[ensembl-dev] Question Regarding Bio::EnsEMBL::Mapper method fastmap.

[Andy Yates]

Hi Will,

The code you have pointed out will only be executed if we are projecting between coordinate systems. DnaAlignFeatureAdaptor::_objs_from_sth() requires the mapper be passed into it from BaseAdaptor::generic_fetch(). This does happen in BaseFeatureAdaptor::_slice_fetch() but only when a feature's coordinate system is not the same as the querying slice's coordinate systems. The schema stores patches/haplotypes as assembly exceptions and therefore are held as mappings between the reference chromosome and the exception. We do not store the relationship of say chromosome 21 from NCBI36 to HSCHR21_2_CTG1_1 in GRCh37.p6 (a coordinate system mapping) so there are no multiple mappings.

Hope this helps,

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 25 Apr 2012, at 11:27, Will Chow wrote:

> Hi dev'ers,
> 
> Regarding Bio::EnsEMBL::Mapper::fastmap method and its use in the DnaAlignFeatureAdaptor.pm.
> 
> from what I gather, the use is to return seq_region_id, start, end, strand information of one coordinate system from information of another coord sys (i.e. project).  However fastmap seems to only return one set of information, as seen in the code.
> 
> I was wondering if there are multiple mappings (like the human patches), which set of information (seq_region_id) will be returned?
> 
> perhaps I'm missing something else from the code, which explains this, if so perhaps you can point me to this.
> 
> much thanks
> 
> Will
> 
> 
> 
> 
> 
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