我正在尝试搜索文本文件并检索包含一组特定单词的行.这是我正在使用的代码:
tyrs = subprocess.check_output('grep "^A" %s | grep TYR' % pocket_location, shell = True).split('\n')
当文件包含grep标识的至少一行时,这可以正常工作.但是当grep没有标识任何行时,grep返回退出状态1并且我收到以下错误:
Traceback (most recent call last): File "../../Python_scripts/cbs_wrapper2.py", line 324, intyrs = subprocess.check_output('grep "^ATOM" %s | grep TYR' % pocket_location, shell = True).split('\n') File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 544, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command 'grep "^ATOM" cbsPrediction_files/1u9c_clean/1u9c_clean_fpocket_out/pockets/pocket0_atm.pdb | grep TYR' returned non-zero exit status 1
我该如何避免这个问题?subprocess.check_output
如果grep找不到任何内容,我只想返回一个空字符串.
谢谢
tyrs = subprocess.check_output('grep "^A" %s | grep TYR || true' % pocket_location, shell = True).split('\n')
我只是希望subprocess.check_output在grep找不到任何内容时返回一个空字符串.
好吧,太糟糕了.grep
认为没有匹配是失败的,并且check
in的重点check_output
是检查失败,所以你明确要求以这种方式做事.以下是相关文档:
如果返回码非零,则会引发CalledProcessError.CalledProcessError对象将具有returncode属性中的返回代码以及output属性中的任何输出.
并为grep
:
The following exit values shall be returned: 0 One or more lines were selected. 1 No lines were selected. >1 An error occurred.
因此,如果您希望将"无行"视为成功,将实际错误视为错误,则必须以1
不同于其他非零值的方式处理该值.并且check_output
不知道你想要那样做.
所以,要么你必须处理CalledProcessError
,要么你必须自己检查.换句话说,要么:
try: tyrs = subprocess.check_output('grep "^A" %s | grep TYR' % pocket_location, shell = True).split('\n') except subprocess.CalledProcessError as e: if e.returncode > 1: raise tyrs = []
… 或这个:
p = subprocess.Popen('grep "^A" %s | grep TYR' % pocket_location, shell=True, stdout=subprocess.PIPE) output, _ = p.communicate() if p.returncode == 1: # no matches found tyrs = [] elif p.returncode == 0: # matches found tyrs = output.split('\n') else: # error, do something with it