The FASTA parsers for the various Bio* all support additional characters; if not then that would definitely be a bug.
Saying that, 'support' completely depends on what the FASTA is and where it comes from (assembly, sequence database, alignment tool, etc), which is something the parser/grammar can't define up front from such a simple format.
Much of the problem comes when validating the sequence for a specific alphabet or symbol set. If the alphabet isn't explicitly defined (again impossible to determine from the format without guessing) then you can certainly run into problems.
This is also an issue when using FASTA for both regular sequence data and for alignments (e.g. length of the sequence would have to take into account possible gap characters generated from various tools like '-?.', or stops in protein seqs like '*').
These are tools that have been in widespread use for ~15 years, so if you have run into problems you should be more explicit in what they are so they can be addressed.
Okay, I think I see the discrepancy. It's a nomenclature thing.
The Bio* refer to the additional stuff after the ID as the sequence 'description'. There is a subtle difference between that and a simple comment, though I have seen even NCBI use this as the 'junk drawer' for any additional seq information (such as the headers in the nr database).
Agreed re: implied superiority. I view all the Bio* are toolkits, frankly, and thus pieces of those toolkits are developed based on the wants/needs of users (some of whom simply do not know perl). BioPerl just happened to be one of the first out of the gates (~1997, in a primordial state), but Biopython and BioJava were also out around 2000 or so IIRC.
Re: FASTA comment support, I haven't ever seen it's use in the wild.
Actually, in the Bio* langs that would be referred to as the 'description'. @dalke is referring to the very rarely-used ';' I believe, which I don't recall any modern-day FASTA parser supporting.
Perl 6 is probably best described as a dialect. The look and design of the language are very Perl-ish, but some of the key sore points from Perl 5 (OO, concurrency, etc) are addressed and it has added a number of killer features. This is not Python 2->32; it is a major overhaul of the language, with no backwards compat beyond a suggested perl 5-compatible layer (I
believe this is called 'v5').
The article touches upon a few (Grammars for instance), but I personally think the concurrency work will also be a real draw.
The other key difference is that Perl 6 is actually a specification with an official test suite and Grammar (STD). I believe the specs indicate that anything that passes the test suite can be deemed to support 'Perl 6', which really opens up the use of various backends. The Rakudo Perl 6 implementation has support for three (MoarVM, Parrot, and JVM).