[Bioperl-l] GenBank db property?

Wiepert, Mathieu Wiepert.Mathieu@mayo.edu
Wed Jan 15 21:29:20 EST 2003


Hi,

I was fetching some sequences with Bio::DB::GenBank, and noticed that though I was requesting nucleotides, the db was being set to protein in the url that was built up.  The parameters, as near as I can tell, are set in the %PARAMSTRING, in the BEGIN block of GenBank.pm.  How can I change the 'db' property when I instantiate the GenBank object?  I tried passing in a parameter 'db' => 'nucleotide', that didn't work, I am sure it is simple to do?  Or do I have to directly access the variable to change it.

$gb = new Bio::DB::GenBank(-db => 'nucleotide');  #don't think this is supposed to do anything
$gb->request_format('gb');  #Did get me the genbank format that I wanted, that was nice.  

Thanks,

-Mat



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