[Bioperl-l] another small question :-)

Ewan Birney birney@ebi.ac.uk
Sun, 30 Jul 2000 16:47:47 +0100 (GMT)

On Sun, 30 Jul 2000, L.Pollak wrote:

> in Bio::SeqIO::swiss:
> what are these functions _id_generation_func, _ac_generation_func,
> _kw_generation_func, ... good for, if they don't contain any useful code
> (or at least i can't see it) ??

So that specialist dumping routines can overload how the Bio::Seq object
writes out this line.

Basically what you are seeing here is the frustration of having to handle
every single last detail in generating an EMBL/GenBank flat file for a
centre like the Sanger Centre without tying the Bio::Seq object
religiously to both the EMBL/GenBank data-model (which ends up being a
pile of lines - not a fun abstraction) and way something like the sanger
uses the flat file format for reasons too annoying to list here.

This area is pretty thick in terms of the code, but it has to be to allow
the same code to be used in different places: there is so much playing
about with formatting specifications for these flat file formats it is
impossible to write one "standard" way - you need a default way and then
ways to provide complete control for the power user.

To get an idea of the complexity sometimes that goes on here, take a look


and the driving script at


from Ensembl.

> thx, lorenz
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420