It's a common misconception that user input can be filtered. PHP even has a (now deprecated) "feature", called magic-quotes, that builds on this idea. It's nonsense. Forget about filtering (or cleaning, or whatever people call it).
What you should do, to avoid problems, is quite simple: whenever you embed a a piece of data within a foreign code, you must treat it according to the formatting rules of that code. But you must understand that such rules could be too complicated to try to follow them all manually. For example, in SQL, rules for strings, numbers and identifiers are all different. For your convenience, in most cases there is a dedicated tool for such an embedding. For example, when you need to use a PHP variable in the SQL query, you have to use a prepared statement, that will take care of all the proper formatting/treatment.
Another example is HTML: If you embed strings within HTML markup, you must escape it with htmlspecialchars. This means that every single echo or print statement should use htmlspecialchars.
A third example could be shell commands: If you are going to embed strings (such as arguments) to external commands, and call them with exec, then you must use escapeshellcmd and escapeshellarg.
Also, a very compelling example is JSON. The rules are so numerous and complicated that you would never be able to follow them all manually. That's why you should never ever create a JSON string manually, but always use a dedicated function, json_encode() that will correctly format every bit of data.
And so on and so forth ...
The only case where you need to actively filter data, is if you're accepting preformatted input. For example, if you let your users post HTML markup, that you plan to display on the site. However, you should be wise to avoid this at all cost, since no matter how well you filter it, it will always be a potential security hole.
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).
Best Answer
If it's 777, that means anyone with an account on the system, or any application running on the system (including PHP scripts, even those owned by those other than you) can modify the file in any way.
So, yes, it's possible someone tinkered with the file. Could it perhaps have been a bug in your PHP script that removed the number?
If you can do so, it would be best to reduce the permissions to something more restrictive, like 644. This will still work if the PHP script that accesses the file is executed as the same user that owns the file. Many webhosts are configured this way, so you might be able to do this. 644 means the owner of the file can read and write to it, while others can only read.