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

Daniel Hughes dsth at ebi.ac.uk
Thu May 2 16:15:04 BST 2013


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
dsth at cpan.org


2013/5/2 Bert Overduin <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> 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
>> T: +44 1223 496827
>>
>>
>>
>>
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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
>
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