Re: [mart-dev] No sequence retrieved using "gene_flank" attribute

[Syed Haider]

Hi Josef,

apologies for the delay in reply,
have you tried the same query on the web interface on Biomart Central 
Portal (www.biomart.org) ? what happens there, i see the query works 
just fine there. please let us know if that works for you.

Best,
Syed


Josef Anrather wrote:
Hi Everyone,

I have troubles with the following code using the biomart perl API

  my $action='clean';
  my $initializer = BioMart::Initializer->new('registryFile'=> 
$confFile, 'action'=>$action);
  my $registry = $initializer->getRegistry;
  my $query = BioMart::Query->new('registry'=> 
$registry,'virtualSchemaName'=>'default');
  my $symbol = 'xxxx';
        
        $query->addAttribute("gene_flank");
        
        $query->addFilter("mgi_symbol", [$symbol]);
        $query->addFilter("upstream_flank",["1000"]);
        $query->addFilter("transcript_status", ["KNOWN"]);
        $query->addFilter("with_entrezgene", ["Only"]);

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

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

# I do not get any data back. If i change the attribute it to anything  
else (eg "cdna" or "peptide" or "5utr") I get actual sequence back.
# "gene_flank" is listed as an attribute of dataset  
"mmusculus_gene_ensembl".

I have tried the code with different genes and on different datasets.  
No success.

Has anybody had a similar experience?

Thanks, Josef