In the UNIX side, when you're processing the files, you just have to do something like this:

while (<INPUT>) {

#removes the UNIX style newline
chomp;

#do something else and then print to the OUTPUT file
#using DOS style new line

print OUTPUT, $line_content, "\r\n";

}
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Here is something to help improve the performance of your program: http://www-128.ibm.com/developerworks/library-combined/l-optperl.html.