[Bioperl-l] Re: UCSC database -> GFF

Allen Day 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.
> Thanks,
>   :Paul

More information about the Bioperl-l mailing list