[Bioperl-l] UCSC database -> GFF

[Allen Day]

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...

-allen


On Thu, 17 Jul 2003, Lincoln Stein wrote:

> I know that this response is rather delayed, but yes, this would work.
> 
> Lincoln
> 
> On Monday 23 June 2003 07:14 pm, Paul Edlefsen wrote:
> > Could we just use our Bio::DB::Das stuff to read in the features, then
> > use the features' gff_string() method to get the string?  Does
> > Bio::DB::GFF dealy allow us to write features back to a GFF db directly?
> >
> > :Paul
> >
> > Lincoln Stein wrote:
> > >Hi Allen,
> > >
> > >I hope someone (Mummi?) will pick it up.  It's necessary now that NCBI has
> > >decided to make their human annotations effectively unloadable.  Maybe
> > >ENSEMBL can have a look at their EMBL output and try to find a way to get
> > >more track info into it?
> > >
> > >Lincoln
> > >
> > >On Tuesday 17 June 2003 04:23 pm, Allen Day wrote:
> > >>I wrote it ~1 year ago.
> > >>
> > >>-Allen
> > >>
> > >>On Tue, 17 Jun 2003, Lincoln Stein wrote:
> > >>>Where did that come from?  I was just talking with Mummi about how badly
> > >>>we need this and how difficult it will be to do it right.
> > >>>
> > >>>Lincoln
> > >>>
> > >>>On Tuesday 17 June 2003 02:07 pm, Jason Stajich wrote:
> > >>>>Does core/scripts/Bio-DB-GFF/load_ucsc.pl work for you?
> > >>>>
> > >>>>On Tue, 17 Jun 2003, Paul Edlefsen wrote:
> > >>>>>The Generic Genome Browser comes with many helpful scripts for
> > >>>>>converting various data sources into GFF format.  I am wondering if
> > >>>>>anyone in the bioperl community has written one for the UCSC data, as
> > >>>>>is available at
> > >>>>>ftp://genome.cse.ucsc.edu/goldenPath/10april2003/database and
> > >>>>>described at http://genome.ucsc.edu/goldenPath/gbdDescriptions.html
> > >>>>>-- I noticed that  Allen Day wrote some handy aggregators for that
> > >>>>>data such as Bio::DB::GFF::ucsc_genscan, so I wanted to check before
> > >>>>>I start writing Generic-Genome-Browser/bin/process_ucsc.PLS.
> > >>>>>
> > >>>>>Thanks,
> > >>>>>
> > >>>>>  :Paul
> 
>