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Hi Duarte,<br>
<br>
Could you copy-paste the exact registry call you have in your
script?<br>
<br>
Using <br>
$registry->load_registry_from_db(<br>
-db_version => 75,<br>
-host => 'ensembldb.ensembl.org',<br>
-user => 'anonymous',<br>
-port => '3306',<br>
);<br>
<br>
I get a list of two genes with the snippet of code you have shown.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 04/11/2014 13:33, Duarte Molha
wrote:<br>
</div>
<blockquote
cite="mid:20141104134430.C185B23017C_458D83EB@hx-mx1.ebi.ac.uk"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 " .
$gene->display_xref->display_id . "\n"; <br>
}<br>
<br>
And got the following results:<br>
Using database homo_sapiens_core_77_37<br>
Found ENSG00000205702 with name CYP2D7P<br>
Found ENSG00000263181 with name CYP2D7P<br>
<br>
This also works on the live GRCh38 database.<br>
<br>
<br>
Regards,<br>
Magali
<div>
<div class="h5"><br>
<br>
<div>On 04/11/2014 12:03, Duarte Molha wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<div dir="ltr">
<div>Dear developer</div>
<div><br>
</div>
<div>I have simple script to fetch gene
information and I am having problems with a
particular gene that I know is correct and on
the database:</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000205702;r=22:42536214-42540576"
target="_blank">http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000205702;r=22:42536214-42540576</a><br>
</div>
<div><br>
</div>
<div>here is the code I use to fecth it:<br>
</div>
<div><br>
</div>
<div>$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>
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</div>
</div>
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