捕获运行期间由 Python 中的子进程生成的内容

Question

我想捕获在运行期间生成的内容而不是输出，因为我意识到程序的输出不幸不是有用的信息。

基本上我的代码：

command = "usearch11 -threads 8 -fastq_filter pmFLP.fastq -fastq_maxee 1  -fastq_minlen 120 -fastq_maxns 0  -fastaout S1--1.QC.fasta"
with Popen(command, stdout=PIPE, stderr=None, shell=True) as process:
    output = process.stdout.readlines()
    print(output)

以及终端中显示的内容 after/during 运行输入代码：

C:\Users\Desktop\Daten\test_Ordner>python test.py
00:00 4.6Mb  FASTQ base 33 for file pmFLP.fastq
00:01 5.3Mb   100.0% Filtering, 98.6% passed
    188650  Reads (188.7k)
      1297  Discarded read with > 0 Ns
      1132  Discarded reads with expected errs > 1.00
    185957  Filtered reads (186.0k, 98.6%)
b'usearch v11.0.667_win64, 137Gb RAM, 64 cores\r\n(C) Copyright 2013-18 Robert C. Edgar, all rights reserved.\r\nhttps://drive5.com/usearch\r\n\r\nLicense: kleine@planton.de\r\n\r\n'

这部分正是我需要的：

00:00 4.6Mb  FASTQ base 33 for file pmFLP.fastq
    00:01 5.3Mb   100.0% Filtering, 98.6% passed
        188650  Reads (188.7k)
          1297  Discarded read with > 0 Ns
          1132  Discarded reads with expected errs > 1.00
        185957  Filtered reads (186.0k, 98.6%)

任何帮助将不胜感激！！

Answer 1

您可能需要捕捉 stderr 而不是 stdout。我还建议使用 subprocess.run() 而不是 subprocess.Popen():

command = "usearch11 -threads 8 -fastq_filter pmFLP.fastq -fastq_maxee 1  -fastq_minlen 120 -fastq_maxns 0  -fastaout S1--1.QC.fasta"
completed_process = run(command, stderr=PIPE, shell=True, text=True)
desired_text = completed_process.stderr
print(desired_text)

如果您想要原始字节，请删除 text=True 标志：

command = "usearch11 -threads 8 -fastq_filter pmFLP.fastq -fastq_maxee 1  -fastq_minlen 120 -fastq_maxns 0  -fastaout S1--1.QC.fasta"
completed_process = run(command, stderr=PIPE, shell=True)
desired_text = completed_process.stderr  # Those are now bytes, not str!
print(desired_text)

将输出写入二进制文件：

command = "usearch11 -threads 8 -fastq_filter pmFLP.fastq -fastq_maxee 1  -fastq_minlen 120 -fastq_maxns 0  -fastaout S1--1.QC.fasta"

with open("summary.txt", "wb") as file:
    run(command, stderr=file, shell=True)

如您所见，您还可以将任何可写文件对象传递给 stderr 或 stdout。

捕获 运行 期间由 Python 中的子进程生成的内容

catch contents generated during run by subprocess in Python

python

subprocess

捕获运行期间由 Python 中的子进程生成的内容