[ensembl-dev] GERP_CONSERVATION_SCORE

[Stephen Fitzgerald]

Hi Chris, your $mlss_adaptor variable is probably undef for some reason.
Have you checked branch-70 for ensembl-compara ?

The code below does not throw an error:
###########
use strict;
use Data::Dumper;
use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->load_registry_from_db(
         -host=>"ensembldb.ensembl.org", -user=>"anonymous",
         -port=>'5306', -db_version=>'70');

my $mlss_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
     "Multi", "compara", "MethodLinkSpeciesSet");

my $mlss = 
$mlss_adaptor->fetch_by_method_link_type_species_set_name("GERP_CONSERVATION_SCORE", 
"mammals");


print $mlss->dbID, "\n";
############

which outputs:

> perl conservation_scores.pl
50043


Cheers,
Stephen.



On Thu, 7 Feb 2013, cj5 at sanger.ac.uk wrote:

> Hi
>
> The example script for getting gerp scores
>
> http://www.ensembl.org/Help/Faq?id=221
>
> seems to have beem removed
>
> I had an old api script which did this using
>
> my $mlss_adaptor = $reg->get_adaptor("Multi", "compara", "MethodLinkSpeciesSet");
> $mlss_adaptor->fetch_by_method_link_type_species_set_name("GERP_CONSERVATION_SCORE", "mammals");'.
>
> But this produces an error in version 70,
>
> "Can't call method "fetch_by_method_link_type_species_set_name" on an undefined value
>
> So how do I get GERP scores using the version 70 API?
>
> Thanks
> Chris Joyce
> Sanger Institute
>
>
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