Bash while循環調用Python腳本

Question

我想從Bash while循環中調用Python腳本。但是，我不太清楚如何正確使用Bash的while循環（也許是變量）語法。我正在尋找的行爲是，雖然文件仍然包含行（DNA序列），但我調用Python腳本來提取序列組，以便另一個程序（dialign2）可以對齊它們。最後，我將對齊添加到結果文件中。注意：我不想遍歷文件。爲了讓Bash while循環正常工作，我應該更改哪些內容？我還想確保while循環將重新檢查每個循環中正在更改的file.txt。這是我的嘗試：

#!/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 

謝謝！

Answer 1

不知道爲什麼要這麼做。

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 

Answer 2

嘗試-gt消除外殼元字符>

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

Answer 3

下應該做的，你說你想要的：

#!/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 

然而，沒有必要使用bash，遍歷文件中的行。你可以很容易地做到這一點，而不必離開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. 

Answer 4

@OP如果你想循環一個文件，只是在讀循環時使用。此外，您不使用變量$ c以及該行。你是否將每一行傳遞給你的Python腳本？或者，只要遇到某一行，就調用Python腳本？ （如果你這樣做，你的腳本會變得很慢）

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 

最後，你可以用Python做所有事情。在Python遍歷文件「file.txt」的方法就是

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()