A general note: Your uses of s/// are overkill. The s and i options are useless on \r and \n, and you could do the same thing with one tr/[\r\n]//d

We monks still can't see what the values are in the variables in question. What I meant for you to provide was an example that we could run to observe the problem. Explicitly set the value of $line to whatever it is when you see the problem, include the relevant lines of code, and show the output, along with what you expected instead.