Their technique is still in use, at https://github.com/bioperl/bioperl-live/blob/master/lib/Bio/... . The key point is they set the input record separator, like this:
local $/ = "\n>";
Raku has a per-filehandle version, according to https://docs.raku.org/language/5to6-perlvar
In principle, since it does more work closer to the machine, it should be faster. I haven't tested it.