use PerlIO::gzip;

open( INPUT, "<:gzip", "old.gz" ) or die "old.gz: $!";
open( OUTPUT, ">:gzip", "new.gz" ) or die "new.gz: $!";

while (<INPUT>) {
    # do something with a line of text...
    s/[\r\n]+/\n/;  # for example, normalize line terminations
    print OUTPUT;
}