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

Thomas Juettemann juettemann at gmail.com
Mon Feb 21 15:07:06 GMT 2011


Thank you Ian.
To clarify, were you suggesting that I should install a local version
of the 54 MySQL DB or only download the 54 Perl API?
I did the later, pointed it to db_version 54 and it seems to work. The
query is quite complex and will take several hours to complete, would
be great to know if I have a bug and query the wrong DB.

Cheers,
Thomas


On Mon, Feb 21, 2011 at 11:45, ian Longden <ianl at ebi.ac.uk> wrote:
> 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
>>
>




More information about the Dev mailing list