[Bioperl-l] UniGene modules and Bio::Cluster

Ewan Birney birney@ebi.ac.uk
Mon, 6 May 2002 08:50:21 +0100 (BST)

On Mon, 6 May 2002, Andrew Macgregor wrote:

> The only thing is what to do with next in the end. What's the general
> consensus? I have to say I like the sound of Hilmar's next_cluster() but if
> there is a move to standardise this across bioperl I am not too worried what
> it is called :) Sound like a good plan?

I vote to stick with next_cluster, meaning we have two votes for (ewan and
hilmar) one against (heikki)

> Other issues:
> Allen Day said on the list:
> > Is there a plan to make general Bio::Cluster and Bio::ClusterIO classes?
> > I see that UnigeneIO is using Bio::SeqIO to do it's reading/writing, and
> > isn't inheriting from the (non-existant) Bio::Cluster class.
> So the steps above would make a more generic ClusterIO class. The only thing
> there is that it currently reads only as I can't see why you would want to
> write UniGene files. This might not be true for other clusters though?
> Should it be able to write?
> What I can't see I'm afraid is how you would code Bio::Cluster::ClusterI
> that was sufficiently generic that UniGene.pm and other clusters could
> inherit from it. Wouldn't the methods I need for a UniGene object be
> completely different for some other cluster. Wouldn't the overlap only come
> on the next_cluster method? And hence ClusterI wouldn't have much in it?
> Sorry if this sounds dumb, I just can't quite get my head around what would
> be in there. Perhaps there is something similar elsewhere in bioperl that
> someone could point me towards.
> Cheers, Andrew.
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420