[Bioperl-l] UCSC database -> GFF

[Lincoln Stein]

The modules are sax based.  For downloading smallish whole genome datasets, 
such as the gene models, bio::das will be fine.  For ESTs and repeats, don't 
even try!

Lincoln


On Friday 18 July 2003 03:46 am, Ewan Birney wrote:
> On Thu, 17 Jul 2003, Allen Day wrote:
> > yes, but there is a problem with the ucsc das server not providing all
> > the information that is available in the tables.  utr info for refgenes,
> > for example.
> >
> > also, my last understanding was that the bio::das packages were dom
> > based... you needed to read the whole xml before gffifying the features.
> > not so desireable with the est tracks...
>
> I (*think*) they are SAX based...
>
>
> DAS is not a good way to download full datasets however... it was never
> designed for that and doesn't scale well.
>
>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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