Question

我需要从python脚本调用bash并将结果存储在变量中（输出是一个数字）。

我需要

output = subprocess.call('command', shell=True)

将命令替换为我的bash one-liner的输出，如下所示：

cat file.sam | grep -v "@" | grep "gi|519666810|ref|NM_001278619.1|"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'

我知道简单的命令可以正常工作：

    output = subprocess.check_output("echo 122;", shell=True)

我的问题是，而不是 122 我需要从我的bash one-liner获得价值。如果我不需要重新格式化它并且只能那么它将是完美的。

以下是我的尝试：

    output = subprocess.check_output("cat file.sam | grep -v "@" | grep "gi|519666810|ref|NM_001278619.1|"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'
    ", shell=True)

      File "script.py", line 9
        output = subprocess.check_output("cat file.sam | grep -v "@" | grep "gi|519666810|ref|NM_001278619.1|"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'
                                                                  ^
    SyntaxError: invalid syntax

尝试二：

    output = subprocess.check_output("cat file.sam | grep -v \"@\" | grep \"gi|519666810|ref|NM_001278619.1|\"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'
", shell=True)

  File "script.py", line 9

    output = subprocess.check_output("cat file.sam | grep -v \"@\" | grep \"gi|519666810|ref|NM_001278619.1|\"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'
                                                                                                                                                                                                                    ^
SyntaxError: EOL while scanning string literal

Answer 1

感谢您的帮助！最后，这有效：

command = "cat file.sam | grep -v \"@\" | grep \"gi|519666810|ref|NM_001278619.1|\"  | perl -lane '$l = 0; $F[5] =~ s/(\d+)[MX=DN]/$l+=$1/eg; print $l' | awk '{ sum+=$1} END {print sum}'";
process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None, shell=True)
#Launch the shell command:
output = process.communicate()[0];

将复杂的bash命令合并到python中

1 个答案: