I've hit a problem with the Ensembl compara Perl API, and was wondering if anyone had any advice. I have a list of UniProt accessions from human proteins, which I've mapped to Ensembl gene IDs using Ensembl Biomart. I'm using the gene IDs, along with the Ensembl Perl API, to extract the homologies for every gene. I have two almost identical scripts, one which accesses the Ensembl database using the API, and one which accesses the Ensembl Genome database using the API. The script which accesses the Ensembl database runs perfectly with all the gene IDs I have. However, the one accessing the Ensembl Genome database fails for some of the gene IDs. For reference these are a few of the ones that it fails with:
ENSG00000223532 ENSG00000206505 ENSG00000224608 ENSG00000231834 ENSG00000228299 ENSG00000206306 ENSG00000206450 ENSG00000235657 ENSG00000206240 ENSG00000223980 ENSG00000224320 ENSG00000228080 ENSG00000229215
The script accessing Ensembl Genome is attempting to return the homologies in the pan-taxonomic database. I've tracked down the problem to the fact that the lines
my $memberAdaptor = Bio::EnsEMBL::Registry->get_adaptor('pan_homology', 'compara', 'Member'); ... # First get the Member object. As we are searching for homology information this is a gene. my $member = $memberAdaptor->fetch_by_source_stable_id("ENSEMBLGENE",$ensemblGene);
$member undefined. My assumption is that this means the gene ID can't be found in the database. However, when I check the Ensembl Genome website it seems to be able to find the gene IDs. I was under the impression that the IDs were meant to be stable, so I'm a bit confused as to why they can't be found.