[Bioperl-l] Re: UCSC database -> GFF
allenday at ucla.edu
Tue Jun 17 14:20:39 EDT 2003
Yes, i have written some files that remap the flatfile table dumps to GFF
format. the script should be in bioperl-live/scripts/Bio-DB-GFF, or in
the GMOD Generic-Genome-Browser CVS. I handed this off to Mummi
Throisson, and I'm not sure where it lives now. It's called load_ucsc.pl,
or something like that.
You might want to hold off on doing any work though. I conversation I had
~2 weeks ago led me to believe that UCSC intends to export GFF directly in
the near future.
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.
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