I would also recommend:

- Loading the file into an array, modifying the array and writing the array back to the file, if the data is small enough to fit into an array;

- Using two files, one for input and one for output, and doing the necessary housekeeping (deleting old file, renaming new one, whatever) afterwards.

In theory, the tie function offers a possibility to edit in-place files. But I have yet to see a case where this solution would be superior to the two others above for this type of problem: for a small file, an array is much simpler and a bit faster; for a very large file, the two-file solution is slightly simpler and much much faster.

Another possible solution in some cases is the -i flag of the command line. But that's really the two-file solution, except that Perl gives you some syntactic sugar in the way of doing the housekeeping for you.