def run_picard():
global infile
mem = mem2(argsmem, '-jdict')
mem['-Djava.io.tmpdir'] = tmpdir
shellpicard = Shell(subcmd = True, dash = '', equal = '=').picard(**mem)
if not (steps.sort or steps.index or steps.markdup or steps.rmdup):
shellpicard.SamFormatConverter(TMP_DIR = tmpdir, I = infile, O = outfile).run()
else:
bamfile = outfile
if steps.sort:
bamfile = path.join(joboutdir, inprefix + '.sorted.bam')
shellpicard.ShortSam(TMP_DIR = tmpdir, I = infile, O = bamfile, SO = sortby).run()
if infile != {{i.infile | quote}}:
shell.rm(f = True, _ = infile)
infile = bamfile
if steps.markdup:
mfile = "/dev/null"
bamfile = path.join(joboutdir, inprefix + '.dedup.bam')
shellpicard.MarkDuplicates(REMOVE_DUPLICATES = 'true' if steps.rmdup else 'false', TMP_DIR = tmpdir, I = infile, O = bamfile, M = mfile).run()
if infile != {{i.infile | quote}}:
shell.rm(f = True, _ = infile)
infile = bamfile
if steps.index:
shellpicard.BuildBamIndex(TMP_DIR = tmpdir, I = infile, O = outfile + '.bai').run()
if infile != outfile:
if path.exists(infile + '.bai'):
shell.mv(infile + '.bai', outfile + '.bai')
shell.mv(infile, outfile)
def run_samtools():
global infile
if not (steps.sort or steps.index or steps.markdup or steps.rmdup):
subshell.samtools.view(b = True, o = outfile, O = 'bam', _ = infile).run()
else:
bamfile = outfile
if steps.sort:
mem = mem2(argsmem, 'M')
bamfile = path.join(joboutdir, inprefix + '.sorted.bam')
subshell.samtools.sort(
m = mem + 'M',
n = sortby == 'queryname',
o = bamfile,
T = tmpdir,
O = 'bam',
_ = infile,
**{'@': nthread}
).run()
if infile != {{i.infile | quote}}:
shell.rm(infile, f = True)
infile = bamfile
if steps.markdup or steps.rmdup:
bamfile = path.join(joboutdir, inprefix + '.dedup.bam')
subshell.rmdup(infile, bamfile).run()
if infile != {{i.infile | quote}}:
shell.rm(infile, f = True)
infile = bamfile
if steps.index:
subshell.samtools.index(bamfile, outfile + '.bai')
if infile != outfile:
if path.exists(infile + '.bai'):
shell.mv(infile + '.bai', outfile + '.bai')
shell.mv(infile, outfile)
def run_gatk():
mem = mem2(argsmem, '-jdict')
intfile = path.join(joboutdir, outprefix + '.intervals')
mem['-Djava.io.tmpdir={}'.format(shell.shquote(tmpdir))] = True
gatksh = Shell(equal=' ', dash='-').gatk
rtcparams = params.get('RealignerTargetCreator', Box())
rtcparams.T = 'RealignerTargetCreator'
rtcparams.R = ref
rtcparams.I = infile
rtcparams.o = intfile
rtcparams.nt = nthread
rtcparams._ = list(mem.keys())
gatksh(**rtcparams).run()
bamfileir = path.join(joboutdir, outprefix + '.ir.bam')
irparams = params.get('IndelRealigner', Box())
irparams.T = 'IndelRealigner'
irparams.R = ref
irparams.I = infile
irparams.o = bamfileir
irparams._ = list(mem.keys())
irparams.targetIntervals = intfile
gatksh(**irparams).run()
recaltable = path.join(joboutdir, outprefix + '.recaltable')
brparams = params.get('BaseRecalibrator', Box())
brparams.T = 'BaseRecalibrator'
brparams.R = ref
brparams.I = bamfileir
brparams.o = recaltable
brparams.nct = nthread
brparams._ = list(mem.keys())
brparams.knownSites = knownSites
gatksh(**brparams).run()
prparams = params.get('PrintReads', Box())
prparams.T = 'PrintReads'
prparams.R = ref
prparams.I = bamfileir
prparams.o = outfile
prparams.nct = nthread
prparams._ = list(mem.keys())
gatksh(**prparams).run()
shell.rm(bamfileir, f=True)
shell.mv(outprefix + '.bai', outfile + '.bai')
def run_sambamba():
global infile
if not (steps.sort or steps.index or steps.markdup or steps.rmdup):
subshell.sambamba.view(S = True, f = 'bam', o = outfile, t = nthread, _ = infile).run()
else:
bamfile = outfile
if infmt == 'sam':
bamfile = path.join(joboutdir, inprefix + '.s2b.bam')
subshell.sambamba.view(S = True, f = 'bam', o = bamfile, t = nthread, _ = infile).run()
infile = bamfile
if steps.sort:
if sortby == 'queryname':
params.n = True
params.N = True
bamfile = path.join(joboutdir, inprefix + '.sorted.bam')
params.m = argsmem
params.tmpdir = tmpdir
params.o = bamfile
params.t = nthread
params._ = infile
subshell.sambamba.sort(**params).run()
if infile != {{i.infile | quote}}:
shell.rm(f = True, _ = infile)
infile = bamfile
if steps.markdup:
bamfile = path.join(joboutdir, inprefix + '.dedup.bam')
subshell.sambamba.markdup(r = steps.rmdup, t = nthread, tmpdir = tmpdir, _ = [infile, bamfile]).run()
if infile != {{i.infile | quote}}:
shell.rm(f = True, _ = infile)
infile = bamfile
if steps.index:
if path.exists(infile + '.bai'):
shell.mv(infile + '.bai', outfile + '.bai')
else:
subshell.sambamba.index(t = nthread, _ = [infile, infile + '.bai'])
if infile != outfile:
if path.exists(infile + '.bai'):
shell.mv(infile + '.bai', outfile + '.bai')
shell.mv(infile, outfile)
shell.mv(outprefix + '.bai', outfile + '.bai')
def run_bamutil():
bush = Shell(subcmd=True, equal=' ').bamutil
if knownSites:
params.dbsnp = knownSites
params['in'] = infile
params.out = outfile
params.refFile = ref
params.verbose = True
refcache = path.splitext(ref)[0] + '-bs.umfa'
if not path.isfile(refcache):
poll = Poll(workdir, joblen, jobindex)
poll.first(lambda **kwargs: bush.recal(**kwargs).run(), **params)
else:
bush.recab(**params).run()
tools = dict(gatk=run_gatk, bamutil=run_bamutil)
try:
tools[tool]()
except KeyError:
raise KeyError('Tool {!r} not supported.'.format(tool))
except Exception as ex:
stderr.write("Job failed: %s" % str(ex))
raise
finally:
shell.rm(tmpdir, r=True, f=True)