[ensembl-dev] gene centred info via slices

Bronwen Aken ba1 at sanger.ac.uk
Mon Oct 11 09:30:32 BST 2010

Hi Hardip,

At a glance your code looks fine. I'm not sure why it is slow. Are you connecting to our MySQL (host ensembldb.ensembl.org port 5306) or do you have local copies of the databases?

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')}){


On 11 Oct 2010, at 06:06, Hardip Patel wrote:

> Dear all
> I am trying to fetch gene centred information using following code. It takes a long time to extract information for all genes from human or mice at least.
> I was wondering if the following code could be optimized to get information faster.
> 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
>         }
>       }
>     }
> }
> ------
> Regards
> -- 
> Hardip R. Patel
> VCCRI 12th International Symposium 
> “Charting the depths of RNA: from molecules to therapies”
> 19 November 2010
> visit http://www.victorchang.edu.au for details
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

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