<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=""><div><blockquote type="cite" class=""><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><br class="">
</div>
<div class="">When you say 100 MB, do you mean 100KB? As in 100,000 bases? </div></div></div></blockquote><div><br class=""></div><div>Yes you are correct I meant 100KB. I’m very sorry for the confusion.</div><div><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class="">I noticed that with the script I have used so far, the longest physical distance between a SNP and one of its LD variants, is 100K. Is this because with the slice, my script will only find SNPs in LD 100K away in either direction? So theoretically,
there can be other LD variants further away from the SNP I am expanding?</div></div></div></blockquote><div><br class=""></div><div>Yes, there could be variants that are further than 100KB away from your given variant and still in LD with the same. You could increase the max SNP distance which would however also increase the computation time. I need to check the literature for information on the distance at which LD decreases (variants are less likely to be in LD).</div><div><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class=""><br class="">
</div>
<div class="">I have mistakenly thought that the default of getting ld SNPs used the entire chromosome as slice. Is this possible (especially given time considerations)? Or is it not any point in doing it, as LD only happen within 100K-blocks anyway?</div></div></div></blockquote><div><br class=""></div><div>It is not possible to pass an entire chromosome for computing LD. I would recommend a slice of length 300 to 500KB. However, 500KB could be almost too large for regions with many variants.</div><div><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Johanne</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">11. mar. 2016 kl. 12.50 skrev Anja Thormann <<a href="mailto:anja@ebi.ac.uk" class="">anja@ebi.ac.uk</a>>:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class="">Dear Johanne,</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">we have released ensembl 84 and you can now make use of our improvements for LD data computation. Just as a reminder, you would like to retrieve all variants that are in LD with a given variant. Depending on how many variants you have for which
you want to compute LD data there are two ways:</div>
<div class=""><br class="">
</div>
<div class="">- If your input list is small (< 1000) you can use fetch_by_VariationFeature($vf, $population). The default setting will create a slice (100MB + variant length + 100MB) expanding the input variant. The API computes LD values between the variant
of interest and all variants surrounding the variant and not further away than 100MB. You could speed this up by decreasing the distance to 50MB:</div>
<div class=""><br class="">
</div>
<div class="">my $ldfc_adaptor = $registry->get_adaptor('homo_sapiens', 'variation', 'ldfeaturecontainer');</div>
<div class="">$ldfc_adaptor->max_snp_distance(50_000);</div>
<div class="">my $ldfc = $ldfc_adaptor->fetch_by_VariationFeature($vf, $ld_population);</div>
<div class=""><br class="">
</div>
<div class="">- If your list of input variants is much longer I would recommend using fetch_by_Slice. You could create overlapping slice objects that cover your chromosomal region of interest and then the API computes all pairwise LD values for all variants
in the region. You need to filter the results for your variants of interest. This requires a little bit more work because you have to choose the correct overlap size to make sure you allow for the same max distance for which you want to compute LD data for
each of your input variants.</div>
<div class=""><br class="">
</div>
<div class="">my $slice_adaptor = $registry->get_adaptor('homo_sapiens', 'core', 'slice');</div>
<div class="">my $chr = 6;</div>
<div class="">my $start = 32_102_292;</div>
<div class="">my $end = 32_402_292;</div>
<div class="">my $slice = $slice_adaptor->fetch_by_region('chromosome', $chr, $start, $end);</div>
<div class="">my $ldfc = $ldfc_adaptor->fetch_by_Slice($slice, $ld_population);</div>
<div class=""><br class="">
</div>
<div class="">The second approach should be faster because it can summarise some of the computations that have do be done: If your input variants are in close proximity you can compute all their LD values in one computation by providing the slice that covers
all of them instead of creating a region for each of them individually and then compute LD values.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Independent of the two approaches you can further speed up your computation: When asking for all ld values pass 1 as an argument. This will prevent the method (get_all_ld_values) from creating variation feature objects and instead will only return
the variant names and their LD values:</div>
<div class=""><br class="">
