Looping through the content of a file in Bash

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

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 here
done

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

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

This is no better than other answers, but is one more way to get the job done in a file without spaces (see comments). I find that I often need one-liners to dig through lists in text files without the extra step of using separate script files.

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

This format allows me to put it all in one command-line. Change the "echo $word" portion to whatever you want and you can issue multiple commands separated by semicolons. The following example uses the file's contents as arguments into two other scripts you may have written.

for word in $(cat peptides.txt); do cmd_a.sh $word; cmd_b.py $word; done

Or if you intend to use this like a stream editor (learn sed) you can dump the output to another file as follows.

for word in $(cat peptides.txt); do cmd_a.sh $word; cmd_b.py $word; done > outfile.txt

I've used these as written above because I have used text files where I've created them with one word per line. (See comments) If you have spaces that you don't want splitting your words/lines, it gets a little uglier, but the same command still works as follows:

OLDIFS=$IFS; IFS=$'\n'; for line in $(cat peptides.txt); do cmd_a.sh $line; cmd_b.py $line; done > outfile.txt; IFS=$OLDIFS

This just tells the shell to split on newlines only, not spaces, then returns the environment back to what it was previously. At this point, you may want to consider putting it all into a shell script rather than squeezing it all into a single line, though.

Best of luck!

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).