[ensembl-dev] ensj-41 chromosome Y

Andy Yates ayates at ebi.ac.uk
Tue Apr 17 09:58:35 BST 2012

Dear Alireza,

I'm very sorry for the trouble you are having with the Ensj API however this is an unsupported piece of software & has been so for the past 5 & 1/2 years. Glenn Proctor's original email outlined that support would be provided on a best effort basis; we cannot offer support at this at the moment in time.

Two alternatives are available which may help you access our data:

* JEnsembl (http://jensembl.sourceforge.net/) from the Roslin Institute

* Ruby Ensembl API (https://github.com/jandot/ruby-ensembl-api) from Jan Aerts

The first is a pure Java implementation so you should have more success with this. The second is the Ruby API which can be accessed using JRuby. You will have to install this along with a number of Ruby Gem dependencies. I would suggest you try the first option & if this fails then try to use the Ruby API.

All the best,


Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 16 Apr 2012, at 23:47, Alireza Khodabakhshi wrote:

> Hi,
> I am using the ensj-41.jar API set to retrieve annotations from the ensembl database. However when I try to fetch data for chromosome Y using the GeneAdaptor I get the following error. I am using core_66_37 version (hg19). It works fine for the core_54_36p (hg18). Any help?
> Thanks,
> Apr 16, 2012 3:14:37 PM org.ensembl.driver.impl.BaseFeatureAdaptorImpl fetch
> WARNING: empty idString for loc = chromosome_GRCh37:Y:1-10000->chromosome_GRCh37:X:60001-2699520->chromosome_GRCh37:Y:2649521-59034049->chromosome_GRCh37:X:154931044-155270560
> Error:     Could not fetch from Exon Adaptor.
> Error:     Message from Java environment (could be null): Failed to execute sql against database homo_sapiens_core_66_37:SELECT e.exon_id, e.seq_region_id, e.seq_region_start, e.seq_region_end, e.seq_region_strand, e.phase, e.end_phase, esi.stable_id, esi.version, esi.created_date, esi.modified_date FROM exon e  LEFT JOIN exon_stable_id esi ON esi.exon_id = e.exon_id WHERE e.seq_region_id IN ()  [41-BCGSC]; nested exception is:
>       com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ')' at line 1
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