def publish():
'''publish files.'''
# publish web pages
P.publish_report()
# publish additional data
web_dir = PARAMS["web_dir"]
project_id = P.getProjectId()
# directory, files
exportfiles = {
"intervals":
glob.glob(os.path.join(PARAMS["exportdir"], "bed", "*.bed.gz")) +
glob.glob(os.path.join(PARAMS["exportdir"], "bed", "*.bed.gz.tbi")),
}
bams = []
for targetdir, filenames in exportfiles.items():
if len(filenames) == 0:
E.warn("no files for target '%s'" % targetdir)
for src in filenames:
dest = "%s/%s/%s" % (web_dir, targetdir, os.path.basename(src))
if dest.endswith(".bam"):
bams.append(dest)
dest = os.path.abspath(dest)
destdir = os.path.dirname(dest)
if not os.path.exists(destdir):
os.makedirs(destdir)
if not os.path.exists(dest):
E.debug("creating symlink from %s to %s" % (src, dest))
os.symlink(os.path.abspath(src), dest)
def publish():
'''publish files.'''
# publish web pages
P.publish_report()
# publish additional data
web_dir = PARAMS["web_dir"]
project_id = P.getProjectId()
# directory, files
exportfiles = {
"intervals": glob.glob(os.path.join(
PARAMS["exportdir"], "bed", "*.bed.gz")) +
glob.glob(os.path.join(PARAMS["exportdir"], "bed", "*.bed.gz.tbi")),
}
bams = []
for targetdir, filenames in exportfiles.iteritems():
if len(filenames) == 0:
E.warn("no files for target '%s'" % targetdir)
for src in filenames:
dest = "%s/%s/%s" % (web_dir, targetdir, os.path.basename(src))
if dest.endswith(".bam"):
bams.append(dest)
dest = os.path.abspath(dest)
destdir = os.path.dirname(dest)
if not os.path.exists(destdir):
os.makedirs(destdir)
if not os.path.exists(dest):
E.debug("creating symlink from %s to %s" % (src, dest))
os.symlink(os.path.abspath(src), dest)
def buildExperimentTable(infiles, outfile):
d = os.getcwd()
try:
project_id = P.getProjectId()
except ValueError:
project_id = "unknown"
with IOTools.openFile(outfile, "w") as outf:
outf.write("id\tname\tproject_id\tdirectory\ttitle\n")
outf.write("\t".join(("1", P.getProjectName(), project_id, d, PARAMS.get("title", ""))) + "\n")
def publish():
'''publish files.'''
# publish web pages
P.publish_report()
# publish additional data
web_dir = PARAMS["web_dir"]
project_id = P.getProjectId()
ucsc_urls = {
"bam":
"""track type=bam name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/%(dirname)s/%(filename)s""",
"bigwig":
"""track type=bigWig name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/%(dirname)s/%(filename)s""",
}
# directory, files
exportfiles = (
("bamfiles",
glob.glob("*/*.genome.bam") + glob.glob("*/*.genome.bam.bai"), "bam"),
("bamfiles", glob.glob("*/*.prep.bam") + glob.glob("*/*.prep.bam.bai"),
"bam"),
("medips", glob.glob("*/*.bigwig"), "bigwig"),
)
ucsc_files = []
for targetdir, filenames, datatype in exportfiles:
for src in filenames:
filename = os.path.basename(src)
dest = "%s/%s/%s" % (web_dir, targetdir, filename)
suffix = os.path.splitext(src)
if suffix in ucsc_urls:
ucsc_files.append((datatype, targetdir, filename))
dest = os.path.abspath(dest)
if not os.path.exists(dest):
os.symlink(os.path.abspath(src), dest)
# output ucsc links
for ucsctype, dirname, filename in ucsc_files:
filename = os.path.basename(filename)
track = P.snip(filename, ucsctype)
print(ucsc_urls[ucsctype] % locals())
def publish():
'''publish files.'''
