[Bioperl-l] Bio::DB::SwissProt

[Chris Fields]

We need to go ahead and remove the expasy code from SwissProt if it's no longer supported.  Any takers?

chris

On Jul 20, 2011, at 11:00 AM, Jason Stajich wrote:

> It is just waiting for someone to code it up. It requires a different, simpler approach. 
> 
> I don't have any time to do this but we welcome volunteers.  
> 
> The simple approach is just to open a file handle and use GET cmd to open the URL with the accession number per the msg I sent before. That filehandle goes to SeqIO and you don't need the Bio::DB module. 
> 
> You can also get Swissprot data via genbank DB handle. 
> 
> Jason Stajich
> 
> 
> On Jul 20, 2011, at 4:23 AM, Oliver Schilling <oliver.schilling at mol-med.uni-freiburg.de> wrote:
> 
>> Dear Jason,
>> 
>> as thankfully pointed out by you on http://old.nabble.com/Fwd%3A-URGENT%21-Update-of-Bio%3A%3ADB%3A%3ASwissProt-td32059436.html#a32059436,
>> 
>> it seems that Bio::DB::SwissProt  is not supported by expasy any more. In a perl script, I used to access Swissprot data and annotations by
>> 
>> $sp = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>>                   '-hostlocation' => 'switzerland');
>>                   $seq = $sp->get_Seq_by_id($id_swiss);
>> 
>> This of course does not work any more. Will Bio::DB::SwissProt  be adapted to the new expasy site in the near future?
>> 
>> Thanks a lot!
>> 
>> Oliver
>> 
>> 
>> Dr. Oliver Schilling
>> Group Leader & Emmy-Noether Research Fellow
>> Institute for Molecular Medicine and Cell Research
>> University of Freiburg
>> Stefan-Meier-Str. 17, Room 02 027
>> D-79104 Freiburg, Germany
>> Tel: +49 761 203 9615
>> email: oliver.schilling at mol-med.uni-freiburg.de
> 
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