[ensembl-dev] question regarding geneadaptor

[mag]

Hi Duarte,

Could you copy-paste the exact registry call you have in your script?

Using
$registry->load_registry_from_db(
-db_version => 75,
-host => 'ensembldb.ensembl.org',
-user => 'anonymous',
-port => '3306',
);

I get a list of two genes with the snippet of code you have shown.


Regards,
Magali

On 04/11/2014 13:33, Duarte Molha wrote:
> I am connected to v75
>
>
> =========================
>      Duarte Miguel Paulo Molha
> http://about.me/duarte
> =========================
>
> On 4 November 2014 13:21, mag <mr6 at ebi.ac.uk <mailto:mr6 at ebi.ac.uk>> 
> wrote:
>
>     Hi Duarte,
>
>     Can you check which database you are connecting to?
>
>     I tried the following:
>     my $registry = "Bio::EnsEMBL::Registry";
>     $registry->load_registry_from_db(
>     -db_version => 77,
>     -host => 'ensembldb.ensembl.org <http://ensembldb.ensembl.org>',
>     -user => 'anonymous',
>     -port => '3337',
>     );
>
>     my $query_gene = "CYP2D7P";
>     my $gene_adaptor = $registry->get_adaptor('human', 'core', 'gene');
>     print "Using database " . $gene_adaptor->dbc->dbname() . "\n";
>     my @fetched_genes =
>     @{$gene_adaptor->fetch_all_by_display_label($query_gene)};
>     foreach my $gene (@fetched_genes) {
>       print "Found " . $gene->stable_id . " with name " .
>     $gene->display_xref->display_id . "\n";
>     }
>
>     And got the following results:
>     Using database homo_sapiens_core_77_37
>     Found ENSG00000205702 with name CYP2D7P
>     Found ENSG00000263181 with name CYP2D7P
>
>     This also works on the live GRCh38 database.
>
>
>     Regards,
>     Magali
>
>
>     On 04/11/2014 12:03, Duarte Molha wrote:
>>     Dear developer
>>
>>     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:
>>
>>     http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000205702;r=22:42536214-42540576
>>
>>     here is the code I use to fecth it:
>>
>>     $query_gene = "CYP2D7P";
>>
>>     my @fetched_genes =
>>     @{$gene_adaptor->fetch_all_by_display_label($query_gene)};
>>
>>     however ...
>>
>>     this method returns an empty list.
>>
>>     Why is this?
>>
>>
>>     I have also tried:
>>
>>     my @fetched_genes =  @{
>>     $gene_adaptor->fetch_all_by_external_name($query_gene) };
>>
>>     and this also fails.
>>
>>     Can someone tell me what I am doing wrong?
>>
>>
>>     Best regards
>>
>>     Duarte
>>
>>
>>     _______________________________________________
>>     Dev mailing listDev at ensembl.org  <mailto:Dev at ensembl.org>
>>     Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>     Ensembl Blog:http://www.ensembl.info/
>
>
>     _______________________________________________
>     Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>     Posting guidelines and subscribe/unsubscribe info:
>     http://lists.ensembl.org/mailman/listinfo/dev
>     Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> 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/20141104/8b0d976f/attachment.html>