[Bioperl-l] Bio::Cluster

[Andrew Macgregor]

Hi Andreas,

Andreas Matern wrote:
 
> The docs 
> (http://docs.bioperl.org/bioperl-live/Bio/Cluster/UniGeneI.html) say
> that the methods cytoband and gene should return strings, however they
> occasionally return hashes....
> 
> Is this a bug or a feature? :)

This would be a feature I guess ;) When the unigene object has a value for
gene or cytoband it returns the value but when there isn't one, it returns a
reference to the unigene object itself, that's when you get the hash. So the
hash shows up when the corresponding unigene record has no value for gene or
cytoband (and also does the same on other attributes).

I'm not 100 percent on why the ref to the object is returned, that's just
something the other bioperl objects do. Perhaps someone who knows better
could let us know?

> I have little experience with Parse::RecDecent so I can't fix it myself...
> I'm using the CVS version of bioperl-live....

Hopefully you'll have the version that uses regexes and not
Parse::RecDescent. I moved away from P::RD for speed reasons. If you are
getting the live version from CVS you should have the right one.

Cheers, Andrew.