Issue

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.

Solution

> 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.

Answered By - dan

Answer Checked By - Marie Seifert (WPSolving Admin)

Saturday, March 12, 2022

[SOLVED] execute a command with each list from a text file

Issue

Solution