def run(self):
liftovertempbed = "%s.bed" % os.path.join(self.genomeoutdir,
self.othergenome)
cmd = "halLiftover %s %s %s %s %s" % (self.halfile, self.genome,
self.bed, self.othergenome,
liftovertempbed)
if len(self.extrafields) > 0:
cmd += " --keepExtra"
else:
cmd += " --outBedVersion %d" % self.numfield
if self.tab:
cmd += " --tab"
system(cmd)
#system("bedSort %s %s" %(liftovertempbed, liftovertempbed))
filterbed = "%s-filtered.bed" % os.path.join(self.genomeoutdir,
self.othergenome)
filterLongIntrons(liftovertempbed, filterbed, 100000, self.tab,
self.options.ucscNames)
# bedSort expects tab-separated beds, so we have to do some
# format gymnastics here.
if not self.tab:
tabifyBed(filterbed)
system("bedSort %s %s" % (filterbed, liftovertempbed))
if not self.tab:
untabifyBed(liftovertempbed)
outbigbed = os.path.join(self.genomeoutdir, "%s.bb" % self.othergenome)
chrsizefile = os.path.join(self.outdir, self.othergenome,
"chrom.sizes")
if not self.asfile:
cmd = "bedToBigBed -type=bed%d %s %s %s" % (
self.numfield, liftovertempbed, chrsizefile, outbigbed)
if self.numfield >= 4:
cmd += " -extraIndex=name"
else:
numextra = len(self.extrafields)
if numextra > 0:
type = "bed%d+%d" % (self.numfield - numextra, numextra)
extraIndex = "name,%s" % ",".join(self.extrafields)
else:
type = "bed%d" % self.numfield
extraIndex = "name"
cmd = "bedToBigBed -as=%s -type=%s -extraIndex=%s %s %s %s" % (
self.asfile, type, extraIndex, liftovertempbed, chrsizefile,
outbigbed)
if self.tab:
cmd += " -tab"
system(cmd)
#Cleanup:
system("rm %s" % liftovertempbed)
system("rm -f %s" % filterbed)
def run(self):
liftovertempbed = "%s.bed" % os.path.join(self.genomeoutdir, self.othergenome)
cmd = "halLiftover %s %s %s %s %s" %(self.halfile, self.genome, self.bed, self.othergenome, liftovertempbed)
if len(self.extrafields) > 0:
cmd += " --keepExtra"
else:
cmd += " --outBedVersion %d" %self.numfield
if self.tab:
cmd += " --tab"
system(cmd)
#system("bedSort %s %s" %(liftovertempbed, liftovertempbed))
filterbed = "%s-filtered.bed" %os.path.join(self.genomeoutdir, self.othergenome)
filterLongIntrons(liftovertempbed, filterbed, 100000, self.tab, self.options.ucscNames)
# bedSort expects tab-separated beds, so we have to do some
# format gymnastics here.
if not self.tab:
tabifyBed(filterbed)
system( "bedSort %s %s" % (filterbed, liftovertempbed) )
if not self.tab:
untabifyBed(liftovertempbed)
outbigbed = os.path.join(self.genomeoutdir, "%s.bb" %self.othergenome)
chrsizefile = os.path.join(self.outdir, self.othergenome, "chrom.sizes")
if not self.asfile:
cmd = "bedToBigBed -type=bed%d %s %s %s" %(self.numfield, liftovertempbed, chrsizefile, outbigbed)
if self.numfield >= 4:
cmd += " -extraIndex=name"
else:
numextra = len(self.extrafields)
if numextra > 0:
type="bed%d+%d" %(self.numfield - numextra, numextra)
extraIndex = "name,%s" % ",".join(self.extrafields)
else:
type="bed%d" %self.numfield
extraIndex = "name"
cmd = "bedToBigBed -as=%s -type=%s -extraIndex=%s %s %s %s" %(self.asfile, type, extraIndex, liftovertempbed, chrsizefile, outbigbed)
if self.tab:
cmd += " -tab"
system(cmd)
#Cleanup:
system("rm %s" % liftovertempbed)
system("rm -f %s" % filterbed)
def run(self):
#beddir has the hierachy: indir/genome/chr1.bed, chr2.bed...
