[Bioperl-l] Unigene proposal and basic implementation

[Ewan Birney]

On Tue, 16 Apr 2002 andrew@anatomy.otago.ac.nz wrote:

> Hi Ewan,
> 
> >does the unigene file come with any actual sequence, or is it just
> >clusters of IDs. And are those IDs dbEST ids?
> 
> It doesn't have the actual sequence but is a collection of IDs, in this case
> accession numbers for Genbank/EMBL.
> 
> 
> >BTW - thinking about it, I suspect that we should have the following
> >abstraction/namespace
> >
> >   Bio::Seq::ClusterI
> >      : methods attached to ClusterI which mainly have
> >      ->seq_ids(); # primary accession of sequences clustered
> >      ->annotation(); # Bio::Annotation::Collection associated with the
> >cluster
> >and I think the name space for unigene is probably best not top level but
> >instead
> >   Bio::Seq::Unigene; # inheriets from Bio::Seq::ClusterI
> >   Bio::Seq::UnigeneIO;
> 
> At the moment at the top level I have:
> Bio::UniGene.pm
> Bio::UniGeneIO.pm
> Bio::UniGene::unigene.pm
> 
> Would it work to make a Cluster namespace like so:
> Bio::Cluster::ClusterI
> Bio::Cluster::UniGene.pm
> Bio::Cluster::UniGeneIO.pm
> Bio::Cluster::UniGene::unigene.pm

I certainly prefer this to the straightforward Unigene one. Let's do it
this way.


What the difference between Bio::Cluster::UniGene and

Bio::Cluster::UniGene::unigene.pm?




> 
> Could this then be used for clusters of other types, less directly related to
> Seq. i.e. perhaps Homologene? which is a kind of cluster of Unigenes (am I
> right there??). I just think looking from the sequence up it is logical to put
> Unigene in Seq but perhaps looking from Unigene down it might be better in
> something like Cluster? As I've said I'm fairly new to the layout of bioperl,
> so I don't know what discussions of this nature have gone before...
> 
> Cheers, Andrew.
> 
> 
> 

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