[mart-dev] upstream_flank length question

[Marcin Piechota]

Dear all,

I have a newbie question.
When I issue this query:

  $input = "ENSG00000204389";
  $query = BioMart::Query->new('registry'=>$registry, 
'virtualSchemaName'=>'default');
  $query->setDataset('hsapiens_gene_ensembl');
  $query->addFilter('ensembl_gene_id', [$input]);
  $query->addFilter('upstream_flank', ["300"]);
  $query->addAttribute('gene_flank');
  $query->formatter('FASTA');

  $query_runner = BioMart::QueryRunner->new();
  $query_runner->uniqueRowsOnly(1);
  $query_runner->execute($query);

  $temp = $query_runner->printResults();

then I get this output:

>
Query ERROR: caught BioMart::Exception::Usage: Requests for flank sequence must 
be accompanied by an upstream_flank or downstream_flank request

5utr and other attributes work fine.
Question:
How to define upstream flank length value?

Marcin Piechota
Department of Molecular Neuropharmacology

Institute of Pharmacology

Polish Academy of Sciences, Krakow