<div dir="ltr">Hi Konrad,<div><br></div><div>Apologies for the delay in getting back to you.</div><div><br></div><div>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.</div><div><br></div><div>my $v = $tva->transcript->version;</div><div><br></div><div><a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#technical">http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#technical</a> contains some details of what data is stripped from transcript objects.<br></div><div><br></div><div>We can easily prevent the gene version being scrubbed in a future VEP version if this would be useful to you.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 9 January 2015 at 08:14, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hello!<div><br></div><div>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.</div><div><br></div><div>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). <span class="HOEnZb"><font color="#888888"><br><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br>-Konrad</div></div>
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<br><div><blockquote type="cite"><div>On Jan 9, 2015, at 2:10 AM, Rocky Bernstein <<a href="mailto:rocky.bernstein@gmail.com" target="_blank">rocky.bernstein@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Comment in line.<br><div><br><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 8, 2015 at 4:47 PM, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><u></u>
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<span><div>Hi VEP team/Will,</div>
<div><br></div>
<div>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?</div></span></div></blockquote><div><br></div><div>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: <span style="font-family:monospace,monospace"><br><br></span><span style="font-family:monospace,monospace"><span style="font-family:monospace,monospace">use Bio::DB::Fasta;<br>my $fasta_file = glob('~/.vep/homo_sapiens/78_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa');<br>my $db = Bio::DB::Fasta->new($fasta_file);<br></span>my @ids = $db->get_all_primary_ids;<br>print join(', ', @ids, "\n");<br></span><span style="font-family:arial,helvetica,sans-serif"><br></span></div><div><span style="font-family:arial,helvetica,sans-serif">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 . <br><br></span></div><div><span style="font-family:arial,helvetica,sans-serif">If you are referring to your input VCF file instead, I don't know.</span><span style="font-family:monospace,monospace"><br><br></span></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><span>
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<div>Thanks!</div></span><div><br></div>
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_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br></div></blockquote></div><br></div></div></div></div><br>_______________________________________________<br>
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