[ensembl-dev] searchin on ensembl with perl API

Animesh Sharma sharma.animesh at gmail.com
Tue Jul 19 19:01:59 BST 2011

Hi Carnë,
I feel most of the useful stuff is mentioned at
http://www.ensembl.org/info/docs/api/core/core_tutorial.html , need to
modify to suit the purpose. Last time I used this approach to get genes in a
region of genome by calling slice via the registry method, something on the
        my @db_adaptors = @{ $registry->get_all_DBAdaptors() };
        my $slice_adaptor = $registry->get_adaptor( $genome, 'Core', 'Slice'
        my $slice = $slice_adaptor->fetch_by_region( 'chromosome', $chr,
$chrs,$chre );
        my @genes = @{ $slice->get_all_Genes() };
Hope this helps,

--------------------------"The Answer Lies In The

2011/7/19 Carnë Draug <carandraug+dev at gmail.com>

> Hi
> I can't find on the tutorials any info on how to something that I hope
> will be very simple.
> On the website, I can enter a query term and I get a list of gene and
> transcripts ids. I'd like to make that search with the perl API.
> However, I can't find any information on to do it on the tutorials.
> Also couldn't find anything when searching for 'query' on the list of
> the core API methods or in the mailing list (by the way, the ensembl
> mailing list archive is not searchable, I had to rely on google. It
> would probably be nice to do that).
> Could someone show me how to do that or point to the right package or
> documentation?
> Thanks in advance,
> Carnë Draug
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