choroba has given you the answer to your question (chomping the variable to get rid of the newline character). I would just want to react to something else that you said.

This mucks up my next task as I want to bubble sort each line to put it in alphabetical order.

Why do you want to bubble sort your lines? Bubble sort is a very inefficient sort algorithm. You may not care about sort efficiency and this may be OK if the amount of data to be sorted is small.

But, yet, why would you want to implement yourself a bubble sort (or any other sort algorithm for that matter) when Perl has a sort built-in function, easy to use and implementing a much more efficient sort algorithm?