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CMDY

从python运行命令的一个方便的包

安装# latest version

pip install git+https://github.com/pwwang/cmdy

# released version

pip install cmdy

为什么在sh之外还有一个？oncotator不与sh一起运行，无论我尝试了什么。

无法用烘焙命令替换参数，请参见以下示例：

fromshimportlsls=ls.bake(l=True)print(ls())# ls -l# but now I somehow want to run `ls` (without `-l`) command with `ls()`ls(l=False)# not work

无法保存命令的配置，因为命令有其可靠的首选项。

无法指定可执行文件的完整路径。

没有管道/重定向标记。

基本用法fromcmdyimportlsprint(ls())

参数

像sh，cmdy可以有非关键字参数，但首选关键字参数。fromcmdyimporttartar("cvf","/tmp/test.tar","/my/home/directory/")

带关键字参数curl("http://duckduckgo.com/",o="page.html",silent=True)# curl http://duckduckgo.com/ -o page.html --silent

order关键字参数：curl("http://duckduckgo.com/","-o","page.html","--silent")# orfromcollectionsimportOrderedDictcurl("http://duckduckgo.com/",OrderedDict([('o','page.html'),('silent',True)]))

关键字参数的前缀和分隔符：fromcmdyimportbedtools,bcftools,lsbedtools.intersect(wa=True,wb=True,a='query.bed',b=['d1.bed','d2.bed','d3.bed'],names=['d1','d2','d3'],sorted=True,_prefix='-')#bedtools intersect -wa -wb -a query.bed -b d1.bed d2.bed d3.bed -names d1 d2 d3 -sortedbcftools.query(_=['a.vcf','b.vcf'],H=True,format='%CHROM\t%POS\t%REF\t%ALT\n')# bcftools query --format '%CHROM\t%POS\t%REF\t%ALT\n' -H a.vcf b.vcf# _prefix defaults to 'auto' ('-' for short options, '--' for long)# You may also define arbitrary prefix:# command(a = 1, bc = 2, _prefix = '---')# command ---a 1 ---bc 2ls(l=True,block_size='KB',_sep='auto')# ls -l --block-size=KB# _sep defaults to ' '. 'auto' means ' ' for short options, '=' for long

一个命令中前缀和分隔符的不同组合：fromcmdyimportjava# Note this is just an example for old verion picard. Picard is changing it's stylejava({'jar':'picard.jar','_prefix':'-','_sep':' '},'SortSam',I='input.bam',O='sorted.bam',SORTED_ORDER='coordinate',_raw=True,_prefix='',_sep='=')# java -jar picard.jar SortSam I=input.bam O=sorted.bam SORT_ORDER=coordinate# The first dictionary usees _prefix and _sep in itself if specified, otherwise uses the ones specified with kwargs.# _raw = True keeps SORTED_ORDER as it is, otherwise, it'll be transformed into SORTED-ORDER# This is useful when some command has option like '--block-size', but you can still use 'block_size' as keyword argument.

列表参数的重复键：fromcmdyimportsortsort(k=['1,1','2,2n'],_='a.bed',_dupkey=True)# sort -k 1,1 -k 2,2n a.bed

返回代码和异常fromcmdyimportxx()... ...

raise CmdyReturnCodeException(self)

│ └

└

cmdy.CmdyReturnCodeException: Unexpected RETURN CODE 127, expecting: [0][PID]38254[CMD] x

[STDERR] /bin/sh: x: command not found

您可以使用try/catch来捕获它：fromcmdyimportx,CmdyReturnCodeExceptiontry:x()exceptCmdyReturnCodeExceptionasexprint('Command returned%s'%ex.cmdy.rc)

您可以通过以下方式允许多个返回代码：x(_okcode = [0, 127])或x(_okcode = '0,127')

重定向fromcmdyimportifconfigifconfig(_out="/tmp/interfaces")# or you can use shell redirection notationifconfig(_out=">")>"/tmp/interfaces"# or# ifconfig(_out = "/tmp/interfaces")## appendifconfig(_out=">")>>"/tmp/interfaces"# or# ifconfig(_out_ = "/tmp/interfaces")# redirect stderrifconfig(_err=">")>"/tmp/ifconfig.errors"# or ifconfig(_err = "/tmp/ifconfig.errors")

输出迭代fromcmdyimporttailforlineintail(_='test.txt',_iter=True):print(line)

后台进程

对于要在非块模式下运行的命令，可能需要使用_bg关键字：forlineintail(_='test.txt',_bg=True,_iter=True):print(line)# blockssleep(3)print("...3 seconds later")# doesn't blockp=sleep(3,_bg=True)print("prints immediately!")p.wait()print("...and 3 seconds later")

后台进程的回调：importtimefromcmdyimportsleepdefcallback(cmdy):print(cmdy.rc)p=sleep(3,_bg=callback)p.wait()# prints 0

烘烤fromcmdyimportjavapicard=java.bake(dict(jar='picard.jar',_sep=' ',_prefix='-'))#picard.SortSam(...)

与sh不同，cmdy保存关键字参数，并在烘焙为新命令时更新它们。这使它能够用新的baked命令替换一些参数。fromcmdyimportlsls=ls.bake(l=True)# or ls = ls(l = True, _bake = True)ls()# ls -l# I don't want -l anymorels(l=False)

注意，非关键字参数是不可更新的。ls=ls.bake('-l')ls()# ls -l# Not work, still ls -lls(l=False)

烘焙整个模块：importcmdycmdy=cmdy(_fg=True)# all commands under new module is running at foreground (stdout = sys.stdout, stderr = stderr)fromcmdyimportlsls()

管道# get the permission columnls(l=True,_pipe=True)|cut(f=1,_fg=True)

子命令fromcmdyimportgitprint(git.branch(v=True))

别名/为命令指定可执行文件的完整路径fromcmdyimportfc_cache,pythonfc_cache(_exe='fc-cache',vf='~/.fonts/',_prefix='-')# fc-cache -vf ~/.fonts/python(_exe='/home/user/miniconda3/bin/python3',version=True)# /home/user/miniconda3/bin/python3 --version

始终将fc_cache别名设为fc-cache，并将python点设为/home/user/miniconda3/bin/python3，将以下内容添加到~/.cmdy.ini[fc_cache]_exe=fc-cache[python]_exe=/home/user/miniconda3/bin/python3

那么您就不需要再关心路径了：fromcmdyimportfc_cache,pythonfc_cache(vf='~/.fonts/',_prefix='-')# fc-cache -vf ~/.fonts/python(version=True)# /home/user/miniconda3/bin/python3 --version

配置

cmdy将首先加载默认参数：{'_okcode':0,'_exe':None,'_sep':' ','_prefix':'auto','_dupkey':False,'_bake':False,'_iter':False,'_pipe':False,'_raw':False,'_timeout':0,'_encoding':'utf-8','_bg':False,'_fg':False,'_out':None,'_out_':None,'_err':None,'_err_':None}

然后尝试加载$HOME/.cmdy.ini、./.cmdy.ini和以CMDY_开头的环境变量，以便可以用临时环境变量覆盖配置。

例如，我希望始终使用原始关键字选项：

~/.cmdy.ini[default]_raw: True

ontotator.py：fromcmdyimportoncotatoroncotator(log_name='/path/to/log',...)# oncotator --log_name LOG_NAME ...# you don't have to specify _raw = True any more.

使用环境变量覆盖设置：exportCMDY_oncotator__raw=False

python oncotator.py

# will run:# oncotator --log-name LOG_NAME ...# ^

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