[ensembl-dev] error with ExonAdaptor fetch_all

[Ian]

This has been fixed on the cvs head and on branch 59. Please update your checkout. alternatively remove the biotype check.

Sorry for the inconvenience.

Ian.

On Oct 30, 2010, at 12:07 AM, Andrea Edwards <edwardsa at cs.man.ac.uk> wrote:

> Hi
> 
> I was trying to fetch all of the exons from my local installation of the ensembl cow database.
> 
> I had this simple code
> 
> ===================
> use Bio::EnsEMBL::Registry;
> use Bio::EnsEMBL::Transcript;
> use Bio::EnsEMBL::Variation::Utils::Sequence qw(unambiguity_code);
> use Bio::EnsEMBL::DBSQL::DBAdaptor;
> use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
> 
> my $registry = 'Bio::EnsEMBL::Registry';
> $registry_file= "....";
> $registry->load_all($registry_file);
> 
> my $exon_adaptor = $registry->get_adaptor( 'bos_taurus', 'Core', 'Exon' );
> my $exons = $exon_adaptor->fetch_all();
> 
> 
> 
> $i = 0;
> foreach $exon(@{$exons}) {
>    $i++;
>    print $exon->display_id, "\n";
> 
> }
> 
> print "done";
> 
> ==================================
> 
> and got this error
> 
> ===================================
> 
> MSG: Detected an error whilst executing SQL 'SELECT  e.exon_id, e.seq_region_id, e.seq_region_start, e.seq_region_end, e.seq_region_strand, e.phase, e.end_phase, e.is_current, e.is_constitutive, esi.stable_id, esi.version, UNIX_TIMESTAMP(created_date), UNIX_TIMESTAMP(modified_date)
> FROM ( (exon e)
>  LEFT JOIN exon_stable_id esi ON esi.exon_id = e.exon_id )
> WHERE e.biotype != "LRG_gene" and e.is_current = 1
> ': DBD::mysql::st execute failed: Unknown column 'e.biotype' in 'where clause' at C:\Perl\site\lib\ensembl-api\ensembl\modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line 521.
> 
> STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch C:\Perl\site\lib\ensembl-api\ensembl\modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:522
> STACK Bio::EnsEMBL::DBSQL::ExonAdaptor::fetch_all C:\Perl\site\lib\ensembl-api\ensembl\modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm:126
> STACK toplevel C:/Documents and Settings/Administrator/Desktop/PHD/java/Code/SNP/get_exons.pl:15
> ---------------------------------------------------
> 
> ===========================================
> The exon table doesn't have a field biotype??
> 
> This is the code for the fetch_all method from the PerlAPI docs
> 
> =========================================
> 
> sub fetch_all {
> 
>  my  ($self)  =@_;
> 
>  my  $constraint  ='e.biotype != "LRG_gene" and e.is_current = 1';
>  my  @exons   = @{  $self->generic_fetch($constraint)  };
> 
>  return\@ exons ;
> 
> }
> 
> ===============================================
> 
> Many thanks in advance for your help
> 
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