[ensembl-dev] gene centred info via slices

[Patrick Meidl]

On Mon, Oct 11 2010, Felix Kokocinski <fsk at sanger.ac.uk> wrote:

> >>my $slice_adaptor = $registry->get_adaptor($spec, 'Core', 'slice');
> >>  foreach my $slice (@{$slice_adaptor->fetch_all('toplevel')}){
> >>    foreach my $gene (@{$slice->get_all_Genes}){
> >>      foreach my $transcript (@{$gene->get_all_Transcripts}){
> >>          foreach my $exon (@{$transcript->get_all_Exons}){
> >>            ####get transcript, UTR, exon, and intron start and
> >>end in cDNA coordinates and genomic coordinates
> >>        }
> >>      }
> >>    }
> >>}
> >
> >If you are only interested in one biotype eg. protein-coding then you
> >could modify your gene-fetch query like:
> >
> >foreach my $gene (@{$slice->get_all_Genes(undef, undef, undef,
> >undef, 'protein_coding')}){
> 
> just to add to this: For specific biotypes you could also do:
> $genes = $slice->get_all_Genes_by_type($type);

probably the most important performance optimisation would be to set
argument 3 for get_all_Genes() to a true value. since you are looping
over all transcripts, you should turn off lazy-loading.

see
http://www.ensembl.org/info/docs/Pdoc/ensembl/modules/Bio/EnsEMBL/Slice.html#POD27

HTH

    patrick

-- 
Patrick Meidl, Mag.
Bioinformatician

Ce-M-M-
Research Centre for Molecular Medicine
of the Austrian Academy of Science

Lazarettgasse 14 / AKH BT 25.3
Vienna, Austria

room 02.205
phone +43 1 40160 70016
email pmeidl at cemm.oeaw.ac.at
web http://www.cemm.at/