To have true portability you should use hex codes:

#DOS to UNIX
perl -i.orig -pe 's/\015\012/\012/g' dosfile.txt
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Take a look at perlrun for the -i switch. And remember the following hash with newline for Windows, UNIX and Mac. I usually declare this on top of my program when i need to do lots of translation or outputting different kind of files

%N = (
    WIN  => "\015\012",
    UNIX => "\012",
    MAC  => "\015"
);
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$|=$_="1g2i1u1l2i4e2n0k",map{print"\7",chop;select$,,$,,$,,$_/7}m{..}g