本文整理汇总了Python中subprocess.Popen.desc方法的典型用法代码示例。如果您正苦于以下问题：Python Popen.desc方法的具体用法？Python Popen.desc怎么用？Python Popen.desc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subprocess.Popen的用法示例。
在下文中一共展示了Popen.desc方法的2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 subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import desc [as 别名]
def main(args):
'''
This script takes in a VCF file (a sample x snp matrux), splits it
into --ref and --imp sets. From the --imp set, it further reduces
the VCF to a set of --tags. Using the --imp X --tags subset, it uses
beagle 4 to impute and discovers the miscalssification rate of the
'''
parser = OptionParser()
parser.add_option('--vcf')
parser.add_option('--ids',default=None)
parser.add_option('--tags',default=None)
parser.add_option('--call_thresh',default=0.45,type='float')
# parse options!
options,args = parser.parse_args(args)
processes = []
# filter imp set into tag set
log('Generating keep and ref sets' + '#'*50)
if not os.path.exists('keep_'+os.path.basename(options.ids)+'.recode.vcf'):
p = Popen([
'vcftools',
'--vcf', options.vcf,
'--keep', options.ids,
'--recode',
'--out', 'keep_' + os.path.basename(options.ids)
])
p.desc = 'vcftools: keep'
processes.append(p)
if not os.path.exists('ref_'+os.path.basename(options.ids)+'.recode.vcf'):
p = Popen([
'vcftools',
'--vcf', options.vcf,
'--remove', options.ids,
'--recode',
'--out', 'ref_' + os.path.basename(options.ids)
])
p.desc = 'vcftools: remove'
processes.append(p)
# Wait for vcftools to be done
wait(processes)
# filter to only tags for keep set
if not os.path.exists('tags_'+os.path.basename(options.ids)+'.recode.vcf'):
log('Genertaing Tag VCF'+ '#'*50)
p = Popen([
'vcftools',
'--vcf', 'keep_' + os.path.basename(options.ids) + '.recode.vcf',
'--snps', options.tags,
'--recode',
'--out', 'tags_' + os.path.basename(options.ids)
])
p.desc = 'vcftools: tags'
processes.append(p)
wait(processes)
# phase the reference pops
log('Phasing reference set' + '#'*50)
if not os.path.exists('ref_phased_'+os.path.basename(options.ids)+'.recode.vcf'):
p = Popen([
'java',
'-jar', '/project/mccuelab/shared/bin/b4.r1274.jar',
'gt=ref_'+os.path.basename(options.ids)+'.recode.vcf',
'out=ref_phased_'+os.path.basename(options.ids)+'.recode'
])
p.desc = 'ref phasing'
processes.append(p)
wait(processes)
unzip('ref_phased_'+os.path.basename(options.ids)+'.recode.vcf.gz',processes)
log('Imputing Tags' + '#'*50)
if not os.path.exists('imputed_'+os.path.basename(options.ids)+'.recode.vcf'):
p = Popen([
'java',
'-jar', '/project/mccuelab/shared/bin/b4.r1274.jar',
'gt=tags_'+os.path.basename(options.ids)+'.recode.vcf',
'ref=ref_phased_'+os.path.basename(options.ids)+'.recode.vcf',
'out=imputed_'+os.path.basename(options.ids)+'.recode',
])
p.desc = 'tag imputation'
processes.append(p)
wait(processes)
unzip('imputed_'+os.path.basename(options.ids)+'.recode.vcf.gz',processes)
# Now do what you came here to do!
tags = TagSet('tags_'+os.path.basename(options.ids)+'.recode.vcf')
print(os.path.basename(options.ids),
tags.misclassification(
VCF("imputed_"+os.path.basename(options.ids)+".recode.vcf"),
VCF("keep_"+os.path.basename(options.ids)+".recode.vcf"),
call_thresh=options.call_thresh
)
)示例2: unzip
# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import desc [as 别名]
def unzip(file,processes):
p = Popen(['gunzip','-f',file])
p.desc = 'unzipping'
processes.append(p)
wait(processes)