[ensembl-dev] Regarding using of local copy of variation database

[Will McLaren]

Hello,

It is possible to use any combination of local and remote databases;
you just need to specify them in your registry file, as you have done.

However, I notice in your registry file the core database you specify
is very old (homo_sapiens_core_47_36i) - it is important that you use
the same version as both the variation database and the API that you
have installed. You should instead use homo_sapiens_core_63_37.

If you need to use a database that is still on the NCBI36 assembly,
then you will need to use release 54 (and download the appropriate
variation database and API).

To use the registry file in your script, you use the load_all() method
in the Bio::EnsEMBL::Registry module:

# load registry from config file
my $reg = 'Bio::EnsEMBL::Registry';
$reg->load_all('ensembl_registry.conf');

# now we can get any adaptors we need from $reg
my $va = $reg->get_adaptor("human", "variation", "variation");
my $vfa = $reg->get_adaptor("human", "variation", "variationfeature");

Hope this helps

Will McLaren
Ensembl Variation


On 18 July 2011 13:06, gaurav thareja <gaurav4thareja at gmail.com> wrote:
> Hi all,
>
> Couple of doubts:
>
> Is it possible to use local version of Variation Database and use online
> version of core database from perl API's?
>
> I am trying to get all LD pairs for given set snps.  (Script Attached:
> ld.pl). I am getting following error:
>
>
> -------------------- WARNING ----------------------
> MSG: Could not find Slice adaptor in the registry for Homo_sapiens variation
>
> FILE: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 899
> CALLED BY: Variation/DBSQL/VariationFeatureAdaptor.pm  LINE: 738
> Ensembl API version = 63
> ---------------------------------------------------
>
> -------------------- EXCEPTION --------------------
> MSG: Could not get adaptor Slice for Homo_sapiens variation
>
> STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD
> /home/gaurav/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:904
> STACK
> Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::_objs_from_sth
> /home/gaurav/ensembl-variation/modules//Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm:738
> STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch
> /home/gaurav/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:528
> STACK
> Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Variation
> /home/gaurav/ensembl-variation/modules//Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm:280
> STACK toplevel ld.pl:51
> Ensembl API version = 63
> ---------------------------------------------------
>
> Please help to resolve above issue. I have also created a registry file
> containing all configuration parameters. (attached ensembl_registry.conf)
>
> While downloading mysql dump of human variation database from ftp site.
> There is no table corresponding to mart_transcript_variation.txt.gz in sql
> file. Can you please let me know, what this file is used for?
>
> --
> Regards
>
> Gaurav Thareja
>
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