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

[Lincoln Stein]

I vote for consistency, which means either next_cluster() or changing 
Bio::SeqIO, Bio::SeqFeatureI, etc to next().

I guess that means next_cluster().

Lincoln

On Monday 06 May 2002 03:50, Ewan Birney wrote:
> 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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>
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> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
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