</div>
<div class="">my $ldfc = $ldfc_adaptor->fetch_by_VariationFeature($vf, $ld_population);</div>
<div class="">my $ld_values = $ldfc->get_all_ld_values(1);</div>
<div class="">foreach my $ld_hash (@$ld_values) {</div>
<div class=""> my $r2 = $ld_hash->{r2};</div>
<div class=""> my $d_prime = $ld_hash->{d_prime};</div>
<div class=""> my $variation_name1 = $ld_hash->{variation_name1};</div>
<div class=""> my $variation_name2 = $ld_hash->{variation_name2};</div>
<div class=""><br class="">
</div>
<div class="">}</div>
<div class=""><br class="">
</div>
<div class="">Don't forget to switch to the new release/84 branches for all ensembl repos.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Anja</div>
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 7 Mar 2016, at 20:02, Anja Thormann <<a href="mailto:anja@ebi.ac.uk" class="">anja@ebi.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class="">Dear Johanne,</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">I was able to reproduce the lost connection error using the following list of 31 variants (concatenating all your input files):</div>
<div class="">rs3117098</div>
<div class="">rs9268516</div>
<div class="">rs3129890</div>
<div class="">rs9272346</div>
<div class="">rs9273349</div>
<div class="">rs7775228</div>
<div class="">rs9275698</div>
<div class="">rs148203517</div>
<div class="">rs3853601</div>
<div class="">rs41268896</div>
<div class="">rs12153855</div>
<div class="">rs176095</div>
<div class="">rs9469099</div>
<div class="">rs4722404</div>
<div class="">rs7000782</div>
<div class="">rs7815944</div>
<div class="">rs549182</div>
<div class="">rs9268480</div>
<div class="">rs9268853</div>
<div class="">rs9268877</div>
<div class="">rs9268923</div>
<div class="">rs2395185</div>
<div class="">rs9271366</div>
<div class="">rs6927022</div>
<div class="">rs1063355</div>
<div class="">rs943072</div>
<div class="">rs6911490</div>
<div class="">rs2858829</div>
<div class="">rs6920220</div>
<div class="">rs798502</div>
<div class="">rs11764116</div>
<div class=""><br class="">
</div>
<div class="">The chromosome names with a different format are called alternate loci. They are stand-alone, accessioned sequences. Several human chromosomal regions exhibit sufficient variability to prevent adequate representation by a single sequence. To address
this, the GRCh38 assembly provides alternate sequence for selected variant regions through the inclusion of alternate loci scaffolds. You can read more about this here:</div>
<div class=""><a href="http://genomeref.blogspot.co.uk/2013/12/announcing-grch38.html" class="">http://genomeref.blogspot.co.uk/2013/12/announcing-grch38.html</a></div>
<div class=""><br class="">
</div>
<div class="">One example is variant s3129890. It maps to the reference sequence and to 6 alternate loci:</div>
<div class=""><a href="http://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=CHR_HSCHR6_8_CTG1:32392790-32393790;v=rs3129890;vdb=variation;vf=146716554" class="">http://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=CHR_HSCHR6_8_CTG1:32392790-32393790;v=rs3129890;vdb=variation;vf=146716554</a></div>
<div class=""><br class="">
</div>
<div class="">The error seems to be caused by variants mapping alternate loci. Until I have figured out what is going on it would be good if you could exclude them from your computations and just use the mappings to the reference sequence:</div>
<div class=""><br class="">
</div>
<div class="">foreach my $vf (@var_features) {</div>
<div class=""> next unless ($vf->slice->is_reference);</div>
<div class=""> ...</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I hope that helps for now. I will get back to you as soon as I have more information. I will also let you know how you can speed up your computation as soon as we release Ensembl 84.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Anja</div>
</div>
<div class=""><br class="">
</div>
<br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 6 Mar 2016, at 12:32, 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="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class="">Dear ensembl team,</div>
<div class=""><br class="">
</div>
<div class="">I have gotten quite some help from you previously with the variation api. I wish to expand variations to include the variants they are in LD with. My script works for the most part, but I am unable to run it on some of my rsID files. I have broken
the files into increasingly smaller parts, but the runs still fails. Could you help me with what I am doing wrong?</div>
<div class=""><br class="">
</div>
<div class="">Some of the issue seems to be connected to the chromosome the rsID is on. In many of the failing files of rsIDs, this is what the script produce (example taken from out_0_Asthma3.txt, full output file attached to this email): </div>
<div class="">6<span class="Apple-tab-span" style="white-space: pre;"> </span>rs3129969<span class="Apple-tab-span" style="white-space: pre;">
