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

zhihua li lzhtom at hotmail.com
Sun Sep 10 22:00:00 EDT 2006


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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