def test_staging(self):
staging_dir, linknames = upload.stage_hub(self.hub)
assert open(os.path.join(
staging_dir, 'example_hub.genomes.txt')).read() == dedent("""\
genome dm3
trackDb dm3/trackDb.txt
""")
assert open(os.path.join(staging_dir,
'example_hub.hub.txt')).read() == dedent("""\
hub hub
shortLabel example hub
longLabel an example hub for testing
genomesFile example_hub.genomes.txt
email [email protected]""")
def test_staging(self):
staging_dir, linknames = upload.stage_hub(self.hub)
assert open(os.path.join(staging_dir, 'example_hub.genomes.txt')).read() == dedent(
"""\
genome dm3
trackDb dm3/trackDb.txt
""")
assert open(os.path.join(staging_dir, 'example_hub.hub.txt')).read() == dedent(
"""\
hub hub
shortLabel example hub
longLabel an example hub for testing
genomesFile example_hub.genomes.txt
email [email protected]""")
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 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)