[ensembl-dev] bug in the Ensembl core API?

[Electra Tapanari]

Hi all,

thanks Bert and Dan for your replies.

I see.. I just think that this is confusing and I don't see the benefits 
of having the strand as a parameter in the 
"$slice_adaptor->fetch_by_region" method if it always returns both strands.

It would be more explicit if you would put the actual strand that you 
are looking for and in case you are interested in both strands call the 
method twice, once for the positive and one for the negative. in my 
opinion of course...

thanks for you input

cheers,
Electra

On 02/05/13 16:15, Daniel Hughes wrote:
> The strand should be refer to the local orientation of your slice 
> object relative to the reference genome and not a specific strand of 
> the underlying sequence.
>
> Dan.
>
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
> -------------------------------------------------------------------------------------
> dsth at cantab.net <mailto:dsth at cantab.net>
> dsth at cpan.org <mailto:dsth at cpan.org>
>
>
> 2013/5/2 Bert Overduin <bert at ebi.ac.uk <mailto:bert at ebi.ac.uk>>
>
>     Hello Electra,
>
>     I don't think this is wrong / a bug as, as far as I know, a slice
>     always encompasses both strands. So, you should do the filtering
>     for features that are located on the forward or reverse strand
>     after retrieving them from the slice.
>
>     But maybe I'm wrong ....
>
>     Cheers,
>     Bert
>
>
>
>
>     On Thu, May 2, 2013 at 4:04 PM, Electra Tapanari <et3 at sanger.ac.uk
>     <mailto:et3 at sanger.ac.uk>> wrote:
>
>
>
>
>         Hi all,
>
>         I came across a problem when using the ensembl core API.
>
>         When I am getting a slice where I define chromosome, start,
>         end and
>         strand and then I get objects from the slice ie,
>         genes/transcripts/introns etc it returns me objects from both
>         strands.
>
>
>         I used this code to test this:
>
>           use strict;
>           use Gencode::Default;
>
>
>           #connect to database
>           my $db = Gencode::Default->dbconnect("ens-livemirror", 3306,
>         "homo_sapiens_core_71_37", "ensro", undef);
>
>           my $sa = $db->get_SliceAdaptor();
>
>           my
>         $slice=$sa->fetch_by_region('chromosome',"3",20000,600000,-1) or
>         die "\n 1.Couldn't get slice\n";
>
>           foreach my $gene (@{$slice->get_all_Genes}){
>
>               $gene=$gene->transform('chromosome');
>               print $gene->stable_id."\t".$gene->strand."\n";
>
>            }
>
>
>         This is the output:
>
>         ENSG00000223587    1
>         ENSG00000224918    -1
>         ENSG00000224318    -1
>         ENSG00000134121    1
>         ENSG00000252017    -1
>         ENSG00000231660    -1
>         ENSG00000234661    -1
>         ENSG00000224957    1
>
>
>         Isn't this wrong? that it returns me genes from both strands
>         since I am
>         defining that I am interested in the slice of the negative
>         strand only?
>
>         many thanks in advance,
>         Electra
>
>         -- 
>         Electra Tapanari
>         Bioinformatician-Gencode Data Coordinator
>         Havana Group
>         Morgan Building
>         Wellcome Trust Sanger Institute
>         Wellcome Trust Genome Campus
>         Hinxton
>         Cambridgeshire
>         CB10 1HH
>
>         E: electra.tapanari at sanger.ac.uk
>         <mailto:electra.tapanari at sanger.ac.uk>
>         T: +44 1223 496827 <tel:%2B44%201223%20496827>
>
>
>
>
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>
>
>
>     -- 
>     Bert Overduin, Ph.D.
>     Vertebrate Genomics Team
>
>     EMBL - European Bioinformatics Institute
>     Wellcome Trust Genome Campus
>     Hinxton, Cambridge CB10 1SD
>     United Kingdom
>
>     http://www.ebi.ac.uk/~bert <http://www.ebi.ac.uk/%7Ebert>
>
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-- 
Electra Tapanari
Bioinformatician-Gencode Data Coordinator
Havana Group
Morgan Building
Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire
CB10 1HH

E: electra.tapanari at sanger.ac.uk
T: +44 1223 496827

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