for each line of output bash code example

Example 1: bash for each line of file

while read p; do
  echo "$p"
done <peptides.txt

Example 2: for line in output bash

Use for in bash for iterating words in a string or values in an array as:
for value in {1, 2, 3}; do echo $value; done
for value in $(cat arguments_files.txt); do [some_command]; done
And use while for iterating lines from a pipe output as:
cat arguments_file.txt | while read line; do [some_command]; done