[Bioperl-l] Bio::RangeI intersection and Bio::DB::GFF

[Sean Davis]

On 5/3/06 11:09 AM, "Cook, Malcolm" <MEC at stowers-institute.org> wrote:

> Marco,
> 
> It appears that your code assumes that the exons as returned from call
> to BIO::DB::GFF::features are sorted by start; I don't think is
> guaranteed (at least not in the documentation I'm reading).  Also I
> think your code will not report overlap between two exons that have an
> intervening overlapping exon.  Depending on what you're application is,
> you may care.  For example, e1, e2, e3 all intersect pairwise, but your
> code won't report on e1's overlap with e3.
> 
> e1 ---*******-------
> e2 -----******------
> e3 ------***--------

I think this can be done (looking for "superexons") via the UCSC table
browser or via Penn State University's Galaxy server (written in python and
downloadable) in case you want a quick solution to what I think is your
problem....

Sean