[ensembl-dev] searching for genes by description field?

[Adam Witney]

Thanks, i am working with bacteria so the number of genes and therefore 
memory usage is not such a problem, but I will give your method a try 
also (I hadn't really got involved with sending bare SQL queries yet, so 
its interesting to see how that can be done).

Thanks again

Adam

On 13/02/2013 11:15, ian Longden wrote:
> The problem with this method (it works fine though) is that it needs to
> get all the genes which will take up a lot of memory.
> An alternative way of doing this is to use the db connection itself and
> use this to query the database directly only getting those genes you want..
> Here is an example:-
> -----------------------------------------------------------------------------------------------------------------
> use Bio::EnsEMBL::Registry;
> use Bio::SeqIO;
> use strict;
> my $reg = "Bio::EnsEMBL::Registry";
>
> my $species = "human";
> my $search_str = "%breast cancer%";
>
> $reg->load_registry_from_db(
>      -host => 'ensembldb.ensembl.org <http://ensembldb.ensembl.org>',
>      -user => 'anonymous');
>
> my $core_ga = $reg->get_adaptor($species,"core","gene");
>
>
> my $sql = 'Select gene_id from gene where description like ?';
> my $sth = $core_ga->dbc->prepare($sql) || die "Could not prepare $sql
> for core database";
> $sth->execute($search_str) or croak( $core_ga->dbc->errstr() );
>
> while (my $gene_id = $sth->fetchrow_array()){
>    my $gene = $core_ga->fetch_by_dbID($gene_id);
>    print $gene->stable_id."\t".$gene->description."\n";
> }
> -----------------------------------------------------------------------------------------------------------------
>
>
>
>
>
>
>
> On Wed, Feb 13, 2013 at 11:09 AM, Adam Witney <awitney at sgul.ac.uk
> <mailto:awitney at sgul.ac.uk>> wrote:
>
>
>     Thanks Andy, in the meantime, I just realised, of course I can just
>     do this:
>
>     my $genes = $dba->get_GeneAdaptor()->__fetch_all();
>
>     foreach my $gene ( @{$genes} ) {
>              if ( $gene->description && $gene->description =~ m/$string/ ) {
>                      # do stuff
>              }
>     }
>
>     Thanks again
>
>     Adam
>
>
>     On 13/02/2013 10:30, Andy Yates wrote:
>
>         Hi Adam,
>
>         Currently we do not support this. The actual code which
>         implements this search is in the DBEntryAdaptor and would
>         require edits in there. I can see a point in having this kind of
>         functionality so we will put it on our to-do list.
>
>         Andy
>
>         On 13 Feb 2013, at 10:24, Adam Witney <awitney at sgul.ac.uk
>         <mailto:awitney at sgul.ac.uk>> wrote:
>
>
>             Hi,
>
>             Is there a method to search the Gene description field. I am
>             currently using fetch_all_by_external_name, but this only
>             works if the gene has been annotated with gyrA:
>
>             my $genes =
>             $dba->get_GeneAdaptor()->__fetch_all_by_external_name('__gyrA');
>
>             What I would like to be able to do is search the data
>             returned by the description method ($gene->description), is
>             this possible? eg something like this:
>
>             my $genes =
>             $dba->get_GeneAdaptor()->__fetch_all_by_description('%__gyrase%');
>
>             Thanks
>
>             Adam
>
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