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<div class="">Dear Ensembl team, </div>
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<div class="">When I do the following call: my @vf_pops = @{ $vf->get_all_LD_Populations() }; I get this error:</div>
<div class=""><font face="Courier New" class="">DBD::mysql::st execute failed: Unknown column 'ip.population_id' in 'field list' at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeature.pm line 1429, <> line 1.DBD::mysql::st execute
failed: Unknown column 'ip.population_id' in 'field list' at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeature.pm line 1429, <> line 1.</font></div>
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<div class="">Here’s the full script:</div>
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<div class=""><font face="Courier New" class="">use strict;</font></div>
<div class=""><font face="Courier New" class="">use warnings;</font></div>
<div class=""><font face="Courier New" class="">use Bio::EnsEMBL::Registry;</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">my $start_run = time();</font></div>
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</font></div>
<div class=""><font face="Courier New" class="">my $registry = 'Bio::EnsEMBL::Registry';</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">$registry->load_registry_from_db(</font></div>
<div class=""><font face="Courier New" class=""> -host => '<a href="http://ensembldb.ensembl.org" class="">ensembldb.ensembl.org</a>',</font></div>
<div class=""><font face="Courier New" class=""> -user => 'anonymous'</font></div>
<div class=""><font face="Courier New" class="">);</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="">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="">my $population_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'population');</font></div>
<div class=""><font face="Courier New" class="">$variation_adaptor->db->use_vcf(1); # To get 1000G phase 3 data also</font></div>
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</font></div>
<div class=""><font face="Courier New" class="">my $ld_populations = $population_adaptor->fetch_all_LD_Populations();</font></div>
<div class=""><font face="Courier New" class="">foreach my $ld_population (@$ld_populations) {</font></div>
<div class=""><font face="Courier New" class=""> print $ld_population->name, "\n";</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=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">my $variation_name = 'rs157580';</font></div>
<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 @vfs = @{ $variation->get_all_VariationFeatures() };</font></div>
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</font></div>
<div class=""><font face="Courier New" class="">foreach my $vf (@vfs) {</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""> print $vf->name, "\n";</font></div>
<div class=""><font face="Courier New" class=""> my @vf_pops = @{ $vf->get_all_LD_Populations() };</font></div>
<div class=""><font face="Courier New" class=""> foreach my $ld_population (@$ld_populations) {</font></div>
<div class=""><font face="Courier New" class=""> print $ld_population->name, "\n";</font></div>
<div class=""><font face="Courier New" class=""> my $ldfc = $ldfc_adaptor->fetch_by_VariationFeature($vf, $ld_population);</font></div>
<div class=""><font face="Courier New" class=""> foreach my $ld_hash (@{$ldfc->get_all_ld_values}) {</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>my $d_prime = $ld_hash->{d_prime};</font></div>
<div class=""><font face="Courier New" class=""> <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>my $variation_name1 = $ld_hash->{variation1}->variation_name;</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>my $variation_name2 = $ld_hash->{variation2}->variation_name;</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>print "$variation_name1 $variation_name2 d_prime=$d_prime r2=$r2\n";</font></div>
<div class=""><font face="Courier New" class=""> }</font></div>
<div class=""><font face="Courier New" class=""> }</font></div>
<div class=""><font face="Courier New" class="">}</font></div>
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</font></div>
<div class=""><font face="Courier New" class="">my $end_run = time();</font></div>
<div class=""><font face="Courier New" class="">my $run_time = $end_run - $start_run;</font></div>
<div class=""><font face="Courier New" class="">print "Job took $run_time seconds\n";</font></div>
</div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class="">If I remove the call to get_all_LD_Populations, the script runs fine again. Do you have any idea on what I am doing wrong? Could it be a bug in the code, like the error I reported yesterday?</div>
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</div>
<div class="">Also, I have visited a lot of forums where LD calculation is discussed. Many users ask for a database one can query to find LD between SNPs, and genomic LD tracks, but all such services are only available on HapMap data. Do you know why there
is none for all SNPs and LD produced up until 1000G phase 3? What kind of restrictions is there that makes it easier to compute LD on the fly, for instance? Space maybe? </div>
<div class="">(If there actually does exist databases/tracks of LD, I would be happy to know!)</div>
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<div class="">Best,</div>
<div class="">Johanne</div>
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