[ensembl-dev] Help with getting cDNA sequences using Biomart perl api's

[pip pipster]

Hello - I'm having trouble getting cDNA sequences using the bioperl/biomart api's.  Here is an example query that I'm building.  It works fine until I add the "cdna" attribute.  Once I add that attribute, I get the message, "Attribute 'cdna' not found in dataset default.hsapiens_gene_ensembl" Perhaps cDNA is in another mart?  I used the Ensembl Biomart 'perl' button to generate the perl query.  



my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action);
my $registry = $initializer->getRegistry;

my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');

        $query->setDataset("hsapiens_gene_ensembl");
        $query->addFilter("biotype", ["pseudogene"]);
        $query->addAttribute("ensembl_transcript_id");
        $query->addAttribute("ensembl_gene_id");
        $query->addAttribute("chromosome_name");
        $query->addAttribute("strand");
        $query->addAttribute("cdna");


$query->formatter("FASTA");

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


Here is my registryFile content.  Does this look OK?
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
  <MartURLLocation database="ensembl_mart_63" default="1" displayName="Ensembl Genes 63" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>

I also tried this mart as well and received the same cdna not found in dataset message:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
  <MartURLLocation database="ensembl_mart_63" default="1" displayName="ENSEMBL GENES 63 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>





Thank you.
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