# publish web pages
P.publish_report()
# publish additional data
web_dir = PARAMS["web_dir"]
project_id = P.getProjectId()
ucsc_urls = {
"bam":
"""track type=bam name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/%(dirname)s/%(filename)s""",
"bigwig":
"""track type=bigWig name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/%(dirname)s/%(filename)s""",
}
# directory, files
exportfiles = (
("bamfiles", glob.glob("*/*.genome.bam") +
glob.glob("*/*.genome.bam.bai"), "bam"),
("bamfiles", glob.glob("*/*.prep.bam") +
glob.glob("*/*.prep.bam.bai"), "bam"),
("medips", glob.glob("*/*.bigwig"), "bigwig"),
)
ucsc_files = []
for targetdir, filenames, datatype in exportfiles:
for src in filenames:
filename = os.path.basename(src)
dest = "%s/%s/%s" % (web_dir, targetdir, filename)
suffix = os.path.splitext(src)
if suffix in ucsc_urls:
ucsc_files.append((datatype, targetdir, filename))
dest = os.path.abspath(dest)
if not os.path.exists(dest):
os.symlink(os.path.abspath(src), dest)
# output ucsc links
for ucsctype, dirname, filename in ucsc_files:
filename = os.path.basename(filename)
track = P.snip(filename, ucsctype)
print(ucsc_urls[ucsctype] % locals())
def publish_tracks(export_files,
prefix="",
project_id=None,
project_name=None):
'''publish a UCSC Track Hub.
*export_files* is a dictionary of filetypes and files.
*prefix* will be added to each track.
'''
if not prefix:
prefix = PARAMS.get("report_prefix", "")
web_dir = PARAMS["web_dir"]
if project_id is None:
project_id = P.getProjectId()
if project_name is None:
project_name = P.getProjectName()
src_export = os.path.abspath("export")
dest_report = prefix + "report"
dest_export = prefix + "export"
hubdir = os.path.join(PARAMS["web_dir"], "ucsc")
if not os.path.exists(hubdir):
E.info("creating %s" % hubdir)
os.mkdir(hubdir)
# write the UCSC hub file
hubfile = os.path.join(hubdir, "hub.txt")
genomesfile = os.path.join(hubdir, "genomes.txt")
trackdir = os.path.join(hubdir, PARAMS["genome"])
trackfile = os.path.join(hubdir, PARAMS["genome"], "trackDb.txt")
trackrelpath = os.path.join(PARAMS["genome"], "trackDb.txt")
if os.path.exists(hubfile):
with IOTools.openFile(hubfile) as infile:
hubdata = PipelineUCSC.readUCSCFile(infile)
else:
hubdata = [('hub', "CGAT-" + project_name),
('shortLabel', "CGAT-" + project_name),
('longLabel', "Data for CGAT project %s" % project_name),
('genomesFile', "genomes.txt"),
('email', '*****@*****.**')]
E.info("writing to %s" % hubfile)
with IOTools.openFile(hubfile, "w") as outfile:
PipelineUCSC.writeUCSCFile(outfile, hubdata)
# create the genomes.txt file - append to it if necessary.
if os.path.exists(genomesfile):
with IOTools.openFile(genomesfile) as infile:
genomes = PipelineUCSC.readUCSCFile(infile)
else:
genomes = []
if ("genome", PARAMS["genome"]) not in genomes:
genomes.append(("genome", PARAMS["genome"]))
genomes.append(("trackDb", trackrelpath))
E.info("writing to %s" % genomesfile)
with IOTools.openFile(genomesfile, "w") as outfile:
PipelineUCSC.writeUCSCFile(outfile, genomes)
# create the track data
if not os.path.exists(trackdir):
os.mkdir(trackdir)
if os.path.exists(trackfile):
E.debug('reading existing tracks from %s' % trackfile)
with IOTools.openFile(trackfile) as infile:
tracks = PipelineUCSC.readTrackFile(infile)
else:
tracks = []
tracks = collections.OrderedDict(tracks)
def getName(name):
if name.endswith(".bam"):
return "bam", name
elif name.endswith(".bw") or name.endswith(".bigwig"):
return "bigWig", name
else:
return None, None
for targetdir, filenames in export_files.items():
for src in filenames:
dest = os.path.join(trackdir, prefix + os.path.basename(src))
dest = os.path.abspath(dest)
# create a symlink
if not os.path.exists(dest):
try:
os.symlink(os.path.abspath(src), dest)
except OSError, msg:
E.warn("could not create symlink from %s to %s: %s" %
(os.path.abspath(src), dest, msg))
ucsctype, trackname = getName(os.path.basename(dest))
# ignore invalid types and other files (.bai files, ...)
if ucsctype is None:
continue
tracks[trackname] = (("bigDataUrl", os.path.basename(dest)),
("shortLabel", trackname),
("longLabel", trackname),
("type", ucsctype))
