[Bioperl-l] (no subject)

Miguel Pignatelli miguel.pignatelli at uv.es
Wed Jun 6 04:36:55 EDT 2012


Hi Hermann,

Sounds like a problem with the registry. Make sure you have the latest 
ensembl code and it is accessible via the PERL5LIB.

Try to diagnose the problem using the -verbose => 1 flag in 
load_registry_from_db or by running the script in running 
ensembl/misc-scripts/ping_ensembl.pl (which tries to diagnose setup 
problems).

You can also try calling a specific version of ensembl and see if there 
is any difference:

$registry->load_registry_from_db(
     -host =>  'ensembldb.ensembl.org',
     -user =>  'anonymous',
     -verbose => 1,
     -db_version => 67,
  );

Hope this helps,

M;


On 05/06/12 22:10, Hermann Norpois wrote:
> use strict;
>
>
> use Bio::EnsEMBL::Registry;
>
>
>      my $registry = 'Bio::EnsEMBL::Registry';
>
>      $registry->load_registry_from_db(
>          -host =>  'ensembldb.ensembl.org', # alternatively'
> useastdb.ensembl.org'
>          -user =>  'anonymous'
>      );
>
>     #my $name = "Bdnf";
>      my $gene_adaptor = $registry ->  get_adaptor( 'Mouse', 'Core', 'Gene');
>         my $gene = $gene_adaptor->fetch_by_stable_id('ENSG00000184129');
>      #my $gene = $gene_adaptor ->  fetch_all_by_external_name ($name);
>      my @dbentries = @{ $gene->get_all_DBEntries() };
>      my $info = join (":", @dbentries);
>      print "$info\n";
> #    print $gene ->  seq(), "\n";



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