[mart-dev] BioMart::Exception::Configuration', 'Attribute \'gene_exon_intron\' not found in dataset default

[Cook, Malcolm]

Does anyone know how to work-around this exception 

 at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.8/Exception/Class.pm line 
269
        Exception::Class::Base::throw('BioMart::Exception::Configuration', 
'Attribute \'gene_exon_intron\' not found in dataset default.m...') called at 
/n/site/inst/shared/bioinfo/ensembl/biomart-perl/release-0_7/lib//BioMart/Registry.pm
 line 490


I'm querying with perl api (/ensembl/biomart-perl/release-0_7 ) using code 
exported from biomart/ensembl from dec2008
        
Below is a URL to the query, which works interactively, followed by (slightly 
editted) perl code exported upon clicking the "perl" button

Thanks for your help....

--Malcolm Cook



http://dec2008.archive.ensembl.org/biomart/martview/f26d676eafa1feaf994ca31a18fcadf0/f26d676eafa1feaf994ca31a18fcadf0/f26d676eafa1feaf994ca31a18fcadf0?VIRTUALSCHEMANAME=default&ATTRIBUTES=mmusculus_gene_ensembl.default.sequences.ensembl_gene_id|mmusculus_gene_ensembl.default.sequences.gene_exon_intron|mmusculus_gene_ensembl.default.sequences.chromosome_name|mmusculus_gene_ensembl.default.sequences.strand|mmusculus_gene_ensembl.default.sequences.start_position|mmusculus_gene_ensembl.default.sequences.end_position&FILTERS=mmusculus_gene_ensembl.default.filters.ensembl_gene_id."ENSMUSG00000083773,ENSMUSG00000081262,ENSMUSG00000082711"&VISIBLEPANEL=filterpanel




                
#!/bin/env perl


# An example script demonstrating the use of BioMart API.
# This perl API representation is only available for configuration versions >=  
0.5 
use strict;
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;

my $confFile = #"PATH TO YOUR REGISTRY FILE UNDER biomart-perl/conf/. For 
Biomart Central Registry navigate to
#  "http://www.biomart.org/biomart/martservice?type=registry";
  
"/n/site/inst/shared/bioinfo/ensembl/biomart-perl/release-0_7/conf/registryURLPointer.xml"
  ;
#
# NB: change action to 'clean' if you wish to start a fresh configuration  
# and to 'cached' if you want to skip configuration step on subsequent runs 
from the same registry
#

my $action='cached';
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 
'action'=>$action);
my $registry = $initializer->getRegistry;

my $query = 
BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');
$query->setDataset("mmusculus_gene_ensembl");
$query->addFilter("ensembl_gene_id", 
["ENSMUSG00000083773","ENSMUSG00000081262","ENSMUSG00000082711"]);
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("gene_exon_intron");
$query->addAttribute("chromosome_name");
$query->addAttribute("strand");
$query->addAttribute("start_position");
$query->addAttribute("end_position");

$query->formatter("FASTA");

my $query_runner = BioMart::QueryRunner->new();

$query_runner->execute($query);
$query_runner->printResults();