()
if 'server' in self.group:
host = host or self.group['server'].get('host')
user = user or self.group['server'].get('user')
rsync_options = rsync_options or self.group['server'].get(
'rsync_options')
hub_remote = hub_remote or self.group['server'].get('hub_remote')
self.hub.remote_fn = hub_remote
self.hub.remote_dir = os.path.dirname(hub_remote)
self.hub.render()
if user == '$USER':
user = os.environ.get('USER')
kwargs = dict(host=host, user=user, rsync_options=rsync_options)
upload_hub(hub=self.hub, **kwargs)
if not hub_only:
for track, level in self.hub.leaves(Track):
upload_track(track=track, **kwargs)
log("Hub can now be accessed via {0}".format(self.hub.url),
style=Fore.BLUE)
def test_upload(self):
d = tempfile.mkdtemp()
upload.upload_hub(
hub=self.hub,
remote_dir=d,
user=None,
host=None,
)
def test_upload(self):
d = tempfile.mkdtemp()
upload.upload_hub(
hub=self.hub,
remote_dir=d,
user=None,
host=None,
)
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)
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)
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_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)
supertrack.add_track(aggregate)
#trackdb.add_tracks(aggregate)
bigBed_files = [track for track in remaining_files 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='Make trackhubs for UCSC browser using bigBed files. \
Outputs to CURRENT DIRECTORY.')
parser.add_argument('inputdir',
metavar='INDIR',
help='Directory containing bigBed files .bb ending')
parser.add_argument('outdir',
metavar='OUTDIR',
help='Directory for staging files')
parser.add_argument('--quiet',
'-q',
action='store_true',
help='Suppress some print statements')
parser.add_argument('--render',
'-r',
action='store_true',
help='Render file to current dir')
parser.add_argument('--upload',
'-u',
action='store_true',
help='Upload file to webserver')
parser.add_argument('--mm9',
'-m',
action='store_true',
help='Switch from mm10 to mm9')
parser.add_argument('--has_strand',
'-s',
action='store_true',
help='Bed has strand (changes from 5 columns to 6)')
parser.add_argument('--suffix',
'-S',
metavar="trackhub label suffix",
default="",
help='Suffix to label, for example H3K4me1')
args = parser.parse_args()
# store command line arguments for reproducibility
CMD_INPUTS = ' '.join(['python'] + sys.argv) # easy printing later
# store argparse inputs for reproducibility / debugging purposes
args_dic = vars(args)
ARG_INPUTS = ['%s=%s' % (key, val) for key, val in args_dic.iteritems()]
# ARG_INPUTS = ['%s=%s' % (key, val) for key, val in args_dic.items()]
ARG_INPUTS = ' '.join(ARG_INPUTS)
# Print arguments supplied by user
if not args.quiet:
print('Command line inputs:')
print(CMD_INPUTS)
print('Argparse variables:')
print(ARG_INPUTS)
# define constants (hard coded)
if args.mm9:
genobuild = "mm9"
else:
genobuild = "mm10"
jsuffix = "%s_%s" % (genobuild, args.suffix)
print("Assigning prefix: %s" % jsuffix)
# dirname: motevo_from_peaks/H3K4me1_peaks
dirname = "motevo_from_peaks/%s_peaks/motevo_motifs_%s" % (args.suffix,
jsuffix)
hubname = "motevo_motifs_%s" % jsuffix
shortlab = "motevo_%s" % jsuffix
longlab = "Motevo motifs %s" % jsuffix
email = "*****@*****.**"
# url = "http://upnaepc2.epfl.ch"
url = "http://upnaesrv1.epfl.ch"
assay = "bigbed"
jvis = "dense"
# bigbed options loaded into ViewTrack
jspectrum = "on"
scoremax = 1000
scoremin = 500
# define URLs
url_main = "%s/%s" % (url, dirname)
url_base = "%s/%s/data" % (url, dirname)
# upload_main = "~/Sites/%s" % dirname
# upload_base = "~/Sites/%s/data" % dirname
upload_main = "%s" % hubname
