[Bioperl-l] BioFetch: Adding databases

Chris Fields cjfields at uiuc.edu
Thu Dec 21 09:28:07 EST 2006


I've added this to the BioFetch FORMATMAP as 'unisave' and committed  
to CVS.  Thanks!

chris

On Dec 21, 2006, at 5:14 AM, Samuel GRANJEAUD - IR/IFR137 wrote:

> Hello!
>
> I needed to query the Unisave database at EBI. Up to date, the only  
> way
> to access it is the dbfetch web service
> (http://www.ebi.ac.uk/cgi-bin/dbfetch). This database is not yet  
> defined
> in the BioFetch package
> (http://doc.bioperl.org/bioperl-live/Bio/DB/BioFetch.html). I wrote
> these few lines to make it work, but I don't think it fits a good
> programming practice. May be it makes sense to defined a method to add
> databases to FORMATMAP, in order to follow the dbfetch service  
> evolutions.
>
> Cheers,
> --Samuel
>
> use Bio::DB::BioFetch;
> $Bio::DB::BioFetch::FORMATMAP{unisave} = {
> default   => 'swiss',
> swissprot => 'swiss',
> fasta     => 'fasta',
> namespace => 'unisave',
> };
> my $bf = new Bio::DB::BioFetch(-db=>'unisave');
> my $seq = $bf->get_Seq_by_id('LAM1_MOUSE');
>
> print $seq->display_id();
> print $seq->seq();
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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