Bioperl: re: fasta def line problem

[Lincoln Stein]

If there were a fast Perl-based XML parser, I'd vote for XML syntax.
Right now there's an interface to a C XML parser, but it is dog slow.
Has anyone looked at BSML (biological sequence markup language)?

Lincoln

Ian Korf writes:
 > I agree with Lincoln, we need a written file forma standard. In some
 > ways I like the fasta format because it's easy to parse knowing that the
 > descriptor is on a single line beginning with ">". If the code is perl-ish
 > then life is even easier. For example:
 > 
 > >name=foo ID=23456 type=nucleotide ...
 > GAATTC...
 > 
 > No problem to use substitution to make this eval-able. I also like the
 > tag=value convention because it is similar to HTML. Of course, if you're
 > going to do that, you might as well be able to use arrays and hashes to
 > get more expressive.
 > 
 > Or even, why not just serialize your object with Data::Dumper and use that
 > as the storage format. True, it doesn't look so good, but you could always
 > have a prettyprinting text (and graphic) tool. I've used this to make a
 > Bio::GSC client-server. It is a trivial operation if you keep the stream
 > on one line and use the print and <> operators (a bit more difficult if
 > you allow newlines). Anyway, if raw perl is too ugly, we could always make
 > it just a bit prettier, do a substitution, and then inflate with eval.
 > 
 > -Ian
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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