#for each genome in beddir, lifeover the bed records of that genome to the coordinate of all other genomes
#liftover bed file of each genome with available beds to all genomes
genomes = self.genome2seq2len.keys()
tempbeds = []
for genome in os.listdir(self.indir):
if genome not in genomes:
continue
genomeindir = os.path.join(self.indir, genome)
assert os.path.isdir(genomeindir)
#Create bed directory for current genome
genomeoutdir = os.path.join(self.bigbeddir, genome)
system("mkdir -p %s" % genomeoutdir)
#get all the bed files (".bed" ext) and as files if available (".as" ext)
bedfiles, asfile, extrafields, numfield = readBedDir(
genomeindir, self.tab)
if numfield < 3:
# This is an empty (probably from an automated
# process) or otherwise malformed bed. Whine to the
# user and then attempt to go as far as possible
# anyway.
self.logToMaster("WARNING: input bed files in %s have less "
"than 3 fields, or are completely empty. "
"Proceeding anyway." % genomeindir)
numfield = 3
#Copy as file to bigbed dir:
if asfile:
system("cp %s %s" %
(asfile, os.path.join(genomeoutdir, "%s.as" % genome)))
elif numfield > 12: #does not have .as file, and have more than 12 fields, just treat as 12 fields
numfield = 12
#Concatenate all the input bed files and convert it into bigbed to outdir/genome/genome.bb
tempbed = "%s-temp.bed" % os.path.join(genomeoutdir, genome)
system("cat %s/*bed | cut -f-%d > %s" %
(genomeindir, numfield, tempbed))
#system( "bedSort %s %s" % (tempbed, tempbed) )
filterbed = "%s-temp-filtered.bed" % os.path.join(
genomeoutdir, genome)
filterLongIntrons(tempbed, filterbed, 100000, self.tab,
self.options.ucscNames)
# bedSort expects tab-separated beds, so we have to do some
# format gymnastics here.
if not self.tab:
tabifyBed(filterbed)
system("bedSort %s %s" % (filterbed, tempbed))
if not self.tab:
untabifyBed(tempbed)
outbigbed = os.path.join(genomeoutdir, "%s.bb" % genome)
chrsizefile = os.path.join(self.outdir, genome, "chrom.sizes")
if not asfile:
# Index on the 'name' field if the bed has one
indexParameter = "-extraIndex=name" if numfield >= 4 else ""
cmd = "bedToBigBed -type=bed%d %s %s %s %s" % (
numfield, indexParameter, tempbed, chrsizefile, outbigbed)
if self.tab:
cmd = "bedToBigBed -tab -type=bed%d %s %s %s %s" % (
numfield, indexParameter, tempbed, chrsizefile,
outbigbed)
system(cmd)
else:
assert numfield >= 4 # -extraIndex=name will fail if this is not true.
numextra = len(extrafields)
if numextra > 0:
type = "bed%d+%d" % (numfield - numextra, numextra)
extraIndex = "name,%s" % ",".join(extrafields)
else:
type = "bed%d" % numfield
extraIndex = "name"
cmd = "bedToBigBed -as=%s -type=%s -extraIndex=%s %s %s %s" % (
asfile, type, extraIndex, tempbed, chrsizefile, outbigbed)
if self.tab:
cmd = "bedToBigBed -tab -as=%s -type=%s -extraIndex=%s %s %s %s" % (
asfile, type, extraIndex, tempbed, chrsizefile,
outbigbed)
system(cmd)
#Liftover to all other genomes:
if not self.noLiftover:
for othergenome in genomes:
if othergenome == genome:
continue
self.addChildTarget(
LiftoverBed(genomeoutdir, tempbed, self.tab, asfile,
extrafields, numfield, genome, othergenome,
self.halfile, self.outdir, self.options))
tempbeds.append(tempbed)
tempbeds.append(filterbed)
self.setFollowOnTarget(CleanupFiles(tempbeds))
def run(self):
#beddir has the hierachy: indir/genome/chr1.bed, chr2.bed...
