[Bioperl-l] Unigene

[Juha Muilu]

Hi Elia and others,

We have a simple proposal for the SeqCluster in a recent OMG submission.
Could you have a look?  Note that it is just a initial proposal, a
starting point for further discussions... 

It would be nice to start to make new bio-entities such a way that all
bio* projects can benefit! This should be possible if we have common
platform independent model behind.

I have been trying to compile ideas into a web-pages and UML diagrams,
but have been busy on doing other things. Anyway here is something:

http://industry.ebi.ac.uk/~muilu/OMG/BSANE/index.html

Note the pages will move somewhere under the wiki-system (very soon I
hope)

Comments are welcome!!

Cheers, Juha

Elia Stupka wrote:
> 
> dear all,
> 
> had very little time to get together a proper proposal, so I will post a
> vague one here. I am trying to parse Unigene entries. It seems to me that
> there is little point in making a Bio::Seq co,pliant object for unigene
> entries since they are a Boentry object which contains many Seq objects.
> The SeqContainerI or SeqClusterI would be hte interface. Unigene would
> inherit from this interface. If people think that there could be lots of
> other SeqCluster objects in other scenarios, we could write
> Bio::SeqCluster and make Bio::Unigene inherit from Bio::SeqCluster. If not
> for now I will write the interface and a Unigene object.
> 
> Hte other thing is that SeqCluster will need its own IO system, which in
> teh case of unigene needs to take in two files, the unigene cluster
> information and the unigene sequences (which can be read  with SeqIO).. I
> have started playing with this idea, and probably on my next plane trip on
> Sunday I will implement the rest of it.  Commens very very welcome,
> because as you see this is not one of those nice mails with bullets and
> precise definitions ;)
> 
> Elia
> 
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 |Juha Muilu, Ph.D., EMBL Outstation| Email:  muilu@ebi.ac.uk         |
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