<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Johanne,<div class=""><br class=""></div><div class="">I replaced the method that was causing the warning. Please refresh your checkout and the message should go away.</div><div class=""><br class=""></div><div class="">The variants for which you cannot compute LD have no reported alternative alleles for the selected population. This means for the given population CEU only the reference allele has been seen in the set of individuals. For example rs116998215: <a href="http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=15:54342925-54343925;v=rs116998215;vdb=variation;vf=23224014" class="">http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=15:54342925-54343925;v=rs116998215;vdb=variation;vf=23224014</a></div><div class=""><br class=""></div><div class="">If you change the population to any of the East Asian populations you could compute LD for the variant.</div><div class=""><br class=""></div><div class="">HTH,</div><div class="">Anja</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 16 Mar 2016, at 07:44, Johanne Håøy Horn <<a href="mailto:johannhh@ifi.uio.no" class="">johannhh@ifi.uio.no</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Dear Ensembl dev team,
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</div>
<div class="">If I use the script below, I get this warning: </div>
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<div class=""><font face="Courier New" class="">Deprecated method call in file /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/LDFeatureContainer.pm line 505.</font></div>
<div class=""><font face="Courier New" class="">Method Bio::EnsEMBL::Slice::get_all_VariationFeatures is deprecated.</font></div>
<div class=""><font face="Courier New" class="">get_all_VariationFeatures is deprecated and will be removed in e88. Please use Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_by_Slice_SO_terms instead.</font></div>
<div class=""><font face="Courier New" class="">Ensembl API version = 84</font></div>
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</div>
<div class="">SCRIPT, where $variation_name is in {rs145155926, rs111309268, rs150384273, rs137966595, rs7675152, rs116998215, rs184066894, rs149535525, rs186235844}:</div>
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</div>
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<div class=""><font face="Courier New" class="">my $variation_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'variation');</font></div>
<div class=""><font face="Courier New" class="">my $ldfc_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'ldfeaturecontainer');</font></div>
<div class=""><font face="Courier New" class="">$ldfc_adaptor->max_snp_distance(100_000);</font></div>
<div class=""><font face="Courier New" class="">my $pop_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'population');</font></div>
<div class=""><font face="Courier New" class="">$variation_adaptor->db->use_vcf(1);</font></div>
</div>
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</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class="">
<div class=""><font face="Courier New" class="">my $variation = $variation_adaptor->fetch_by_name($variation_name);</font></div>
<div class=""><font face="Courier New" class="">my @var_features;</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">if ($variation) {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>@var_features = @{ $variation->get_all_VariationFeatures() };</font></div>
<div class=""><font face="Courier New" class="">} else {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>print 'failing variation name: ', $variation_name, "\n";</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>next;</font></div>
<div class=""><font face="Courier New" class="">}</font></div>
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</font></div>
<div class=""><font face="Courier New" class="">foreach my $vf (@var_features) {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>if ($vf->slice->is_reference) {</font></div>
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</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $rsid = $vf->name;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>print $rsid, "\n";</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $start = $vf->start;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $region = $vf->seq_region_name;</font></div>
<div class=""><span class="Apple-tab-span" style="white-space: pre;"><font face="Courier New" class=""></font></span></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $ldfc = $ldfc_adaptor->fetch_by_VariationFeature($vf, $ld_population);</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my @ld_values = @{ $ldfc->get_all_ld_values() };</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span> <span class="Apple-tab-span" style="white-space:pre"> </span>foreach my $ld_hash (@ld_values) {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space: pre;">
</span>my $r2 = $ld_hash->{r2};</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $variation_name1 = $ld_hash->{variation_name1};</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $variation_name2 = $ld_hash->{variation_name2};</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $pos1 = $ld_hash->{variation1}->seq_region_name();</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $pos2 = $ld_hash->{variation2}->seq_region_name();</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $start1 = $ld_hash->{variation1}->start;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>my $start2 = $ld_hash->{variation2}->start;</font></div>
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</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>if ($variation_name1 eq $rsid) {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>print OUT "$pos2\t$start2\t$start2\t$variation_name2\t$rsid\t$r2\n";</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>} else {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>print OUT "$pos1\t$start1\t$start1\t$variation_name1\t$rsid\t$r2\n";</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>}</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> }</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>} else {</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>print "Failed to get, not a reference allele: ", $vf->name;</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>}</font></div>
<div class=""><font face="Courier New" class="">}</font></div>
</div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class="">The issue seems to be related to get_all_ld_values(). If I use get_all_ld_values(1), no warning occurs. I also tried get_all_ld_values(0), but with the same warning of deprecated method call appeared.</div>
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</div>
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<div class="">I am trying to expand variations with their variations in LD. However, quite a few rsids seem to have no LD. A list of these is included in this email. Could you help me with why they get no LD variations? Is it because they do not have any? Or
is it a technical limitation that cause this?</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Johanne Håøy Horn</div>
<div class=""></div>
</div>
<span id="cid:1522A7015E356B41A1C3E3CD48D25A34@mail.uio.no"><unaccounted_old.txt></span><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""></div></div>_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""></div></body></html>