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Hi Michael,<br>
<br>
The ENSESTG stable IDs are present in the otherfeatures database,
can you please check which database you are connecting to?<br>
<br>
The following snippet:<br>
my $registry = "Bio::EnsEMBL::Registry";<br>
<br>
$registry->load_registry_from_db(<br>
-host => 'ensembldb.ensembl.org',<br>
-user => 'anonymous',<br>
);<br>
<br>
my $gene_adaptor = $registry->get_adaptor('homo_sapiens', 'core',
'Gene');<br>
my $genes = $gene_adaptor->fetch_all();<br>
<br>
should return genes with ENSG stable IDs.<br>
<br>
The status property has been retired earlier this year, please see
Andy's email for more detail:
<a class="moz-txt-link-freetext" href="http://lists.ensembl.org/pipermail/dev/2017-April/012421.html">http://lists.ensembl.org/pipermail/dev/2017-April/012421.html</a><br>
<br>
<br>
I hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 25/10/2017 20:18, Michael Yourshaw
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CANcs_JKNaYZ0ipyUqcbDgzt+bU2z6GnVetwnVyKF4kXmvF89Kg@mail.gmail.com">
<div dir="ltr">I have taken a few years off from bioinformatics to
grow stem cells. Things in the ensembl api/db seem to have
changed a bit in my absence.
<div><br>
</div>
<div>1. When I make an API query in homo_sapiens_90_38 such as
$gene_adapter->fetch_all(), I get genes with stable_ids in
the form ENSESTG*.</div>
<div><br>
</div>
<div>However when I query the sql db with select *
from homo_sapiens_core_90_38.gene, the ids have the
conventional form ENSG*.</div>
<div><br>
</div>
<div>2. The property gene->{status} seems not to exist. This
used to contain KNOWN, PUTATIVE, or NOVEL.</div>
<div><br>
</div>
<div>My question is, is it possible to use the API to get, say,
all ensembl genes that are KNOWN and their ENSG ids?</div>
<div> </div>
<div><br>
</div>
<div><br clear="all">
<div>
<div class="gmail_signature">
<div dir="ltr">
<div>ॐ<br>
Michael Yourshaw<br>
<a href="mailto:myourshaw@ucla.edu" target="_blank"
moz-do-not-send="true">myourshaw@gmail.com</a><br>
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<br>
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