[ensembl-dev] downloading old Ensembl version using Perl API

[ian Longden]

You should install the 54 version of the database if you want to use
the perl API on release 54 databases. You can have multiple APIs
installed you will just need to set the PERL5LIB path for which ever
one you want to use.

Sometimes you can use different versions of the API and databases but
if there are any schema changes between these versions then the API
may fail, which sounds like the case you have here.


-Ian Longden.

On Mon, Feb 21, 2011 at 8:23 AM, Thomas Juettemann <juettemann at gmail.com> wrote:
> Dear all,
>
> another newbie question.
>
> I'd like to use the Perl API to fetch data from Release 54 (NCBI36/hg18).
> I tried to connect with db_version 54 (I read the disclaimer in API docs):
>
> <code>
>  my $registry = 'Bio::EnsEMBL::Registry';
>  $registry->load_registry_from_db(
>      -host => 'ensembldb.ensembl.org',
>      -user => 'anonymous',
>      -port => 5306,
>      -db_version => 54
>      );
>  return($registry)
> </code>
>
> but fetching a slice fails (2nd line):
>
> <code>
>  my $slice_adaptor  = $registry->get_adaptor( 'Human', 'Core', 'Slice' );
>  my $slice = $slice_adaptor->fetch_by_region( 'chromosome', $chr);
> </code>
>
> Any help/pointers much appreciated.
>
> Best wishes,
> Thomas
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
>