Bioperl: re: fasta def line problem

[Ian Korf]

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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