execute a command with each list from a text file-CodePudding

I would like to execute a command with each list from a text file. I tried doing this code but it is not giving me any output. Can you help me? Thank you!

for i in $(cat list_of_text.txt)
do
    commandtool some_input_file $i> new_"$i".fa

    cat > final.list
    echo -e "new_"$i"\t " >> final.list
done

list_of_text.txt looks like this

nameabc
namedef
nameghi
namejkl

while final.list looks like this

new_nameabc.fa   
new_namedef.fa   
new_nameghi.fa   
new_namejkl.fa

In summary the long version of the code is like this and I'm trying to make a shortcut:

commandtool some_input_file nameabc> new_nameabc.fa
commandtool some_input_file namedef> new_namedef.fa
commandtool some_input_file nameghi> new_nameghi.fa
commandtool some_input_file namejkl> new_namejkl.fa

echo -e "new_nameabc.fa\t " > final.list
echo -e "new_namedef.fa\t " >> final.list
echo -e "new_nameghi.fa\t " >> final.list
echo -e "new_namejkl.fa\t " >> final.list

Edit: It is working now. I just replaced cat > final.list to echo > final.list and moved it at the beginning as suggested in the answer.

CodePudding user response：

Moving cat out of the loop and replacing with echo, I believe you want:

echo > final.list
for i in $(cat list_of_text.txt)
do
    commandtool some_input_file $i > new_"$i".fa
    echo -e "new_${i}.fa\t " >> final.list
done

CodePudding user response：

Perhaps something like this to calculate the output filename only once and to use printf instead of echo -e for portability

#!/bin/bash
true > final.list
for i in $(< list_of_text.txt)
do
    out="new_${i}.fa"
    commandtool some_input_file "$i" > "$out"
    printf '%s\t \n' "$out" >> final.list
done

CodePudding user response：

> final.list

while IFS= read -r name; do
    new_name=new_${name}.fa

    cmd input-file "$name" > "$new_name"
    printf '%s\t\n' "$new_name" >> final.list
done < list_of_text.txt

> final.list truncates (empties) the file before it gets appended.
while IFS= read -r line; ... loop is the canonical method of processing one line of an input stream at a time. It is also far more robust compared to looping over an unquoted command substitution.
< list_of_text.txt redirects the list as input for the while read loop.