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Hi Mahmood,<br>
<br>
To access all genes in a species, you can use directly the
GeneAdaptor.<br>
This will allow you to loop through all the genes without having to
retrieve the chromosomes first.<br>
<br>
Additionally, there is a method called fetch_all_by_external_name<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1GeneAdaptor.html#a940d6dc7e9273ad373a23eb563a455e6">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1GeneAdaptor.html#a940d6dc7e9273ad373a23eb563a455e6</a><br>
which allows you to retrieve all Gene objects for a gene symbol.<br>
<br>
An example script would look like:<br>
$registry->load_registry_from_db(<br>
-host => 'ensembldb.ensembl.org',<br>
-user => 'anonymous',<br>
-port => 3337<br>
);<br>
my $gene_adaptor = $registry->get_adaptor('human', 'core',
'Gene');<br>
my @genes = @{ $gene_adaptor->fetch_all() };<br>
my @brca_genes = @{
$gene_adaptor->fetch_all_by_external_name('BRCA2') };<br>
while (my $brca_gene = shift @brca_genes) {<br>
print ">" . $brca_gene->stable_id . " " .
$brca_gene->display_xref->display_id . "\n";<br>
print $brca_gene->seq . "\n";<br>
}<br>
<br>
I would recommend looking through our API course to get more
familiar with it.<br>
We have slides from our in-person workshops<br>
<a class="moz-txt-link-freetext" href="https://github.com/Ensembl/ensembl-presentation/tree/master/API/Core">https://github.com/Ensembl/ensembl-presentation/tree/master/API/Core</a><br>
a tutorial<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/core/core_tutorial.html">http://www.ensembl.org/info/docs/api/core/core_tutorial.html</a><br>
and videos<br>
<a class="moz-txt-link-freetext" href="http://www.ebi.ac.uk/training/online/course/ensembl-filmed-api-workshop">http://www.ebi.ac.uk/training/online/course/ensembl-filmed-api-workshop</a><br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 28/06/2017 19:36, Mahmood Naderan
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CADa2P2Wk2uhTtgmaOrS2vywtLcfU3195MUkiSaaTHM50c2+GmA@mail.gmail.com">
<div dir="ltr">
<div class="gmail_default" style="font-family:tahoma,sans-serif">Hi,<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">Is
exonerate the only tool to get the stable_id by the gene name?
I was wondering if an ensemble perl api does this job. <br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">Also,
I didn't see an api to access the database by the gene name.
It seems that I have to get the chromosome first and then
iterate over all genes in it.<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif"><br
clear="all">
</div>
<div>
<div class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr"><font face="tahoma,sans-serif">Regards,<br>
Mahmood</font><br>
<br>
<br>
</div>
</div>
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<br>
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