</span>32414832<span class="Apple-tab-span" style="white-space: pre;"> </span>r2=0.538176</div>
<div class="">6<span class="Apple-tab-span" style="white-space:pre"> </span>rs3763312<span class="Apple-tab-span" style="white-space:pre">
</span>32408571<span class="Apple-tab-span" style="white-space:pre"> </span>r2=0.074106</div>
<div class="">6<span class="Apple-tab-span" style="white-space:pre"> </span>rs553071835<span class="Apple-tab-span" style="white-space:pre">
</span>32487947<span class="Apple-tab-span" style="white-space:pre"> </span>r2=0.058328</div>
<div class="">CHR_HSCHR6_MHC_DBB_CTG1<span class="Apple-tab-span" style="white-space:pre">
</span>rs3129890<span class="Apple-tab-span" style="white-space:pre"> </span>32421214</div>
<div class="">CHR_HSCHR6_MHC_MANN_CTG1<span class="Apple-tab-span" style="white-space:pre">
</span>rs3129890<span class="Apple-tab-span" style="white-space:pre"> </span>32485127</div>
<div class="">CHR_HSCHR6_MHC_MCF_CTG1<span class="Apple-tab-span" style="white-space:pre">
</span>rs3129890<span class="Apple-tab-span" style="white-space:pre"> </span>32521873</div>
<div class="">CHR_HSCHR6_MHC_QBL_CTG1<span class="Apple-tab-span" style="white-space:pre">
</span>rs3129890<span class="Apple-tab-span" style="white-space:pre"> </span>32403957</div>
<div class="">CHR_HSCHR6_MHC_SSTO_CTG1<span class="Apple-tab-span" style="white-space:pre">
</span>rs3129890<span class="Apple-tab-span" style="white-space:pre"> </span>32453108</div>
<div class="">CHR_HSCHR6_8_CTG1<span class="Apple-tab-span" style="white-space:pre">
</span>rs3129890<span class="Apple-tab-span" style="white-space:pre"> </span>32393290</div>
<div class="">6<span class="Apple-tab-span" style="white-space:pre"> </span>rs9272346<span class="Apple-tab-span" style="white-space:pre">
</span>32636595</div>
<div class=""><br class="">
</div>
<div class="">In stead of getting a line of <chromosome> <rsID> <position> <r2> for the variation, the same SNP is repeated multiple times with a chromosome/region of a different format than what I get in the scripts that do not fail.</div>
<div class=""><br class="">
</div>
<div class="">I have attached some of the GWAS disease files of rsIDs I wish to expand, but which seem to produce errors, and some error printouts I have gotten is pasted below. Two output files belonging to the erroneous input files, with out_0_<inputfilename>
as filename is also attached. </div>
<div class=""><br class="">
</div>
<div class="">Is it something related to the rsIDs I am using? Are you able to run the script with these input files?</div>
<div class="">I noticed that longer files of rsIDs were more prone to fail, as the connection to the database was broken. Therefore, I have divided the files into multiple small files. For most of the GWAS data, this worked fine, and I get output files on the
format I want. But I am now left with 10-15 files of 10-20 rsIDs which fail with various error messages. I have tried calling my script with them multiple times, and as they fail consistently, I do not think it is my internet connection that is the problem. </div>
<div class=""><br class="">
</div>
<div class="">_START TERMINAL PRINT ERROR 1_</div>
<div class=""><font face="Courier New" class="">inputfile Asthma3.txt</font></div>
<div class=""><font face="Courier New" class="">outputfile out_0_Asthma3.txt</font></div>
<div class=""><font face="Courier New" class="">DBD::mysql::st execute failed: Lost connection to MySQL server during query at /Users/Johanne/src/ensembl/modules//Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line 482, <OUT> line 3739.</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">-------------------- EXCEPTION --------------------</font></div>
<div class=""><font face="Courier New" class="">MSG: Detected an error whilst executing SQL 'SELECT v.variation_id, v.name AS v_name, v.class_attrib_id AS v_class_attrib_id, v.source_id AS v_source_id, v.somatic AS v_somatic, v.flipped AS v_flipped, v.ancestral_allele
AS v_ancestral_allele, vs.moltype AS vs_moltype, vs.name AS vs_name, s2.name AS vs_source_name, v.minor_allele, v.minor_allele_freq, v.minor_allele_count, v.clinical_significance, v.evidence_attribs</font></div>
<div class=""><font face="Courier New" class="">FROM (( (variation v, source s1)</font></div>
<div class=""><font face="Courier New" class=""> LEFT JOIN variation_synonym vs ON v.variation_id = vs.variation_id )</font></div>
<div class=""><font face="Courier New" class=""> LEFT JOIN source s2 ON vs.source_id = s2.source_id )</font></div>
<div class=""><font face="Courier New" class=""> WHERE v.name = ? AND</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""> s1.source_id = v.source_id</font></div>
<div class=""><font face="Courier New" class=""> AND v.display = 1</font></div>
