[Bioperl-l] UCSC database -> GFF

[Paul Edlefsen]

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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+-----O------------------------------------+
|    o-o     Paul T. Edlefsen
|    o---o   Computational Biologist
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| O----O     Institute for Systems Biology
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