<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hello - I'm having trouble getting cDNA sequences using the bioperl/biomart api's. <span class="tab"></span><span class="tab">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, "<span style="color: rgb(192, 0, 0);">Attribute 'cdna' not found in dataset default.hsapiens_gene_ensembl</span>" Perhaps cDNA is in another mart? I used the Ensembl Biomart 'perl' button to generate the perl query. <br><br></span></div><div style="color: rgb(0, 0, 127);"><br><span class="tab"></span></div><div style="margin-left: 80px; color: rgb(0, 0, 127);"><span class="tab"></span>my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action);<br>my $registry =
$initializer->getRegistry;<br><br>my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');<br><br> $query->setDataset("hsapiens_gene_ensembl");<br> $query->addFilter("biotype", ["pseudogene"]);<br> $query->addAttribute("ensembl_transcript_id");<br> $query->addAttribute("ensembl_gene_id");<br> $query->addAttribute("chromosome_name");<br> $query->addAttribute("strand");<br> $query->addAttribute("cdna");<br><br><br>$query->formatter("FASTA");<br><br>my $query_runner = BioMart::QueryRunner->new();</div><div><br></div><div><br></div><div>Here is my registryFile content. Does this look
OK?</div><div style="color: rgb(0, 0, 127);"><?xml version="1.0" encoding="UTF-8"?><br><!DOCTYPE MartRegistry><br><MartRegistry><br> <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" /><br></MartRegistry></div><div><br></div><div>I also tried this mart as well and received the same cdna not found in dataset message:</div><div><span style="color: rgb(0, 0, 127);"><?xml version="1.0" encoding="UTF-8"?></span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);"><!DOCTYPE MartRegistry></span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);"><MartRegistry></span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);"> <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" /></span><br style="color: rgb(0, 0, 127);"><span style="color: rgb(0, 0, 127);"></MartRegistry></span><br style="color: rgb(0, 64, 127);"><br></div><div><br></div><div><br></div><div><br></div><div>Thank you.</div><div><br></div></div></body></html>