[ensembl-dev] Gene ID version

[Konrad Karczewski]

Hello!

Yes, I figured I could do by going into the API (with VEP, that would involve writing a plugin), but thought maybe it's already implemented in native VEP.

In any case, I found a partial solution, the --hgvs flag appears to write out the version number for transcripts (e.g. ENST00000302118.5:c.-26G>A), which is most of what I need (though it doesn't have this for genes). 

-Konrad

> On Jan 9, 2015, at 2:10 AM, Rocky Bernstein <rocky.bernstein at gmail.com> wrote:
> 
> Comment in line.
> 
> 
> On Thu, Jan 8, 2015 at 4:47 PM, Konrad Karczewski <konradk at broadinstitute.org <mailto:konradk at broadinstitute.org>> wrote:
> Hi VEP team/Will,
> 
> In some applications, Ensembl Gene IDs have a version number (i.e. ENSG00000000001.2) - is there a way I can get this information from a particular run of VEP? Or at least figure out which particular version of each gene I have in a cache?
> 
> I know very little about VEP, and am not sure I even totally understand what you are asking. However since half of the VEP team is out until the end of the month, I'll give it a shot; I can read a manual page. The following code is pretty much straight out of man Bio::DB::Fasta: 
> 
> use Bio::DB::Fasta;
> my $fasta_file = glob('~/.vep/homo_sapiens/78_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa');
> my $db = Bio::DB::Fasta->new($fasta_file);
> my @ids      = $db->get_all_primary_ids;
> print join(', ', @ids, "\n");
> 
> If you aren't using Fasta, them I imagine you if read the man page for whatever DB you are using , it probably has  $db->get_all_primary_id . 
> 
> If you are referring to your input VCF file instead, I don't know.
> 
> 
> Thanks!
> 
> 
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