[ensembl-dev] How to get AlignSlice objects

[Javier Herrero]

Hi Marc

The AlignSliceAdaptor has a method to produce an AlignSlice from a 
GenomicAlignBlock:

my $align_slice_adaptor =
    $registry->get_adaptor("Multi", "compara", "AlignSlice");

my $align_slice =
    $align_slice_adaptor->fetch_by_GenomicAlignBlock($gab);

Javier

On Monday 29 Aug 2011 09:17:59 Marc P. Hoeppner wrote:
> Hi,
> 
> so I continue on my quest to wrap my head around the PERL Api...
> 
> My current problem concerns the AlignSlice class and how to get get such
> an object starting from a GenomicAlignBlock. All I was able to produce
> are single slices, but no align slices. I'd be glad if anyone could
> point out (conceptually, no detailed code required) how AlignSlices are
> obtained from blocks of individual genomic aligns.
> 
> Cheers,
> Marc
> 
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-- 
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK