<div dir="ltr">I think that just introduced a can of worms into my script. Where are these VCF files stored? I am running the code from a locally stored ensembl database.<div><br></div><div>Do I need to retrieve additional data when creating my database to get these files?</div><div><br></div><div>Thanks</div><div><br></div><div>Duarte</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><table border="0" cellpadding="0" cellspacing="0" style="margin:0px;padding:0px;border:0px;outline:0px;font-size:14px;font-family:proxima-nova-1,proxima-nova-2,Tahoma,Helvetica,Verdana,sans-serif;vertical-align:baseline;border-spacing:0px;color:rgb(51,51,51);line-height:18.2000007629395px"><tbody style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-size:0px;font-family:inherit;vertical-align:baseline;width:auto;height:30px"> </td></tr><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-family:inherit;vertical-align:baseline;width:auto"><div style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;line-height:0"><a href="https://about.me/duarte?promo=email_sig" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;color:rgb(43,130,173);text-decoration:none;display:inline-block" target="_blank"><table border="0" cellpadding="0" cellspacing="0" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;border-spacing:0px"><tbody style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><td align="left" valign="top" style="padding:0px;border:0px;outline:0px;font-style:inherit;font-family:inherit;vertical-align:top;width:auto;line-height:1"><img alt="--" width="0" height="0" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;display:block;width:0px;height:0px;overflow:hidden"><div style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:bold;font-style:inherit;font-size:18px;font-family:proxima-nova-1,Proxima-Nova,Helvetica,Arial,sans-serif;vertical-align:baseline;line-height:1;color:rgb(51,51,51)">Duarte Molha</div><div style="margin:3px 0px 0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-size:12px;font-family:proxima-nova-1,Proxima-Nova,Helvetica,Arial,sans-serif;vertical-align:baseline"><img alt="https://" width="0" height="0" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;display:block;width:0px;height:0px;overflow:hidden">about.me/duarte</div></td></tr><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><td align="left" valign="top" style="padding:8px 0px 0px;border:0px;outline:0px;font-style:inherit;font-family:inherit;vertical-align:top;width:auto;line-height:1"><div style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;text-align:right;height:4px;background-color:rgb(197,208,224)"><img src="https://d13pix9kaak6wt.cloudfront.net/signature/colorbar.png" alt="" width="88" height="4" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;float:right;display:block"></div></td></tr></tbody></table></a> </div></td></tr><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline"><td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-size:0px;font-family:inherit;vertical-align:baseline;width:auto;height:20px"><img src="https://about.me/t/sig?u=duarte" width="1" height="1" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;overflow:hidden"></td></tr></tbody></table></div></div></div></div>
<br><div class="gmail_quote">On 6 March 2018 at 17:16, Sarah Hunt <span dir="ltr"><<a href="mailto:seh@ebi.ac.uk" target="_blank">seh@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<p><br>
</p>
<p>Hi Duarte,</p>
<p>We store large scale genotype and frequency data in VCF now, so
you need to set an extra flag on the API:<br>
</p>
<pre class="m_-6538029127110316456code m_-6538029127110316456sh_perl m_-6538029127110316456sh_sourceCode"><span class="m_-6538029127110316456sh_variable">$variation_adaptor</span><span class="m_-6538029127110316456sh_symbol">-></span><span class="m_-6538029127110316456sh_function">db</span><span class="m_-6538029127110316456sh_symbol">-></span><span class="m_-6538029127110316456sh_function">use_<wbr>vcf</span><span class="m_-6538029127110316456sh_symbol">(</span><span class="m_-6538029127110316456sh_number">1</span><span class="m_-6538029127110316456sh_symbol">);
</span></pre>
to access it. More details are available here:<br>
<br>
<a class="m_-6538029127110316456moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ag" target="_blank">http://www.ensembl.org/info/<wbr>docs/api/variation/variation_<wbr>tutorial.html#ag</a><br>
<div class="m_-6538029127110316456moz-cite-prefix"><br>
Best wishes,<br>
<br>
Sarah<div><div class="h5"><br>
<br>
On 06/03/2018 17:00, Duarte Molha wrote:<br>
</div></div></div>
<blockquote type="cite"><div><div class="h5">
<div dir="ltr">Hi Guys
<div><br>
</div>
<div>I am retrieving variations using the API that have a
certain value of MAF</div>
<div><br>
</div>
<div>for example rs770602</div>
<div><br>
</div>
<div>If you retrieve this variation </div>
<div><br>
</div>
<div>like so: $vf->minor_allele_<wbr>frequency</div>
<div><br>
</div>
<div>it reports a MAF of 0.495807</div>
<div><br>
</div>
<div>but when I get each allele <br>
<br>
</div>
<div>
<div>my @alleles = @{$vf->get_all_Alleles};</div>
</div>
<div><br>
</div>
<div>and I cycle through them, their frequency is undef</div>
<div><br>
</div>
<div>
<div>foreach my $a (@alleles){</div>
<div><span style="white-space:pre-wrap"> </span>my $freq =
$a->frequency();</div>
<div><span style="white-space:pre-wrap"> </span>print <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span> </span>$freq;</span></div>
<div>}</div>
</div>
<div><br>
</div>
<div>How do I retrieve the frequency calculated for each
individual alleles on the variation?</div>
<div><br>
</div>
<div>Many thanks</div>
<div><br>
</div>
<div>Duarte<br>
</div>
<div>
</div>
</div>
<br>
<fieldset class="m_-6538029127110316456mimeAttachmentHeader"></fieldset>
<br>
</div></div><pre>______________________________<wbr>_________________
Dev mailing list <a class="m_-6538029127110316456moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="m_-6538029127110316456moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/<wbr>mailman/listinfo/dev</a>
Ensembl Blog: <a class="m_-6538029127110316456moz-txt-link-freetext" href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</div>
<br>______________________________<wbr>_________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/<wbr>mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>