[Bioperl-l] UCSC database -> GFF

[Paul Edlefsen]

It's possible to pass a callback to apply to each feature as it is returned.

Allen Day wrote:

>the problem is that there is no event handling with bio::das (or wasn't
>the last time i had a look), so you don't get any objects until you've
>slurped up the whole xml file.  this means that if you want, say, all the
>EST alignments of chrX, you're going to run out of memory before you have
>a chance to dump as gff.
>
>-Allen
>
>
>On Mon, 23 Jun 2003, 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
>>>>>>>         
>>>>>>>
>>>>>>>              
>>>>>>>
>>> 
>>>
>>>      
>>>
>>    
>>
>
>  
>

-- 
+-----O------------------------------------+
|    o-o     Paul T. Edlefsen
|    o---o   Computational Biologist
|  o----o    mailto:paul at systemsbiology.org
| O----O     Institute for Systems Biology
| 0--o       1441 North 34th Street
|   O        Seattle, Washington 98103-8904
|  o-o       callto:1-206-732-1336
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