[ensembl-dev] Problem with DBAdaptor

Luc Merenda merenda.luc at gmail.com
Wed Jun 29 10:01:29 BST 2011


Hi Ensembl,

I've been using a perl script that uses the ensembl compara api to retrieve
protein trees. It worked fine until last week, now it exits with the
following error:

Can't call method "get_adaptor" on an undefined value at
/home/luc/Code/gene2proteintree line 22, <FILE> line 43.

It seems that there is a problem connecting to the server.
The line of code where the error occurs is the last one of the following
snippet:


    my $compara_dba;
    foreach my $dba( @{Bio::EnsEMBL::Registry->get_all_DBAdaptors()} ){
        if( $dba->isa('Bio::EnsEMBL::Compara::DBSQL::DBAdaptor') ){
          $compara_dba = $dba;
          last;
        }
    }

    my $member_adaptor   = $compara_dba->get_adaptor('Member');


Many thanks in advance

Luc
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