[ensembl-dev] Fwd: Help with Bio::EnsEMBL::Mapper Class

[Javier Herrero]

Hi Andrés

The Mapper returned by the GenomicAlign object maps between two 
coordinate types called "sequence" and "alignment". I believe in your 
case, $type should be "sequence".

You may want to consider usng the map_coordinates() method rather than 
the list_pairs() one. The map_coordinates() method will trim the 
mappings such that they match your query region (start and end of the 
gene) while list_pairs() will return all the pairs that overlap. Also, 
list_pairs() returns a reference to an array, not the start position of 
the 1st mapping.

I hope this helps

Javier

On 02/04/13 18:30, Andrés Arturo Lanzós Camaioni wrote:
> Hi.
>
> My name is Andrés Lanzós and I am using the Ensembl API for the first 
> time.
>
> I want to map genes from primates in a genomic align.
>
> First, I use the method get_Mapper () to transform the coordinates 
> from each original sequence to the alignment.
>
> $this_mapper = $genomic_align->get_Mapper();
>
> Then, I use the method list_pairs () to find the coordinates for each 
> gene in the alignment.
>
> my $start0=$this_mapper->list_pairs($gene_id,$gene_start,$gene_end,$type);
>
>
>
> But I have a problem with the fourth argument: $type, i do not know 
> which value to put.
>
> Could yo help me with this?
>
> My final objective is to extract the common regions between the genes 
> for the different species of the alignment.
>
> Thank you.
>
> Kind regards,
> Andrés Lanzós.
>
>
>
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-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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