SHELL

bash loop lines in file

#!/bin/bash
filename='peptides.txt'
echo Start
while read p; do 
    echo $p
done < $filename

bash read file line by line

#!/bin/bash
while read line
do
  echo $line
done < /path/to/file

bash for each line of file

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

read file line loop in bash

for word in $(cat peptides.txt); do echo $word; done