Looping through the content of a file in Bash

One way to do it is:

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

As pointed out in the comments, this has the side effects of trimming leading whitespace, interpreting backslash sequences, and skipping the last line if it's missing a terminating linefeed. If these are concerns, you can do:

while IFS="" read -r p || [ -n "$p" ]do  printf '%s\n' "$p"done < peptides.txt

Exceptionally, if the loop body may read from standard input, you can open the file using a different file descriptor:

while read -u 10 p; do  ...done 10<peptides.txt

Here, 10 is just an arbitrary number (different from 0, 1, 2).

cat peptides.txt | while read line do   # do something with $line heredone

and the one-liner variant:

cat peptides.txt | while read line; do something_with_$line_here; done

These options will skip the last line of the file if there is no trailing line feed.

You can avoid this by the following:

cat peptides.txt | while read line || [[ -n $line ]];do   # do something with $line heredone

Option 1a: While loop: Single line at a time: Input redirection

#!/bin/bashfilename='peptides.txt'echo Startwhile read p; do     echo "$p"done < "$filename"

Option 1b: While loop: Single line at a time:
Open the file, read from a file descriptor (in this case file descriptor #4).

#!/bin/bashfilename='peptides.txt'exec 4<"$filename"echo Startwhile read -u4 p ; do    echo "$p"done