upload_base = "%s/data" % hubname
if not args.has_strand:
ftype = "bigBed 5"
else:
ftype = "bigBed 6"
# host = "circadian.epfl.ch"
# user = "******"
host = "upnaesrv1.epfl.ch"
user = "******"
# define constants
genomebuild = genobuild
files_dic = get_files_from_dir(args.inputdir, ext=".bb")
samples_dic = {}
for sample in files_dic.keys():
samples_dic[sample] = sample
# init hub genomes file genome trackdb
# Make my hub
hub = Hub(hub=hubname,
short_label=shortlab,
long_label=longlab,
email=email)
# url = "%s/%s" % (url, dirname))
hub.url = os.path.join(url_main, "%s.hub.txt" % hub.hub)
genomes_file = GenomesFile()
genome = Genome(genomebuild)
trackdb = TrackDb()
# add remote fn
# hub.remote_fn = os.path.join(upload_main, "hub.txt")
# genomes_file.remote_fn = os.path.join(upload_main, "genomes.txt")
hub.remote_fn = upload_main
genomes_file.remote_fn = upload_main
trackdb.remote_fn = os.path.join(upload_main, genomebuild, "trackDb.txt")
hub.add_genomes_file(genomes_file)
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
# init composite
composite = CompositeTrack(name=hubname,
short_label=shortlab,
long_label=longlab,
tracktype=ftype)
# make subgroups
subgroups = [
SubGroupDefinition(name="sample", label="sample", mapping=samples_dic),
]
composite.add_subgroups(subgroups)
# make viewTrack, a hierarchy containing my files, for example
view = ViewTrack(
name="%sViewTrack" % assay,
view="%s" % assay,
visibility=jvis,
tracktype=ftype,
short_label="%s" % assay,
long_label="%s assay" % assay,
# big bed labels
spectrum=jspectrum,
scoreMin=scoremin,
scoreMax=scoremax)
composite.add_view(view)
# make track
for sample, wfs in files_dic.iteritems():
for wf in wfs:
sampname = os.path.basename(wf)
bname = sampname.split(".")[0]
track = Track(name=bname,
tracktype=ftype,
url=os.path.join(url_base, "%s" % sampname),
local_fn=os.path.abspath(wf),
remote_fn=os.path.join(upload_base, "%s" % sampname),
visibility=jvis,
shortLabel=bname,
longLabel=bname,
spectrum=jspectrum,
scoreMin=scoremin,
scoreMax=scoremax,
subgroups={"sample": sample})
view.add_tracks(track)
trackdb.add_tracks(composite)
print('Track looks like this:')
print(trackdb)
if args.render:
# print('Rendering to %s' % hub.local_fn)
# results = hub.render()
# upload_hub(hub=hub, host='localhost', remote_dir='example_grouping_hub')
stage_hub(hub, staging=args.outdir)
if args.upload:
print('Uploading to [email protected]')
# for track in trackdb.tracks:
# upload_track(track = track, host = host, user = user)
upload_hub(hub=hub,
host=host,
user=user,
remote_dir="/data/web/sites/motevo_from_peaks")
print('Subgroups:')
for sg in subgroups:
print(sg)
print("Staging to path: %s" % args.outdir)
name=sanitize(k),
label=sanitize(k, strict=False),
mapping={sanitize(i): sanitize(i, False)
for i in list(v)}))
sample_composite.add_subgroups(sample_subgroups)
sample_composite.add_params(
dimensions='dimX=bait dimY=kind dimA=sample dimB=inter',
sortOrder='bait=+ sample=+',
filterComposite='dimA dimB',
)
bait_subgroups = []
for k, v in bait_subgroup_values.items():
bait_subgroups.append(
SubGroupDefinition(
name=sanitize(k),
label=sanitize(k, strict=False),
mapping={sanitize(i): sanitize(i, False)
for i in list(v)}))
bait_composite.add_subgroups(bait_subgroups)
bait_composite.add_params(
dimensions='dimX=bait dimY=kind dimA=treatment',
sortOrder='bait=+',
filterComposite='dimA',
)
f = hub.render()
linknames = upload.upload_hub(host=config['trackhub']['upload']['host'],
user=config['trackhub']['upload']['user'],
hub=hub)
local_fn = datadir + f,
remote_fn = remote_dir + bname,
