[ensembl-dev] gene centred info via slices
Hardip Patel
H.Patel at victorchang.edu.au
Mon Oct 11 06:06:52 BST 2010
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20101011/2452f663/attachment.html>
More information about the Dev
mailing list