[Bioperl-l] ensembl perl API - very slow retrival of data?

Tim Erwin taerwin at gmail.com
Mon Sep 11 02:36:17 EDT 2006


Hi Zhihua

Is this using the remote ensembl databases? I have done a similar thing
using a local copy of the Arabidopsis ensembl and it only took about 30
seconds.

This question would also be better on the ensembl-dev mailing list:
http://www.ensembl.org/info/about/contact.html

Regards,

Tim


On 9/11/06, zhihua li <lzhtom at hotmail.com> wrote:
>
> hi netters,
>
> has anyone had any experience in using ensembl perl API (based on bioperl)
> to retrieve and analyse data from ensembl?  i wanted to retrieve all the
> genes from ensembl core database. to do this i used a slice adaptor:
>
> $db=new Bio::EnsEMBL::DBSQL::DBAdaptor (...);
> my $slice_adaptor = $db->get_SliceAdaptor();
> my @slices = @{$slice_adaptor->fetch_all('chromosome')};
> foreach my $slice (@slices){
> my @genes=@{$slice->get_all_Genes};
> do something......
> }
>
> it took several hours for the script to get all the genes from
> ensembl.  if
> i'd used the website of BioMart and had the same task done, it'd be just a
> matter of minutes.  So is there a better way of coding? or ensembl modules
> are just extremely slow?
>
> Thanks a lot!
>
>
>
>
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