[ensembl-dev] stable_id by gene name

[Emily Perry]

Hi Mahmood

The gene sequence page displays 600 bp upstream and downstream of the 
gene. You can get this extra 600 bp by altering your slice adapter call to:
my $slice = $slice_adaptor->fetch_by_gene_stable_id( 'ENSG00000139618', 
600);

This is described in the docs here:
http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1SliceAdaptor.html#a744a0044ea95082ce090e31007417d60

All the best

Emily

On 29/06/2017 10:42, Mahmood Naderan wrote:
> Thanks for the feedback. I have read the tutorial and understood most 
> of it (at least this is what I think!). The main manual which contains 
> all class names and member functions is comprehensive though and need 
> more elaboration...
>
> What $brca_gene->seq prints is not the same as the website. That perl 
> command prints GGGCTTGTGGC.... however the sequence section of the web 
> frontend 
> (http://grch37.ensembl.org/Homo_sapiens/Gene/Sequence?db=core;g=ENSG00000139618;r=13:32889611-32973805) 
> starts withTACCAAGCCC...
>
>
> ​I have to say that ​GGGCTTGTGGC.... is the start of an exon which is 
> inside the printed sequence from the web page.
>
> ​I also double checked with
>
> my $slice = $slice_adaptor->fetch_by_gene_stable_id( 'ENSG00000139618');
> my $sequence = $slice->seq();
> print $sequence, "\n";
>
> ​and it was not the same as the web's output. Is seq() the same as 
> Gene/Sequence?db=core in the URL?​
>
> Regards,
> Mahmood
>
>
>
> On Thu, Jun 29, 2017 at 12:38 PM, mag <mr6 at ebi.ac.uk 
> <mailto:mr6 at ebi.ac.uk>> wrote:
>
>     Hi Mahmood,
>
>     To access all genes in a species, you can use directly the
>     GeneAdaptor.
>     This will allow you to loop through all the genes without having
>     to retrieve the chromosomes first.
>
>     Additionally, there is a method called fetch_all_by_external_name
>     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>
>     which allows you to retrieve all Gene objects for a gene symbol.
>
>     An example script would look like:
>     $registry->load_registry_from_db(
>       -host => 'ensembldb.ensembl.org <http://ensembldb.ensembl.org>',
>       -user => 'anonymous',
>       -port => 3337
>     );
>     my $gene_adaptor = $registry->get_adaptor('human', 'core', 'Gene');
>     my @genes = @{ $gene_adaptor->fetch_all() };
>     my @brca_genes = @{
>     $gene_adaptor->fetch_all_by_external_name('BRCA2') };
>     while (my $brca_gene = shift @brca_genes) {
>       print ">" . $brca_gene->stable_id . " " .
>     $brca_gene->display_xref->display_id . "\n";
>       print $brca_gene->seq . "\n";
>     }
>
>     I would recommend looking through our API course to get more
>     familiar with it.
>     We have slides from our in-person workshops
>     https://github.com/Ensembl/ensembl-presentation/tree/master/API/Core
>     <https://github.com/Ensembl/ensembl-presentation/tree/master/API/Core>
>     a tutorial
>     http://www.ensembl.org/info/docs/api/core/core_tutorial.html
>     <http://www.ensembl.org/info/docs/api/core/core_tutorial.html>
>     and videos
>     http://www.ebi.ac.uk/training/online/course/ensembl-filmed-api-workshop
>     <http://www.ebi.ac.uk/training/online/course/ensembl-filmed-api-workshop>
>
>
>     Hope that helps,
>     Magali
>
>
>
>
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-- 
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK

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