[Bioperl-l] UCSC database -> GFF

[Lincoln Stein]

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

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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