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))
hub=args.hub,
short_label=args.short_label,
long_label=args.long_label,
email=args.email,
)
genomes_file = GenomesFile()
genome = Genome(GENOME)
trackdb = TrackDb()
supertrack = SuperTrack(name=args.hub,
short_label=args.hub,
long_label=args.hub)
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
hub.upload_fn = upload_dir
files = args.files
#logic for doing pos and neg as the same multi trackhub
#process bw files first, do the rest with old logic
bw_files = [
track for track in files
if track.endswith(".bw") or track.endswith(".bigWig")
]
remaining_files = [
track for track in files
if not (track.endswith(".bw") or track.endswith(".bigWig"))
]
key_func = lambda x: x.split(args.sep)[:args.num_sep]
GENOME = args.genome
hub = Hub(hub=args.hub,
short_label=args.short_label,
long_label=args.long_label,
email = args.email,
)
genomes_file = GenomesFile()
genome = Genome(GENOME)
trackdb = TrackDb()
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
hub.upload_fn = upload_dir
files = args.files
#logic for doing pos and neg as the same multi trackhub
#process bw files first, do the rest with old logic
bw_files = [track for track in files if track.endswith(".bw") or track.endswith(".bigWig")]
remaining_files = [track for track in files if not (track.endswith(".bw") or track.endswith(".bigWig"))]
key_func = lambda x: x.split(".")[:-2]
for bw_group, files in groupby(sorted(bw_files, key=key_func), key_func):
long_name = os.path.basename(bw_group[0])
aggregate = AggregateTrack(
name=long_name,
tracktype='bigWig',
short_label=long_name,
long_label=long_name,
