Bash while 循环调用 Python 脚本
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Bash while loop calling a Python script
提问by Morlock
I would like to call a Python script from within a Bash while loop. However, I do not understand very well how to use appropriately the while loop (and maybe variable) syntax of the Bash. The behaviour I am looking for is that, while a file still contains lines (DNA sequences), I am calling a Python script to extract groups of sequences so that another program (dialign2) can align them. Finally, I add the alignments to a result file. Note: I am not trying to iterate over the file. What should I change in order for the Bash while loop to work? I also want to be sure that the while loop will re-check the changing file.txt on each loop. Here is my attempt:
我想从 Bash while 循环中调用 Python 脚本。但是，我不太明白如何适当地使用 Bash 的 while 循环（可能还有变量）语法。我正在寻找的行为是，虽然文件仍然包含行（DNA 序列），但我正在调用 Python 脚本来提取序列组，以便另一个程序 (dialign2) 可以对齐它们。最后，我将对齐添加到结果文件中。注意：我不是要遍历文件。我应该更改什么才能使 Bash while 循环正常工作？我还想确保 while 循环会在每个循环中重新检查不断变化的 file.txt。这是我的尝试：
#!/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
Thanks!
谢谢！
回答by MattH
No idea why you want to do this.
不知道你为什么要这样做。
c=1
while [[ -s file.txt ]] ; # Stop when file.txt has no more lines
do
echo "Python script called $c times"
python script.py # Uses file.txt and removes lines from it
c=$(($c + 1))
done
回答by Joe Koberg
try -gtto eliminate the shell metacharacter >
尝试-gt消除 shell 元字符>
while [ `wc -l file.txt` -gt 0 ]
do
...
c=$[c + 1]
done
回答by vezult
The following should do what you say you want:
以下应该做你说你想要的：
#!/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
However, there is no need to use bash, to iterate over the lines in a file. You can do that quite easily without ever leaving python:
但是，不需要使用 bash 来遍历文件中的行。你可以很容易地做到这一点，而无需离开 python：
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.
回答by ghostdog74
@OP if you want to loop through a file , just use while read loop. Also, you are not using the variables $c as well as the line. Are you passing each line to your Python script? Or you just calling your Python script whenever a line is encountered? (your script going to be slow if you do that)
@OP 如果你想遍历一个文件，只需使用 while read 循环。此外，您没有使用变量 $c 以及行。您是否将每一行都传递给您的 Python 脚本？或者你只是在遇到一行时调用你的 Python 脚本？（如果你这样做，你的脚本会很慢）
while true
do
while read -r line
do
# if you are taking STDIN in myscript.py, then something must be passed to
# myscript.py, if not i really don't understand what you are doing.
echo "$line" | python myscript.py > temp.txt
dialign -f temp.txt # aligns DNA sequences
cat temp.txt >>results.txt
done <"file.txt"
if [ ! -s "file.txt" ]; break ;fi
done
Lastly, you could have done everything in Python. the way to iterate "file.txt" in Python is simply
最后，您可以用 Python 完成所有工作。在 Python 中迭代“file.txt”的方法很简单
f=open("file.txt"):
for line in f:
print "do something with line"
print "or bring what you have in myscript.py here"
f.close()
