CMDY
從python運作指令的一個友善的包
安裝# latest version
pip install git+https://github.com/pwwang/cmdy
# released version
pip install cmdy
為什麼在sh之外還有一個？oncotator不與sh一起運作，無論我嘗試了什麼。
無法用烘焙指令替換參數，請參見以下示例：
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
無法儲存指令的配置，因為指令有其可靠的首選項。
無法指定可執行檔案的完整路徑。
沒有管道/重定向标記。
基本用法fromcmdyimportlsprint(ls())
參數
像sh，cmdy可以有非關鍵字參數，但首選關鍵字參數。fromcmdyimporttartar("cvf","/tmp/test.tar","/my/home/directory/")
帶關鍵字參數curl("http://duckduckgo.com/",o="page.html",silent=True)# curl http://duckduckgo.com/ -o page.html --silent
order關鍵字參數：curl("http://duckduckgo.com/","-o","page.html","--silent")# orfromcollectionsimportOrderedDictcurl("http://duckduckgo.com/",OrderedDict([('o','page.html'),('silent',True)]))
關鍵字參數的字首和分隔符：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
一個指令中字首和分隔符的不同組合：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.
清單參數的重複鍵：fromcmdyimportsortsort(k=['1,1','2,2n'],_='a.bed',_dupkey=True)# sort -k 1,1 -k 2,2n a.bed
傳回代碼和異常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來捕獲它：fromcmdyimportx,CmdyReturnCodeExceptiontry:x()exceptCmdyReturnCodeExceptionasexprint('Command returned%s'%ex.cmdy.rc)
您可以通過以下方式允許多個傳回代碼：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")
輸出疊代fromcmdyimporttailforlineintail(_='test.txt',_iter=True):print(line)
背景程序
對于要在非塊模式下運作的指令，可能需要使用_bg關鍵字：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")
背景程序的回調：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(...)
與sh不同，cmdy儲存關鍵字參數，并在烘焙為新指令時更新它們。這使它能夠用新的baked指令替換一些參數。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，非關鍵字參數是不可更新的。ls=ls.bake('-l')ls()# ls -l# Not work, still ls -lls(l=False)
烘焙整個子產品：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)
子指令fromcmdyimportgitprint(git.branch(v=True))
别名/為指令指定可執行檔案的完整路徑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
始終将fc_cache别名設為fc-cache，并将python點設為/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
那麼您就不需要再關心路徑了：fromcmdyimportfc_cache,pythonfc_cache(vf='~/.fonts/',_prefix='-')# fc-cache -vf ~/.fonts/python(version=True)# /home/user/miniconda3/bin/python3 --version
配置
cmdy将首先加載預設參數：{'_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}
然後嘗試加載$HOME/.cmdy.ini、./.cmdy.ini和以CMDY_開頭的環境變量，以便可以用臨時環境變量覆寫配置。
例如，我希望始終使用原始關鍵字選項：
~/.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.
使用環境變量覆寫設定：exportCMDY_oncotator__raw=False
python oncotator.py
# will run:# oncotator --log-name LOG_NAME ...# ^
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