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

[gaurav thareja]

Hi all,

Couple of doubts:


   1. 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20110718/244d6091/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ld.pl
Type: application/x-perl
Size: 2515 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20110718/244d6091/attachment.pl>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ensembl_registry.conf
Type: application/octet-stream
Size: 842 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20110718/244d6091/attachment.obj>