本文整理匯總了Python中jcvi.apps.grid.MakeManager.clean方法的典型用法代碼示例。如果您正苦於以下問題：Python MakeManager.clean方法的具體用法？Python MakeManager.clean怎麽用？Python MakeManager.clean使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類jcvi.apps.grid.MakeManager的用法示例。
在下文中一共展示了MakeManager.clean方法的1個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: lobstr
# 需要導入模塊: from jcvi.apps.grid import MakeManager [as 別名]
# 或者: from jcvi.apps.grid.MakeManager import clean [as 別名]
def lobstr(args):
"""
%prog lobstr lobstr_index1 lobstr_index2 ...
Run lobSTR on a big BAM file. There can be multiple lobSTR indices. In
addition, bamfile can be S3 location and --lobstr_home can be S3 location
(e.g. s3://hli-mv-data-science/htang/str-build/lobSTR/)
"""
p = OptionParser(lobstr.__doc__)
p.add_option("--chr", help="Run only this chromosome")
p.set_home("lobstr", default="s3://hli-mv-data-science/htang/str-build/lobSTR/")
p.set_cpus()
p.set_aws_opts(store="hli-mv-data-science/htang/str-data")
opts, args = p.parse_args(args)
bamfile = opts.input_bam_path
if len(args) < 1 or bamfile is None:
sys.exit(not p.print_help())
lbindices = args
s3mode = bamfile.startswith("s3")
store = opts.output_path
cleanup = not opts.nocleanup
workdir = opts.workdir
mkdir(workdir)
os.chdir(workdir)
lhome = opts.lobstr_home
if lhome.startswith("s3://"):
lhome = pull_from_s3(lhome, overwrite=False)
exec_id, sample_id = opts.workflow_execution_id, opts.sample_id
prefix = [x for x in (exec_id, sample_id) if x]
if prefix:
pf = "_".join(prefix)
else:
pf = bamfile.split("/")[-1].split(".")[0]
if s3mode:
gzfile = pf + ".{0}.vcf.gz".format(lbindices[-1])
remotegzfile = "{0}/{1}".format(store, gzfile)
if check_exists_s3(remotegzfile):
logging.debug("Object `{0}` exists. Computation skipped."\
.format(remotegzfile))
return
localbamfile = pf + ".bam"
localbaifile = localbamfile + ".bai"
if op.exists(localbamfile):
logging.debug("BAM file already downloaded.")
else:
pull_from_s3(bamfile, localbamfile)
if op.exists(localbaifile):
logging.debug("BAM index file already downloaded.")
else:
remotebaifile = bamfile + ".bai"
if check_exists_s3(remotebaifile):
pull_from_s3(remotebaifile, localbaifile)
else:
remotebaifile = bamfile.rsplit(".")[0] + ".bai"
if check_exists_s3(remotebaifile):
pull_from_s3(remotebaifile, localbaifile)
else:
logging.debug("BAM index cannot be found in S3!")
sh("samtools index {0}".format(localbamfile))
bamfile = localbamfile
chrs = [opts.chr] if opts.chr else (range(1, 23) + ["X", "Y"])
for lbidx in lbindices:
makefile = "makefile.{0}".format(lbidx)
mm = MakeManager(filename=makefile)
vcffiles = []
for chr in chrs:
cmd, vcffile = allelotype_on_chr(bamfile, chr, lhome, lbidx)
mm.add(bamfile, vcffile, cmd)
filteredvcffile = vcffile.replace(".vcf", ".filtered.vcf")
cmd = "python -m jcvi.variation.str filtervcf {}".format(vcffile)
cmd += " --lobstr_home {}".format(lhome)
mm.add(vcffile, filteredvcffile, cmd)
vcffiles.append(filteredvcffile)
gzfile = bamfile.split(".")[0] + ".{0}.vcf.gz".format(lbidx)
cmd = "vcf-concat {0} | vcf-sort".format(" ".join(vcffiles))
cmd += " | bgzip -c > {0}".format(gzfile)
mm.add(vcffiles, gzfile, cmd)
mm.run(cpus=opts.cpus)
if s3mode:
push_to_s3(store, gzfile)
if cleanup:
mm.clean()
sh("rm -f {} {} *.bai *.stats".format(bamfile, mm.makefile))