open my $FH, '>', 'afile.pl';
print $FH <<EOHDR;
Some header stuff
EOHDR

while (<>) {
    if (/^RPT/) { print $FH, "another line of your script" }
    elsif (/^FOO/) { print $FH, "something completely different" }
    elsif (/^Q/) { last; }
}

##</code><code>##

my $SCRIPT = <<EOHDR
Some header stuff
EOHDR;

$SCRIPT .= "More script stuff";