<div dir="ltr">I am connected to v75<div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br>     Duarte Miguel Paulo Molha      <br></font><div><font style="background-color:rgb(255,255,255)" color="#999999">         <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>         <br>=========================</font></div></div></div>
<br><div class="gmail_quote">On 4 November 2014 13:21, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div bgcolor="#FFFFFF" text="#000000">
    Hi Duarte,<br>
    <br>
    Can you check which database you are connecting to?<br>
    <br>
    I tried the following:<br>
    my $registry = "Bio::EnsEMBL::Registry";<br>
    $registry->load_registry_from_db(<br>
    -db_version => 77,<br>
    -host => '<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a>',<br>
    -user => 'anonymous',<br>
    -port => '3337',<br>
    );<br>
    <br>
    my $query_gene = "CYP2D7P";<br>
    my $gene_adaptor = $registry->get_adaptor('human', 'core',
    'gene');<br>
    print "Using database " . $gene_adaptor->dbc->dbname() . "\n";<span class=""><br>
    my @fetched_genes =
    @{$gene_adaptor->fetch_all_by_display_label($query_gene)};<br></span>
    foreach my $gene (@fetched_genes) {<br>
      print "Found " . $gene->stable_id . " with name " .
    $gene->display_xref->display_id . "\n"; <br>
    }<br>
    <br>
    And got the following results:<br>
    Using database homo_sapiens_core_77_37<br>
    Found ENSG00000205702 with name CYP2D7P<br>
    Found ENSG00000263181 with name CYP2D7P<br>
    <br>
    This also works on the live GRCh38 database.<br>
    <br>
    <br>
    Regards,<br>
    Magali<div><div class="h5"><br>
    <br>
    <div>On 04/11/2014 12:03, Duarte Molha
      wrote:<br>
    </div>
    </div></div><blockquote type="cite"><div><div class="h5">
      <div dir="ltr">
        <div>Dear developer</div>
        <div><br>
        </div>
        <div>I have simple script to fetch gene information and I am
          having problems with a particular gene that I know is correct
          and on the database:</div>
        <div><br>
        </div>
        <div><a href="http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000205702;r=22:42536214-42540576" target="_blank">http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000205702;r=22:42536214-42540576</a><br>
        </div>
        <div><br>
        </div>
        <div>here is the code I use to fecth it:<br>
        </div>
        <div><br>
        </div>
        <div>$query_gene = "CYP2D7P";</div>
        <div><span style="white-space:pre-wrap"><br>
          </span></div>
        <div><span style="white-space:pre-wrap"> </span>my
          @fetched_genes =
          @{$gene_adaptor->fetch_all_by_display_label($query_gene)};<br>
        </div>
        <div><br>
        </div>
        <div>however ...</div>
        <div><br>
        </div>
        <div>this method returns an empty list.</div>
        <div><br>
        </div>
        <div>Why is this?</div>
        <div><br>
        </div>
        <div><br>
        </div>
        <div>I have also tried:</div>
        <div><br>
        </div>
        <div>
          <div><span style="white-space:pre-wrap"> </span>my
            @fetched_genes =  @{
            $gene_adaptor->fetch_all_by_external_name($query_gene) };</div>
        </div>
        <div><br>
        </div>
        <div>and this also fails.</div>
        <div><br>
        </div>
        <div>Can someone tell me what I am doing wrong?</div>
        <div><br>
        </div>
        <div><br>
        </div>
        <div>Best regards</div>
        <div><br>
        </div>
        <div>Duarte</div>
      </div>
      <br>
      <fieldset></fieldset>
      <br>
      </div></div><pre>_______________________________________________
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</pre>
    </blockquote>
    <br>
  </div>

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<br></blockquote></div><br></div>