[Bioperl-l] UCSC database -> GFF

[Paul Edlefsen]

Hmm.  I've been working with them and they have assumed that they are 
Sax based.  Which is it?

Allen Day wrote:

>yes, but there is a problem with the ucsc das server not providing all the 
>information that is available in the tables.  utr info for refgenes, for 
>example.
>
>also, my last understanding was that the bio::das packages were dom
>based... you needed to read the whole xml before gffifying the features.  
>not so desireable with the est tracks...
>
>-allen
>
>
>On Thu, 17 Jul 2003, Lincoln Stein wrote:
>
>  
>
>>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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+-----O------------------------------------+
|    o-o     Paul T. Edlefsen
|    o---o   Computational Biologist
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| O----O     Institute for Systems Biology
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