[英]Bash process substitution in Python with subprocess.run() and shared input
I have a question regarding bash process substitution in python using subprocess. 我有一个关于使用子进程在python中进行bash进程替换的问题。 I'm trying to write it in a way that both the main function and the subprocess use the same input from stdin (which in the code is a string variable).
我正在尝试以一种方式编写它,即主函数和子进程都使用来自stdin的相同输入(在代码中是字符串变量)。 Here is the code:
这是代码:
p1 = subprocess.run(['cat'],
stdout=subprocess.PIPE, input=in_fa.encode())
p2 = subprocess.run(['bwa samse reference/C57BL_6J.fa <(bwa aln -l 20 reference/C57BL_6J.fa -) -'],
shell=True, executable="/bin/bash", input=p1.stdout,
stdout=subprocess.PIPE)
In this example, in_fa
is a string like the following: 在此示例中,
in_fa
是类似于以下的字符串:
>header\ntTCAGCCTTCCCTTCCATTTCTCTCCCCTTCCCTCTCCTCCCCATTTCAGAGTTTCTTTAGAATCTGTATTCTGGCACCCAAAGTGAACTATGTGTCTGACTCAGGGGCTCTTTGTTTCACTGCAGGGCTGTGGTG
In this code, both '-' in the main process and the subprocess refer to in_fa
, but while the main process is reading it correctly, the subprocess is not. 在此代码中,主进程和子进程中的“-”都引用
in_fa
,但是当主进程正确读取它时,子进程却没有。
This, for example, would work, but it's not dynamic and it's reading from a file instead than a variable: 例如,这可以工作,但它不是动态的,它是从文件而不是变量中读取的:
p1 = subprocess.run(['''cat fasta/input.fasta |
bwa samse reference/C57BL_6J.fa <(
cat fasta/input.fasta |
bwa aln -l 20 reference/C57BL_6J.fa -) -'],
shell=True, executable="/bin/bash", stdout=subprocess.PIPE)
Any help would be appreciated! 任何帮助,将不胜感激! Meanwhile, I will keep trying.
同时,我会继续尝试。
You cannot consume standard input from two distinct processes; 您不能使用来自两个不同过程的标准输入; they need to receive a copy each.
他们需要各自收到一份副本。
My approach to this would be to write the string to a temporary file and take it from there. 我的解决方法是将字符串写入临时文件,然后从那里获取。
In addition, your subprocess
calls have a couple of problems. 此外,您的
subprocess
调用还有两个问题。
You need to pass in either a string or a list of tokens. 你需要在一个字符串或标记列表通过。 What you have looks like it's working, but it's really not well-defined.
您所看到的似乎正在运行,但实际上定义不明确。
The cat
performs no useful purpose here; cat
在这里没有任何用处。 the purpose of cat
is to combine multiple files, and you only have one file. cat
的目的是合并多个文件,而您只有一个文件。 ( It wasn't useful in the shell either. ) ( 它在shell中也没有用。 )
import tempfile
import os
with tempfile.TemporaryDirectory() as tmpdirname:
fa_tmp = os.path.join([tmpdirname, 'in.fa'])
with open(fa_tmp, 'wb') as handle:
handle.write(in_fa.encode())
proc = subprocess.run(
'''bwa samse reference/C57BL_6J.fa <(
bwa aln -l 20 reference/C57BL_6J.fa {0})
{0}'''.format(fa_tmp),
shell=True, executable="/bin/bash",
check=True, stdout=subprocess.PIPE)
See also Running Bash commands in Python where I have an answer which outlines some of the problems you are having in more detail. 另请参见在Python中运行Bash命令,在这里我有一个答案,概述了您遇到的一些更详细的问题。
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