[ensembl-dev] Get Oligo probes

[njohnson]

Hi Sebastian

That method call doesn't appear in ur example script and seems to have been missed when we updated the API wrt removing the stable_id tables. I have updated now, and it will be available in v76. Here is the now working version:

sub fetch_all_by_linked_transcript_Gene{
  my $self = shift;
  my $gene = shift;
  assert_ref($gene, 'Bio::EnsEMBL::Gene'); 
  #No need to pass params here as we known the gene ID is an int from the db 
  my $tx_sids = $gene->adaptor->db->dbc->sql_helper->execute_simple('select t.stable_id from transcript t where t.gene_id='.$gene->dbID);
  return $self->fetch_all_by_external_names($tx_sids, $self->db->species.'_core_Transcript');
}

Or alternatively a link to the master check in, if you want to cherry pick the commit over on your local repo:

	https://github.com/Ensembl/ensembl-funcgen/commit/7ac1eba97fa00913de8f00b6a149e0a82753ee9f

Incidentally, I will also be updating the example script, as this seems to have aged a little bit.


Nathan Johnson

Ensembl Regulation
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

http://www.ensembl.info/
http://twitter.com/#!/ensembl
https://www.facebook.com/Ensembl.org

On 1 Apr 2014, at 09:22, njohnson <njohnson at ebi.ac.uk> wrote:

> Hi Sebastian
> 
> You probably want to have a look at our example script, found here:
> 
> 	ensembl-funcgen/scripts/examples/microarray_annotation_example.pl
> 
> I will have a look at that error asap.
> 
> Thanks
> 
> Nathan Johnson
> 
> Ensembl Regulation
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> 
> http://www.ensembl.info/
> http://twitter.com/#!/ensembl
> https://www.facebook.com/Ensembl.org
> 
> On 1 Apr 2014, at 08:50, Sébastien Moretti <sebastien.moretti at unil.ch> wrote:
> 
>> Hi
>> 
>> I wonder how to retrieve all gene_id and related probeset id for a given species and a particular chip type.
>> Usually I get that from BioMart but cannot find the equivalent way of doing that with the Ensembl API
>> e.g. Ensembl Gene ID 	Affy HG U95AV2 probeset
>>    ENSG00000261657 	39195_s_at
>>    ENSG00000234627 	37079_at
>>    ENSG00000256305 	31325_at
>>    ...
>> 
>> I tried the method fetch_all_by_linked_transcript_Gene but it fails with this error message:
>> DBD::mysql::db selectcol_arrayref failed: Table 'homo_sapiens_core_75_37.transcript_stable_id' doesn't exist at /usr/local/ensembl/ensembl-funcgen/modules//Bio/EnsEMBL/Funcgen/DBSQL/BaseAdaptor.pm line 922.
>> And the status of the method is "at risk".
>> 
>> 
>> Any idea how to do that?
>> Thanks
>> 
>> 
>> 
>> PS for the API documentation of fetch_all_by_linked_transcript_Gene() & fetch_all_by_linked_Transcript() a '}'  is missing at the end of the code example.
>> 
>> -- 
>> Sébastien Moretti
>> Department of Ecology and Evolution,
>> Biophore, University of Lausanne,
>> CH-1015 Lausanne, Switzerland
>> Tel.: +41 (21) 692 4221/4079
>> http://selectome.unil.ch/ http://bgee.unil.ch/
>> 
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> 
> 
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