def run(self):
options = self.options
localHalfile = os.path.join(self.outdir, os.path.basename(self.halfile))
if os.path.abspath(localHalfile) != os.path.abspath(self.halfile):
if os.path.exists(localHalfile):
system("rm %s" %localHalfile)
if options.cpHal:
system("cp %s %s" %(os.path.abspath(self.halfile), localHalfile))
else:
system("ln -s %s %s" %(os.path.abspath(self.halfile), localHalfile))
#Create lod files if useLod is specified
lodtxtfile, loddir = getLod(options, localHalfile, self.outdir)
#Get the maximum window size to display SNPs
if lodtxtfile:
snpwidth = getLodLowestLevel(lodtxtfile) - 1
if snpwidth > -1:
options.snpwidth = snpwidth
genomes = sortByProperName(self.genomes, self.options.properName)
#Create documentation files:
docdir = os.path.join(self.outdir, "documentation")
system("mkdir -p %s" %docdir)
writeDocFiles(docdir, self.options)
#Create genomes.txt file
filename = os.path.join(self.outdir, "genomes.txt")
f = open(filename, 'w')
#for genome in self.genomes:
for genome in genomes:
genomedir = os.path.join(self.outdir, genome)
f.write("genome %s\n" %genome)
f.write("twoBitPath %s/%s.2bit\n" % (genome, genome))
#create trackDb for the current genome:
if lodtxtfile == '':
self.addChildTarget( WriteTrackDbFile(self.genomes, "../%s" % os.path.basename(self.halfile), genomedir, options) )
else:
self.addChildTarget( WriteTrackDbFile(self.genomes, "../%s" % os.path.basename(lodtxtfile), genomedir, options) )
f.write("trackDb %s/trackDb.txt\n" %genome)
#other info
f.write("groups groups.txt\n")
writeDescriptionFile(genome, genomedir)
f.write("htmlPath %s/description.html\n" % genome)
f.write("description %s\n" % getProperName(genome, self.options.properName))
f.write("organism %s\n" % getProperName(genome, self.options.properName))
f.write("orderKey 4800\n")
f.write("scientificName %s\n" % genome)
seq2len = self.genome2seq2len[genome]
(seq, l) = getLongestSeq(seq2len)
f.write("defaultPos %s:1-%d\n" %(seq, min(l, 1000)))
f.write("\n")
f.close()
def writeTrackDb_compositeStart(f, shortLabel, longLabel, bbdirs, bwdirs, genomes, properName, url, img):
#Composite track includes all annotations in BED & WIGGLE formats, their lifted-over tracks, and Snake tracks
f.write("track hubCentral\n")
f.write("compositeTrack on\n")
f.write("shortLabel %s\n" %shortLabel)
f.write("longLabel %s\n" %longLabel)
f.write("group comphub\n")
bedtracktypes = [os.path.basename(b.rstrip('/')) for b in bbdirs]
bedstr = " ".join(["%s=%s" %(item, item) for item in bedtracktypes])
wigtracktypes = [os.path.basename(b.rstrip('/')) for b in bwdirs]
wigstr = " ".join(["%s=%s" %(item, item) for item in wigtracktypes])
f.write("subGroup1 view Track_Type Snake=Alignments %s %s\n" %(bedstr, wigstr))
genomeStr = " ".join(["%s=%s" %(g, getProperName(g, properName)) for g in genomes])
f.write("subGroup2 orgs Organisms %s\n" %genomeStr)
f.write("dragAndDrop subTracks\n")
f.write("#allButtonPair on\n")
#f.write("sortOrder view=+ orgs=+\n")
f.write("dimensions dimensionX=view dimensionY=orgs\n")
f.write("noInherit on\n")
f.write("priority 0\n")
f.write("centerLabelsDense on\n")
f.write("visibility full\n")
f.write("html ../documentation/hubCentral\n")
if url and img:
imgurl = os.path.join(url, os.path.basename(img))
f.write("treeImage %s\n" %imgurl)
f.write("type bigBed 3\n")
f.write("\n")
def writeTrackDb_compositeStart(f, shortLabel, longLabel, bbdirs, bwdirs, genomes, properName, url, img):
#Composite track includes all annotations in BED & WIGGLE formats, their lifted-over tracks, and Snake tracks
f.write("track hubCentral\n")
f.write("compositeTrack on\n")
f.write("shortLabel %s\n" %shortLabel)
