[ensembl-dev] gene stable_ids and status?

[mag]

Hi Michael,

The ENSESTG stable IDs are present in the otherfeatures database, can 
you please check which database you are connecting to?

The following snippet:
my $registry = "Bio::EnsEMBL::Registry";

$registry->load_registry_from_db(
   -host => 'ensembldb.ensembl.org',
   -user => 'anonymous',
);

my $gene_adaptor = $registry->get_adaptor('homo_sapiens', 'core', 'Gene');
my $genes = $gene_adaptor->fetch_all();

should return genes with ENSG stable IDs.

The status property has been retired earlier this year, please see 
Andy's email for more detail: 
http://lists.ensembl.org/pipermail/dev/2017-April/012421.html


I hope that helps,
Magali

On 25/10/2017 20:18, Michael Yourshaw wrote:
> 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.
>
> 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*.
>
> However when I query the sql db with select * 
> from homo_sapiens_core_90_38.gene, the ids have the conventional form 
> ENSG*.
>
> 2. The property gene->{status} seems not to exist. This used to 
> contain KNOWN, PUTATIVE, or NOVEL.
>
> My question is, is it possible to use the API to get, say, all ensembl 
> genes that are KNOWN and their ENSG ids?
>
>
> ॐ
> Michael Yourshaw
> myourshaw at gmail.com <mailto:myourshaw at ucla.edu>
>
> This message is intended only for the use of the addressee and may 
> contain information that is PRIVILEGED and CONFIDENTIAL, and/or may 
> contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, 
> you are hereby notified that any dissemination of this communication 
> is strictly prohibited. If you have received this communication in 
> error, please erase all copies of the message and its attachments and 
> notify us immediately. Thank you.
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20171026/e1f3c70f/attachment.html>