[ensembl-dev] Slow get_adaptor

Genomeo Dev genomeodev at gmail.com
Tue Jan 7 19:01:30 GMT 2014


Hi all,

I am finding this code very slow. I am using Ensembl VM 74:

$gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
"gene" );

my $genes =
$gene_adaptor->fetch_all_by_stable_id_list(["ENSG00000249352","ENSG00000109576"]);

while ( my $gene = shift @{$genes} ) {
my $gstring = feature2string($gene);
print "$gstring\n";
my $transcripts = $gene->get_all_Transcripts();
while ( my $transcript = shift @{$transcripts} ) {
my $tstring = feature2string($transcript);
print "\t$tstring\n";
}
}

I suspect the first line is the problem. Any advice on how I can run this
faster? especially for a large set of genes?

Thanks,

Genomeo
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