f.write("longLabel %s\n" %longLabel)
f.write("group comphub\n")
bedtracktypes = [os.path.basename(b.rstrip('/')) for b in bbdirs]
bedstr = " ".join(["%s=%s" %(item, item) for item in bedtracktypes])
wigtracktypes = [os.path.basename(b.rstrip('/')) for b in bwdirs]
wigstr = " ".join(["%s=%s" %(item, item) for item in wigtracktypes])
f.write("subGroup1 view Track_Type Snake=Alignments %s %s\n" %(bedstr, wigstr))
genomeStr = " ".join(["%s=%s" %(g, getProperName(g, properName)) for g in genomes])
f.write("subGroup2 orgs Organisms %s\n" %genomeStr)
f.write("dragAndDrop subTracks\n")
f.write("#allButtonPair on\n")
#f.write("sortOrder view=+ orgs=+\n")
f.write("dimensions dimensionX=view dimensionY=orgs\n")
f.write("noInherit on\n")
f.write("priority 0\n")
f.write("centerLabelsDense on\n")
f.write("visibility full\n")
f.write("html ../documentation/hubCentral\n")
if url and img:
imgurl = os.path.join(url, os.path.basename(img))
f.write("treeImage %s\n" %imgurl)
f.write("type bigBed 3\n")
f.write("\n")
def writeTrackDb_bigbeds(f, bigbeddir, genomes, currgenome, properName,
composite, tab):
annotation = os.path.basename(bigbeddir)
genome2priority = getPriorities(genomes, currgenome)
for genome in os.listdir(bigbeddir):
bbfile = os.path.join(bigbeddir, genome, "%s.bb" % currgenome)
if not os.path.exists(bbfile):
continue
searchIndexStr, fields, numfield = getSearchIndexInfo(
bigbeddir, genome, bbfile, tab)
#start writing track
genomeProperName = getProperName(genome, properName)
priority = 1
if genome in genome2priority:
priority = genome2priority[genome]
indent = ''
if composite:
indent = "\t\t"
f.write("%strack %s%s\n" % (indent, annotation, genome))
if genome == currgenome:
f.write("%slongLabel %s %s\n" %
(indent, genomeProperName, annotation))
else:
f.write("%slongLabel %s Lifted-over %s\n" %
(indent, genomeProperName, annotation))
f.write("%spriority %d\n" % (indent, priority))
f.write("%stype bigBed %s\n" % (indent, fields))
f.write("%sgroup annotation%s\n" % (indent, annotation))
if numfield >= 4:
f.write("%ssearchIndex %s\n" % (indent, searchIndexStr))
f.write("%sitemRgb On\n" % indent)
if genome == currgenome:
f.write("%svisibility dense\n" % indent)
else:
f.write("%svisibility hide\n" % indent)
if composite: #Composite
f.write("%sshortLabel %s%s\n" %
(indent, genomeProperName, annotation))
f.write("%sbigDataUrl ../liftoverbed/%s\n" %
(indent,
os.path.join(annotation, genome, "%s.bb" % currgenome)))
if genome == currgenome:
f.write("%sparent hubCentral%s\n" % (indent, annotation))
else:
f.write("%sparent hubCentral%s off\n" % (indent, annotation))
f.write("%ssubGroups view=%s orgs=%s\n" %
(indent, annotation, genome))
else:
f.write("%sshortLabel %s\n" % (indent, genomeProperName))
f.write("%sbigDataUrl ../liftoverbed2/%s\n" %
(indent,
os.path.join(annotation, genome, "%s.bb" % currgenome)))
f.write("\n")
def writeTrackDb_bigbeds_hackFakeRow(f, bigbeddir, genomes, currgenome, properName, tab):
annotation = os.path.basename(bigbeddir)
genome2priority = getPriorities(genomes, currgenome)
bedGenomes = os.listdir(bigbeddir)#HACK
bedGenomes2 = os.listdir(bigbeddir)#HACK
if currgenome not in bedGenomes2:#HACK
bedGenomes2.append(currgenome)#HACK
for genome in bedGenomes2:#HACK
bbfile = os.path.join(bigbeddir, genome, "%s.bb" %currgenome)
if genome == currgenome and currgenome not in bedGenomes:#HACK
bbfile = os.path.join(bigbeddir, bedGenomes[1], "%s.bb" %currgenome)#HACK
if not os.path.exists(bbfile):
continue
searchIndexStr, fields, numfield = getSearchIndexInfo(bigbeddir, genome, bbfile, tab)
#start writing track
genomeProperName = getProperName(genome, properName)
priority = 1
if genome in genome2priority:
