from sys import stderr
from pyppl import Box
from os import path
from bioprocs.utils import shell, mem2
from bioprocs.utils.poll import Poll
from bioprocs.utils.shell import Shell
from bioprocs.utils.reference import bamIndex
infile = {{i.infile | quote}}
bamIndex(infile, samtools=None)
outfile = {{o.outfile | quote}}
outprefix = {{o.outfile | prefix | quote}}
tool = {{args.tool | quote}}
gatk = {{args.gatk | quote}}
samtools = {{args.samtools | quote}}
picard = {{args.picard | quote}}
bamutil = {{args.bamutil | quote}}
params = {{args.params | repr}}
ref = {{args.ref | quote}}
tmpdir = {{args.tmpdir | quote}}
knownSites = {{args.knownSites | quote}}
argsmem = {{args.mem | quote}}
nthread = {{args.nthread | quote}}
joboutdir = {{job.outdir | quote}}
joblen = {{proc.size | repr}}
jobindex = {{job.index | repr}}
workdir = {{proc.workdir | quote}}
tmpdir = path.join(tmpdir, "{{proc.id}}.{{i.infile | fn}}.{{job.index}}")
# pass the index file
shell.ln_s(infile + '.bai', outfile + '.bai')
if not path.exists(tmpdir):
from pyppl import Box
from bioprocs.utils import shell, runcmd, cmdargs
from bioprocs.utils.reference import bamIndex
infiles = {{i.infiles | repr}}
exbaits = {{args.exbaits | repr}}
accfile = {{args.accfile | repr}}
ref = {{args.ref | repr}}
params = {{args.params | repr}}
prefix = {{i.infiles | fs2name | quote}}
outdir = {{job.outdir | quote}}
cnvkit = {{args.cnvkit | quote}}
nthread = {{args.nthread | repr}}
for infile in infiles:
bamIndex(infile)
shell.TOOLS['cnvkit'] = cnvkit
envs = dict(OPENBLAS_NUM_THREADS=str(nthread),
OMP_NUM_THREADS=str(nthread),
NUMEXPR_NUM_THREADS=str(nthread),
MKL_NUM_THREADS=str(nthread))
ckshell = shell.Shell(subcmd=True, equal=' ', envs=envs, cwd=outdir).cnvkit
# generate target file
params_t = params.target
params_t.o = path.join(outdir, prefix + '.bed')
ckshell.target(exbaits, **params_t).run()
# generate access file
if not accfile:
prefix = {{i.infile | fn2 | quote}}
tool = {{args.tool | quote}}
gz = {{args.gz | bool}}
outfile = {{o.outfile | quote}}
params = {{args.params | repr}}
samtools = {{args.samtools | quote}}
mem = {{args.mem | quote}}
nthread = {{args.nthread | repr}}
gatk = {{args.gatk | quote}}
cfgParams = {{args.cfgParams | repr}}
platypus = {{args.platypus | quote}}
ssniffer = {{args.snvsniffer | quote}}
strelka = {{args.strelka | quote}}
vardict = {{ args.vardict | quote}}
joboutdir = {{job.outdir | quote}}
bamIndex(infile, samtools = None, nthread = nthread)
shell.TOOLS.update(dict(
gatk = gatk,
platypus = platypus,
ssniffer = ssniffer,
strelka = strelka,
vardict = vardict
))
if not path.exists(ref):
raise ValueError("Reference file not specified")
tmpdir = path.join(tmpdir, "{procid}.{prefix}.{jobindex}".format(
jobindex = jobindex,
procid = procid,
prefix = prefix
nprefix = {{i.normal | fn2 | quote}}
tool = {{args.tool | quote}}
gz = {{args.gz | bool}}
outfile = {{o.outfile | quote}}
params = {{args.params | repr}}
samtools = {{args.samtools | quote}}
mem = {{args.mem | quote}}
nthread = {{args.nthread | repr}}
gatk = {{args.gatk | quote}}
ssniper = {{args.somaticsniper | quote}}
ssniffer = {{args.snvsniffer | quote}}
strelka = {{args.strelka | quote}}
virmid = {{ args.virmid | quote}}
vardict = {{ args.vardict | quote}}
joboutdir = {{job.outdir | quote}}
bamIndex(tumor, samtools = None, nthread = nthread)
bamIndex(normal, samtools = None, nthread = nthread)
if tprefix == nprefix:
tprefix = tprefix + '_TUMOR'
nprefix = nprefix + '_NORMAL'
if gz:
# remove ending .gz
outfile = outfile[:-3]
if not path.exists (ref):
stderr.write ("Reference file not specified")
exit (1)
tmpdir = path.join (tmpdir, "{procid}.{tprefix}.{nprefix}.{jobindex}".format(
{% python from os import path %}
itvfile = {{ i.itvfile | quote}}
prefix = {{ o.outdir | path.join: fn(i.itvfile) | quote }}
tumbam = {{ i.tumbam | quote}}
tumsnp = {{ o.outdir | path.join: fn(i.tumbam) | @append: '.bamrc' | quote}}
normbam = {{ i.normbam | quote}}
normsnp = {{ o.outdir | path.join: fn(i.normbam) | @append: '.bamrc' | quote}}
outdir = {{ o.outdir | quote}}
params = {{ args.params | repr}}
bamrc = {{ args.bam_readcount | quote }}
nthread = {{ args.nthread | repr}}
affysnps = {{ args.affysnps | quote}}
ref = {{ args.ref | quote}}
theta = {{ args.theta | quote}}
bamIndex(tumbam, samtools = None, nthread = nthread)
bamIndex(normbam, samtools = None, nthread = nthread)
if not path.isfile(ref):
raise ValueError('A reference fasta file is required to extract allele counts.')
if not path.isfile(affysnps):
raise ValueError('A snp list is required.')
def getAlleleCount(bamfile, snpfile, outfile):
brcparams = Box()
brcparams.f = ref
brcparams.w = 0
brcparams.l = snpfile
brcparams[''] = bamfile