url = uploadbase+'bw/'+ bname,
shortLabel = '%s_%s' %( name,rep) ,
color = col)
signal_view.add_tracks(track)
for b in chipseq_bbfiles:
bname = os.path.basename(b)
name = bname.split('.')[0]
col = maps[name]
track = Track(
name = '%s_peak' % name,
tracktype='bigBed',
local_fn = datadir+ f,
remote_fn = remote_dir + bname,
url = uploadbase + 'bb/'+bname,
shortLabel = '%s_peaks' % name,
color=col)
bed_view.add_tracks(track)
#need to add in the RNAseq to same composite groups
trackdb.add_tracks(comp)
print trackdb
hub.render()
kwargs = dict(host='kure.its.unc.edu', user='******')
upload_hub(hub=hub, **kwargs)
for track, level in hub.leaves(Track):
upload_track(track=track, **kwargs)
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)
bigBed_files = [track for track in remaining_files if track.endswith(".bb") or track.endswith(".bigBed")]
for bigBed_file in bigBed_files:
base_track = os.path.basename(bigBed_file)
track = Track(
name = base_track,
url = os.path.join(URLBASE, GENOME, base_track),
tracktype = "bigBed",
short_label = base_track,
long_label = base_track,
color = color,
local_fn = track,
remote_fn = os.path.join(upload_dir, GENOME, base_track)
)
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)
long_label='{0} {1} postfilter normalized signal'.format(
algorithm, label),
tracktype='bigWig',
source=postfilter_wig,
subgroups=subgroup,
color=decide_color(postfilter_wig),
altColor=decide_color(postfilter_wig),
maxHeightPixels='8:35:100',
viewLimits='0:500'))
supplemental = hub_config.get('supplemental', [])
if supplemental:
composite.add_view(supplemental_view)
for block in supplemental:
supplemental_view.add_tracks(Track(**block))
# Tie everything together
composite.add_subgroups(subgroups)
trackdb.add_tracks(composite)
composite.add_view(signal_view)
composite.add_view(peaks_view)
# Render and upload using settings from hub config file
hub.render()
kwargs = hub_config.get('upload', {})
if kwargs.get('remote_dir', False):
upload_hub(hub=hub, **kwargs)
else:
stage_hub(hub, 'staging')
def make_hub(self, result_map):
genome_db = 'hg19'
hub_url = self.baseurl + '/'
hub, genomes_file, genome, trackdb = default_hub(
hub_name=self.name,
short_label=self.name,
long_label=self.name,
email='email',
genome=genome_db)
hub.remote_dir = self.uploadpath
# build higher order track types
composite = CompositeTrack(
name=self.sanitize_name(self.name),
short_label = self.sanitize_name(self.name),
long_label = str(self.name),
tracktype="bed 3",
dragAndDrop='subtracks',
visibility='full',
)
trackdb.add_tracks(composite)
subgroups = self.add_subgroups(composite)
view_type = None
view = None
for track in self.get_tracks():
if track['file_type'] not in TRACKTYPES:
LOGGER.info('Unrecognized file type %s', track['file_type'])
continue
view = self.add_new_view_if_needed(composite, view, track)
track_name = self.make_track_name(track)
track_subgroup = self.make_track_subgroups(subgroups, track)
track_type = self.make_track_type(track)
if 'file_label' in track:
track_label = self.sanitize_name(track['file_label'])
else:
track_label = track_name
attributes = {
'name': track_name,
'tracktype': track_type,
'url': hub_url + str(track['relative_path']),
'short_label': str(track['library_id']),
'long_label': str(track_label),
'subgroups': track_subgroup,
}
LOGGER.debug('track attributes: %s', pformat(attributes))
newtrack = Track(**attributes)
view.add_tracks([newtrack])
results = hub.render()
if hub.remote_dir:
LOGGER.info("Uploading to %s @ %s : %s",
self.user, self.host, hub.remote_dir)
upload_hub(hub=hub, host=self.host, user='******')