[ensembl-dev] Gene ID version

Will McLaren wm2 at ebi.ac.uk
Mon Jan 26 11:21:17 GMT 2015


Hi Konrad,

Apologies for the delay in getting back to you.

The gene version currently gets scrubbed from the data in the VEP cache,
unfortunately. The transcript version is still attached to the transcript
object, however, so you can pull this out in a plugin if necessary, e.g.

my $v = $tva->transcript->version;

http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#technical
contains some details of what data is stripped from transcript objects.

We can easily prevent the gene version being scrubbed in a future VEP
version if this would be useful to you.

Regards

Will McLaren
Ensembl Variation



On 9 January 2015 at 08:14, Konrad Karczewski <konradk at broadinstitute.org>
wrote:

> 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> 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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