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_star():
params.genomeDir = ref + '.star'
params.readFilesIn = [infile1, infile2]
params.readFilesCommand = ("cat", "zcat", "bzcat")[
1 if infile1.endswith('.gz') else 2 if infile1.endswith('.bz2') else 0
]
params.readNameSeparator = '.'
params.outFileNamePrefix = outdir + '/'
params.outSAMtype = [outfmt.upper(), 'Unsorted']
Shell(equal = ' ').star(**params).run()
starout = path.join(outdir, "Aligned.out.{}".format(outfmt))
if path.isfile(starout):
shell.mv(starout, outfile)
def run_strelka():
# config
cfgParams.bam = infile
cfgParams.referenceFasta = ref
cfgParams.runDir = joboutdir
Shell().strelka(**cfgParams).run()
# run the pipeline
params.m = 'local'
params.j = nthread
params.g = mem2(mem, 'G')[:-1]
Shell({'runWorkflow': path.join(joboutdir, 'runWorkflow.py')}).runWorkflow(**params).run()
# mv output file to desired outfile
ofile = path.join(joboutdir, 'results', 'variants', 'genome.S1.vcf.gz')
shell.mv(ofile, outfile + '.gz')
if not gz: shell.gunzip(outfile + '.gz')
def vcfIndex(vcf, tabix='tabix'):
# /path/to/some.vcf -> some.vcf
# /path/to/some.vcf.gz -> some.vcf
bname = path.basename(
vcf[:-3]) if vcf.endswith('.gz') else path.basename(vcf)
# /path/to/some.bam -> /path/to/
dname = path.dirname(vcf)
# some.vcf -> some
# some.vcf.gz -> some
fname = path.splitext(bname)[0]
# some -> some
# [1]some -> some
rname = fname.split(']', 1)[1] if fname.startswith('[') else fname
expectedIndex = path.join(dname, rname + '.vcf.gz.tbi')
if path.isfile(expectedIndex):
return vcf
# if vcf is not a link, there is nowhere else to find index, create it using tabix
tabix = shell.Shell({'tabix': tabix}).tabix
gt = gztype(vcf)
if gt == 'bgzip':
if path.islink(vcf):
linkvcf = path.readlink(vcf)
if path.isfile(linkvcf + '.tbi'):
shell.ln_s(linkvcf + '.tbi', expectedIndex)
return vcf
realvcf = path.realpath(vcf)
if path.isfile(realvcf + '.tbi'):
shell.ln_s(realvcf + '.tbi', expectedIndex)
return vcf
tabix(p='vcf', _=vcf).run()
return vcf
if gt == 'gzip':
tmpvcf = path.join(dname, bname + '.tmp.vcf')
shell.gunzip_to(vcf, tmpvcf)
shell.bgzip(tmpvcf)
tabix(p='vcf', _=tmpvcf + '.gz').run()
shell.mv(tmpvcf + '.gz.tbi', expectedIndex)
return vcf
shell.bgzip(vcf, c=True, _stdout=vcf + '.gz')
tabix(p='vcf', _=vcf + '.gz').run()
return vcf + '.gz'
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)