Preprocessing

        sub preprocess{
                while (<INFILE>){
                        chomp;
                s/$/;/g if (/apply/);
                print OUTFILE ("$_\n");
                last if ( /^SCAN_CELLS/);
                }
                close OUTFILE;
        }

It appends a ; to the end of lines that match apply
It stops copying when it sees SCAN_CELLS
For this we needed a subroutine and an extra file?