Bash中的while循环调用Python脚本

Question

我想在Bash的while循环中调用一个Python脚本。不过，我对Bash的while循环（还有变量）语法不是很了解。我希望的效果是，当一个文件里还有内容（DNA序列）时，我就调用Python脚本来提取这些序列组，以便另一个程序（dialign2）可以对它们进行比对。最后，我会把这些比对结果添加到一个结果文件里。注意：我并不是想逐行处理这个文件。我该怎么改才能让Bash的while循环正常工作？我还想确保每次循环时，while循环都会重新检查变化的file.txt。以下是我的尝试：

#!/bin/bash
# Call a python script as many times as needed to treat a text file

c=1
while [ `wc -l file.txt` > 0 ] ; # Stop when file.txt has no more lines
do
    echo "Python script called $c times"
    python script.py # Uses file.txt and removes lines from it
    # The Python script also returns a temp.txt file containing DNA sequences
    c=$c + 1
    dialign -f temp.txt # aligns DNA sequences
    cat temp.fa >>results.txt # append DNA alignements to result file
done

谢谢！

Answer 1

下面的代码应该能实现你想要的功能：

#!/bin/bash

c=1
while read line; 
do
    echo "Python script called $c times"
    # $line contains a line of text from file.txt
    python script.py 
    c=$((c + 1))
done < file.txt

不过，其实你不需要用bash来遍历文件中的每一行。你可以直接在python里轻松做到这一点：

myfile = open('file.txt', 'r')

for count, line in enumerate(myfile):
    print '%i lines in file' % (count + 1,)
    # the variable "line" contains the line of text from the file.txt 

    # Do your thing here.

Answer 2

试试用 -gt 来去掉命令行中的特殊符号 >

while [ `wc -l  file.txt`  -gt 0 ]
do
    ...
    c=$[c + 1]
done

Answer 3

我不知道你为什么想这么做。

c=1
while [[ -s file.txt ]] ; # Stop when file.txt has no more lines
do
    echo "Python script called $c times"
    python script.py # Uses file.txt and removes lines from it
    c=$(($c + 1))
done