priority = genome2priority[genome]
f.write("\t\ttrack %s%s\n" % (annotation, genome))
if genome == currgenome:
if currgenome not in bedGenomes:#HACK
f.write("\t\tlongLabel %s Lifted-over %s\n" % (properName[bedGenomes[1]], annotation))#HACK
else:#HACK
f.write("\t\tlongLabel %s %s\n" % (genomeProperName, annotation))#HACK
else:
f.write("\t\tlongLabel %s Lifted-over %s\n" % (genomeProperName, annotation))
f.write("\t\tpriority %d\n" %priority)
f.write("\t\tshortLabel %s%s\n" % (genomeProperName, annotation))
if genome == currgenome and genome not in bedGenomes:#HACK
f.write("\t\tbigDataUrl ../liftoverbed/%s\n" % os.path.join( annotation, bedGenomes[1], "%s.bb" % currgenome ) )#HACK
else:#HACK
f.write("\t\tbigDataUrl ../liftoverbed/%s\n" % os.path.join( annotation, genome, "%s.bb" % currgenome ) )#HACK
f.write("\t\ttype bigBed %s\n" %fields)
f.write("\t\tgroup annotation%s\n" %annotation)
if numfield >=4:
f.write("\t\tsearchIndex %s\n" %searchIndexStr)
f.write("\t\titemRgb On\n")
if genome == currgenome:
if genome in bedGenomes:
f.write("\t\tvisibility dense\n")
f.write("\t\tparent hubCentral%s\n"%annotation)
else:
f.write("\t\tvisibility hide\n")
f.write("\t\tparent hubCentral%s off\n"%annotation)
else:
f.write("\t\tvisibility hide\n")
f.write("\t\tparent hubCentral%s off\n"%annotation)
f.write("\t\tsubGroups view=%s orgs=%s\n" %(annotation, genome))
f.write("\n")
def writeTrackDb_bigbeds(f, bigbeddir, genomes, currgenome, properName, composite, tab):
annotation = os.path.basename(bigbeddir)
genome2priority = getPriorities(genomes, currgenome)
for genome in os.listdir(bigbeddir):
bbfile = os.path.join(bigbeddir, genome, "%s.bb" %currgenome)
if not os.path.exists(bbfile):
continue
searchIndexStr, fields, numfield = getSearchIndexInfo(bigbeddir, genome, bbfile, tab)
#start writing track
genomeProperName = getProperName(genome, properName)
priority = 1
if genome in genome2priority:
priority = genome2priority[genome]
indent = ''
if composite:
indent = "\t\t"
f.write("%strack %s%s\n" % (indent, annotation, genome))
if genome == currgenome:
f.write("%slongLabel %s %s\n" % (indent, genomeProperName, annotation))
else:
f.write("%slongLabel %s Lifted-over %s\n" % (indent, genomeProperName, annotation))
f.write("%spriority %d\n" %(indent, priority))
f.write("%stype bigBed %s\n" %(indent, fields))
f.write("%sgroup annotation%s\n" %(indent, annotation))
if numfield >=4:
f.write("%ssearchIndex %s\n" %(indent, searchIndexStr))
f.write("%sitemRgb On\n" %indent)
if genome == currgenome:
f.write("%svisibility dense\n" %indent)
else:
f.write("%svisibility hide\n" %indent)
if composite: #Composite
f.write("%sshortLabel %s%s\n" % (indent, genomeProperName, annotation))
f.write("%sbigDataUrl ../liftoverbed/%s\n" % (indent, os.path.join( annotation, genome, "%s.bb" % currgenome )) )
if genome == currgenome:
f.write("%sparent hubCentral%s\n" %(indent, annotation))
else:
f.write("%sparent hubCentral%s off\n" %(indent, annotation))
f.write("%ssubGroups view=%s orgs=%s\n" %(indent, annotation, genome))
else:
f.write("%sshortLabel %s\n" % (indent, genomeProperName))
f.write("%sbigDataUrl ../liftoverbed2/%s\n" % (indent, os.path.join( annotation, genome, "%s.bb" % currgenome )) )
f.write("\n")
def getProperName_tree(tree, properName):
from hal.assemblyHub.assemblyHubCommon import getProperName
for node in tree.find_clades():
if node.name:
node.name = getProperName(node.name, properName)
return
def getProperName_tree(tree, properName):
from hal.assemblyHub.assemblyHubCommon import getProperName
for node in tree.find_clades():
if node.name:
node.name = getProperName(node.name, properName)
return