#for each genome in beddir, lifeover the bed records of that genome to the coordinate of all other genomes
#liftover bed file of each genome with available beds to all genomes
genomes = self.genome2seq2len.keys()
tempbeds = []
for genome in os.listdir(self.indir):
if genome not in genomes:
continue
genomeindir = os.path.join(self.indir, genome)
assert os.path.isdir(genomeindir)
#Create bed directory for current genome
genomeoutdir = os.path.join(self.bigbeddir, genome)
system("mkdir -p %s" %genomeoutdir)
#get all the bed files (".bed" ext) and as files if available (".as" ext)
bedfiles, asfile, extrafields, numfield = readBedDir(genomeindir, self.tab)
if numfield < 3:
# This is an empty (probably from an automated
# process) or otherwise malformed bed. Whine to the
# user and then attempt to go as far as possible
# anyway.
self.logToMaster("WARNING: input bed files in %s have less "
"than 3 fields, or are completely empty. "
"Proceeding anyway." % genomeindir)
numfield = 3
#Copy as file to bigbed dir:
if asfile:
system("cp %s %s" %(asfile, os.path.join(genomeoutdir, "%s.as" %genome)))
elif numfield > 12: #does not have .as file, and have more than 12 fields, just treat as 12 fields
numfield = 12
#Concatenate all the input bed files and convert it into bigbed to outdir/genome/genome.bb
tempbed = "%s-temp.bed" % os.path.join(genomeoutdir, genome)
system( "cat %s/*bed | cut -f-%d > %s" %(genomeindir, numfield, tempbed) )
#system( "bedSort %s %s" % (tempbed, tempbed) )
filterbed = "%s-temp-filtered.bed" %os.path.join(genomeoutdir, genome)
filterLongIntrons(tempbed, filterbed, 100000, self.tab,
self.options.ucscNames)
# bedSort expects tab-separated beds, so we have to do some
# format gymnastics here.
if not self.tab:
tabifyBed(filterbed)
system( "bedSort %s %s" % (filterbed, tempbed) )
if not self.tab:
untabifyBed(tempbed)
outbigbed = os.path.join(genomeoutdir, "%s.bb" %genome)
chrsizefile = os.path.join(self.outdir, genome, "chrom.sizes")
if not asfile:
# Index on the 'name' field if the bed has one
indexParameter = "-extraIndex=name" if numfield >= 4 else ""
cmd = "bedToBigBed -type=bed%d %s %s %s %s" %(numfield, indexParameter, tempbed, chrsizefile, outbigbed)
if self.tab:
cmd = "bedToBigBed -tab -type=bed%d %s %s %s %s" %(numfield, indexParameter, tempbed, chrsizefile, outbigbed)
system( cmd )
else:
assert numfield >= 4 # -extraIndex=name will fail if this is not true.
numextra = len(extrafields)
if numextra > 0:
type="bed%d+%d" %(numfield - numextra, numextra)
extraIndex = "name,%s" % ",".join(extrafields)
else:
type="bed%d" %numfield
extraIndex = "name"
cmd = "bedToBigBed -as=%s -type=%s -extraIndex=%s %s %s %s" %(asfile, type, extraIndex, tempbed, chrsizefile, outbigbed)
if self.tab:
cmd = "bedToBigBed -tab -as=%s -type=%s -extraIndex=%s %s %s %s" %(asfile, type, extraIndex, tempbed, chrsizefile, outbigbed)
system( cmd )
#Liftover to all other genomes:
if not self.noLiftover:
for othergenome in genomes:
if othergenome == genome:
continue
self.addChildTarget( LiftoverBed(genomeoutdir, tempbed, self.tab, asfile, extrafields, numfield, genome, othergenome, self.halfile, self.outdir, self.options) )
tempbeds.append( tempbed )
tempbeds.append( filterbed )
self.setFollowOnTarget( CleanupFiles(tempbeds) )