Hi Malcolm,
We need more information from you in order to find out the cause of the problem.
Could you send me the registry file you used in the perl API code? It's
specified in the line like this:
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile,
'action'=>$action);
Cheers,
Junjun
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of Cook, Malcolm
> Sent: Tuesday, April 27, 2010 10:01 AM
> To: '[email protected]'
> Subject: [mart-dev] BioMart::Exception::Configuration',
> 'Attribute \'gene_exon_intron\' not found in dataset default
>
> Does anyone know how to work-around this exception
>
> at
> /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.8/Exception/Cl
> ass.pm line 269
>
> Exception::Class::Base::throw('BioMart::Exception::Configurati
> on', 'Attribute \'gene_exon_intron\' not found in dataset
> default.m...') called at
> /n/site/inst/shared/bioinfo/ensembl/biomart-perl/release-0_7/l
> ib//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/f26d676eaf
> a1feaf994ca31a18fcadf0/f26d676eafa1feaf994ca31a18fcadf0/f26d67
> 6eafa1feaf994ca31a18fcadf0?VIRTUALSCHEMANAME=default&ATTRIBUTE
S=mmusculus_gene_ensembl.default.sequences.ensembl_gene_id|mmusculus_gene_ensembl.default.sequences.gene_exon_int>
ron|mmusculus_gene_ensembl.default.sequences.chromosome_name|m
> musculus_gene_ensembl.default.sequences.strand|mmusculus_gene_
> ensembl.default.sequences.start_position|mmusculus_gene_ensemb
> l.default.sequences.end_position&FILTERS=mmusculus_gene_ensemb
> l.default.filters.ensembl_gene_id."ENSMUSG00000083773,ENSMUSG0
> 0000081262,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();
>
