def run(self, fileStore):
#GC content & Alignability
for genome in self.genomes:
genomedir = os.path.join(self.outdir, genome)
if self.options.gcContent:
self.addChild(GetGCpercent(genomedir,
genome)) #genomedir/genome.gc.bw
if self.options.alignability:
self.addChild(GetAlignability(
genomedir, genome,
self.halfile)) #genomedir/genome.alignability.bw
#Compute conservation track:
if self.options.conservation:
#if self.options.conservation or self.options.conservationDir:
conservationDir = os.path.join(self.outdir, "conservation")
if not self.options.conservationDir:
system("mkdir -p %s" % conservationDir)
self.addChild(
GetConservationFiles(self.halfile, conservationDir,
self.options))
else:
if os.path.abspath(self.options.conservationDir
) != os.path.abspath(conservationDir):
system("ln -s %s %s" % (os.path.abspath(
self.options.conservationDir), conservationDir))
#system("cp -r %s %s" %(self.options.conservationDir, conservationDir))
#Make bed tracks:
preprocessAnnotationInputs(self.options, self.outdir, "bed")
self.addChild(
MakeAnnotationTracks(self.options, self.outdir, self.halfile,
self.genome2seq2len, "bed"))
#Make bed2 tracks:
preprocessAnnotationInputs(self.options, self.outdir, "bed2")
self.addChild(
MakeAnnotationTracks(self.options, self.outdir, self.halfile,
self.genome2seq2len, "bed2"))
#Make wig tracks:
preprocessAnnotationInputs(self.options, self.outdir, "wig")
self.addChild(
MakeAnnotationTracks(self.options, self.outdir, self.halfile,
self.genome2seq2len, "wig"))
#Make clade-exclusive tracks:
if self.options.tree and self.options.cladeExclusive:
self.addChild(
GetCladeExclusiveRegions(
self.halfile, self.options.tree,
os.path.join(self.outdir, "liftoverbeds"),
self.options.maxOut, self.options.minIn))
self.options.bigbeddirs.append(
os.path.join(self.outdir, "liftoverbeds", "CladeExclusive"))
#Get LOD if needed, and Write trackDb files
self.addFollowOn(
WriteGenomesFile(self.genomes, self.genome2seq2len, self.halfile,
self.options, self.outdir))
def run(self):
# GC content & Alignability
for genome in self.genomes:
genomedir = os.path.join(self.outdir, genome)
if self.options.gcContent:
self.addChildTarget(GetGCpercent(genomedir, genome)) # genomedir/genome.gc.bw
if self.options.alignability:
self.addChildTarget(
GetAlignability(genomedir, genome, self.halfile)
) # genomedir/genome.alignability.bw
# Compute conservation track:
if self.options.conservation:
# if self.options.conservation or self.options.conservationDir:
conservationDir = os.path.join(self.outdir, "conservation")
if not self.options.conservationDir:
system("mkdir -p %s" % conservationDir)
self.addChildTarget(GetConservationFiles(self.halfile, conservationDir, self.options))
else:
if os.path.abspath(self.options.conservationDir) != os.path.abspath(conservationDir):
system("ln -s %s %s" % (os.path.abspath(self.options.conservationDir), conservationDir))
# system("cp -r %s %s" %(self.options.conservationDir, conservationDir))
# Make bed tracks:
preprocessAnnotationInputs(self.options, self.outdir, "bed")
self.addChildTarget(MakeAnnotationTracks(self.options, self.outdir, self.halfile, self.genome2seq2len, "bed"))
# Make bed2 tracks:
preprocessAnnotationInputs(self.options, self.outdir, "bed2")
self.addChildTarget(MakeAnnotationTracks(self.options, self.outdir, self.halfile, self.genome2seq2len, "bed2"))
# Make wig tracks:
preprocessAnnotationInputs(self.options, self.outdir, "wig")
self.addChildTarget(MakeAnnotationTracks(self.options, self.outdir, self.halfile, self.genome2seq2len, "wig"))
# Make clade-exclusive tracks:
if self.options.tree and self.options.cladeExclusive:
self.addChildTarget(
GetCladeExclusiveRegions(
self.halfile,
self.options.tree,
os.path.join(self.outdir, "liftoverbeds"),
self.options.maxOut,
self.options.minIn,
)
)
self.options.bigbeddirs.append(os.path.join(self.outdir, "liftoverbeds", "CladeExclusive"))
# Get LOD if needed, and Write trackDb files
self.setFollowOnTarget(
WriteGenomesFile(self.genomes, self.genome2seq2len, self.halfile, self.options, self.outdir)
)