本文整理汇总了Python中multiprocessing.Pool.endswith方法的典型用法代码示例。如果您正苦于以下问题：Python Pool.endswith方法的具体用法？Python Pool.endswith怎么用？Python Pool.endswith使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类multiprocessing.Pool的用法示例。
在下文中一共展示了Pool.endswith方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: __main__
# 需要导入模块: from multiprocessing import Pool [as 别名]
# 或者: from multiprocessing.Pool import endswith [as 别名]
#.........这里部分代码省略.........
logging.error("Insert Sizes needs to undefined or match input file count")
sys.exit(1)
sampleTags = args.sampleTags
if len(sampleTags) != len(inputBamFiles):
logging.error("Sample Tags need to match input file count")
sys.exit(1)
tempDir = tempfile.mkdtemp(dir=args.workdir, prefix="pindel_work_")
print(tempDir)
try:
meanInsertSizes = []
seq_hash = {}
newInputFiles = []
i = 0
#make sure the BAMs are indexed and get the mean insert sizes
for inputBamFile, inputBamIndex, insertSize, sampleTag in zip(inputBamFiles, inputBamFileIndexes, insertSizes, sampleTags ):
inputFastaFile, inputBamFile = indexBam(args.workdir, args.inputFastaFile, inputBamFile, i, inputBamIndex)
i += 1
newInputFiles.append(inputBamFile)
if insertSize==None:
meanInsertSize = getMeanInsertSize(inputBamFile)
else:
meanInsertSize=insertSize
meanInsertSizes.append( meanInsertSize )
for seq in get_bam_seq(inputBamFile, args.min_chrom_size):
seq_hash[seq] = True
seqs = seq_hash.keys()
configFile = config(newInputFiles, meanInsertSizes, sampleTags, tempDir)
#run pindel
pindel_files = []
if args.procs == 1:
cmd, pindelFileBase = pindel(inputFastaFile, configFile, args, tempDir)
execute(cmd)
for suffix in ["_D", "_SI", "_LI", "_INV", "_TD"]:
if os.path.exists(pindelFileBase + suffix):
pindel_files.append( pindelFileBase + suffix )
else:
cmds = []
runs = []
for a in seqs:
cmd, pindelFileBase = pindel(inputFastaFile, configFile, args, tempDir, a)
cmds.append(cmd)
runs.append(pindelFileBase)
p = Pool(args.procs)
values = p.map(execute, cmds, 1)
for pindelFileBase in runs:
for suffix in ["_D", "_SI", "_LI", "_INV", "_TD"]:
if os.path.exists(pindelFileBase + suffix):
pindel_files.append( pindelFileBase + suffix )
#run pindel2vcf
with open(os.path.join(args.workdir, "pindel_all"), "w") as handle:
for p in pindel_files:
with open(p) as ihandle:
for line in ihandle:
handle.write(line)
if args.outputRaw is not None:
shutil.copy(os.path.join(args.workdir, "pindel_all"), args.outputRaw)
if args.outputVcfFile is not None:
cmd = pindel2vcf(inputFastaFile, args.inputFastaName, os.path.join(args.workdir, "pindel_all"), args.outputVcfFile)
execute(cmd)
if args.outputSomaticVcfFile is not None:
with open(os.path.join(args.workdir, "pindel_somatic"), "w") as handle:
for p in pindel_files:
if p.endswith("_D"):
with open(p) as ihandle:
for line in ihandle:
if re.search("ChrID", line):
handle.write(line)
for p in pindel_files:
if p.endswith("_SI"):
with open(p) as ihandle:
for line in ihandle:
if re.search("ChrID", line):
handle.write(line)
with open(os.path.join(args.workdir, "somatic.indel.filter.config"), "w") as handle:
handle.write("indel.filter.input = %s\n" % os.path.join(args.workdir, "pindel_somatic"))
handle.write("indel.filter.vaf = %s\n" % (args.somatic_vaf))
handle.write("indel.filter.cov = %s\n" % (args.somatic_cov))
handle.write("indel.filter.hom = %s\n" % (args.somatic_hom))
handle.write("indel.filter.pindel2vcf = %s\n" % (which("pindel2vcf")))
handle.write("indel.filter.reference = %s\n" % (inputFastaFile))
handle.write("indel.filter.referencename = %s\n" % (args.inputFastaName))
handle.write("indel.filter.referencedate = %s\n" % (datetime.datetime.now().strftime("%Y%m%d")) )
handle.write("indel.filter.output = %s\n" % (args.outputSomaticVcfFile))
# The hard-coded paths need to be removed.
execute("%s ~/bin/somatic_indelfilter.pl %s" % (which("perl"), os.path.join(args.workdir, "somatic.indel.filter.config")) )
finally:
if not args.no_clean and os.path.exists(tempDir):
shutil.rmtree(tempDir)