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

[Andrew Macgregor]

Hi Allen,

Allen Day wrote:

>> 1. rename UniGeneIO.pm --> IO.pm
> 
> By convention of SeqIO, I think it should be called unigene (note
> lowercase), and should be under ClusterIO.  Have a look at how the
> SeqIO::game classes are laid out.  So I think it should go something like:
> 
> Bio/
> 
> Cluster/
> ...
> ClusterIO.pm
> ClusterIO/
> unigene.pm
> ungene/
> ...

I'll put it in  lowercase (like the format module is) the mixed case has
been used because it is called UniGene by NCBI.

It does seem looking around bioperl that the IO.pm method of Variation is
less common than putting a ClusterIO.pm at the top level then format modules
in a directory like SeqIO.pm and SeqIO. If I change the UniGeneIO.pm to be
ClusterIO.pm at the top level I'll just need the format module in the
ClusterIO directory.

So then for other clusters only a format module should need to be written,
is that right? My layout then would be:

Bio/
|   ClusterIO.pm
|   ClusterIO/
    |   unigene.pm

|   Cluster/
...

>I'd like a next_component() method that can be
Can you show  me how that would be done? Are there examples of similar
things elsewhere in bioperl?

Cheers, Andrew.