[ensembl-dev] Gene ID version

[Rocky Bernstein]

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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