<div class=""><font face="Courier New" class="">': DBD::mysql::st execute failed: Lost connection to MySQL server during query at /Users/Johanne/src/ensembl/modules//Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line 482, <OUT> line 3739.</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch /Users/Johanne/src/ensembl/modules//Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:483</font></div>
<div class=""><font face="Courier New" class="">STACK Bio::EnsEMBL::Variation::DBSQL::VariationAdaptor::fetch_by_name /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationAdaptor.pm:497</font></div>
<div class=""><font face="Courier New" class="">STACK Bio::EnsEMBL::Variation::DBSQL::LDFeatureContainerAdaptor::_ld_calc /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/LDFeatureContainerAdaptor.pm:865</font></div>
<div class=""><font face="Courier New" class="">STACK Bio::EnsEMBL::Variation::DBSQL::LDFeatureContainerAdaptor::fetch_by_Slice /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/LDFeatureContainerAdaptor.pm:177</font></div>
<div class=""><font face="Courier New" class="">STACK Bio::EnsEMBL::Variation::DBSQL::LDFeatureContainerAdaptor::fetch_by_VariationFeature /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/LDFeatureContainerAdaptor.pm:246</font></div>
<div class=""><font face="Courier New" class="">STACK toplevel expandSNPs.pl:42</font></div>
<div class=""><font face="Courier New" class="">Date (localtime) = Sat Mar 5 18:03:25 2016</font></div>
<div class=""><font face="Courier New" class="">Ensembl API version = 83</font></div>
<div class=""><font face="Courier New" class="">---------------------------------------------------</font></div>
<div class=""><font face="Courier New" class="">rs3117098</font></div>
<div class=""><font face="Courier New" class="">rs3117098</font></div>
<div class=""><font face="Courier New" class="">rs3117098</font></div>
<div class=""><font face="Courier New" class="">rs3117098</font></div>
<div class=""><font face="Courier New" class="">rs3117098</font></div>
<div class=""><font face="Courier New" class="">rs9268516</font></div>
<div class=""><font face="Courier New" class="">rs9268516</font></div>
<div class=""><font face="Courier New" class="">rs9268516</font></div>
<div class=""><font face="Courier New" class="">rs9268516</font></div>
<div class=""><font face="Courier New" class="">rs9268516</font></div>
<div class=""><font face="Courier New" class="">rs9268516</font></div>
<div class=""><font face="Courier New" class="">rs9268516</font></div>
<div class=""><font face="Courier New" class="">rs9268516</font></div>
<div class=""><font face="Courier New" class="">rs9268516</font></div>
<div class=""><font face="Courier New" class="">rs3129890</font></div>
<div class=""><font face="Courier New" class="">rs3129890</font></div>
<div class=""><font face="Courier New" class="">rs3129890</font></div>
<div class=""><font face="Courier New" class="">rs3129890</font></div>
<div class=""><font face="Courier New" class="">rs3129890</font></div>
<div class=""><font face="Courier New" class="">rs3129890</font></div>
<div class=""><font face="Courier New" class="">rs3129890</font></div>
<div class=""><font face="Courier New" class="">rs9272346</font></div>
<div class="">_END TERMINAL PRINT ERROR 1_</div>
<div class=""><br class="">
</div>
<div class="">_START TERMINAL PRINT ERROR 2_</div>
<div class="">
<div class=""><font face="Courier New" class="">inputfile Atopicdermatitis3.txt</font></div>
<div class=""><font face="Courier New" class="">outputfile out_0_Atopicdermatitis3.txt</font></div>
<div class=""><font face="Courier New" class="">connect:</font><span style="font-family: 'Courier New';" class=""> Network is unreachable</span></div>
<div class=""><font face="Courier New" class="">rs1050654</font></div>
</div>
<div class="">_END TERMINAL PRINT ERROR 2_</div>
<div class=""><br class="">
</div>
<div class="">_START TERMINAL PRINT ERROR 3_</div>
<div class="">
<div class=""><font face="Courier New" class="">inputfile textfiles/Atopicdermatitis3.txt</font></div>
<div class=""><font face="Courier New" class="">outputfile textfiles/out_0_Atopicdermatitis3.txt</font></div>
<div class=""><font face="Courier New" class="">Can't call method "get_all_VariationFeatures" on an undefined value at expandSNPs.pl line 33, <IN> line 3.</font></div>
<div class=""><font face="Courier New" class="">rs1050654</font></div>
<div class=""><font face="Courier New" class="">rs3853601</font></div>
<div class=""><font face="Courier New" class="">rs3853601</font></div>
<div class=""><font face="Courier New" class="">rs3853601</font></div>
<div class=""><font face="Courier New" class="">rs3853601</font></div>
<div class=""><font face="Courier New" class="">rs3853601</font></div>
<div class=""><font face="Courier New" class="">rs3853601</font></div>
<div class=""><font face="Courier New" class="">rs3853601</font></div>
<div class=""><font face="Courier New" class="">rs3853601</font></div>
</div>
<div class="">_END TERMINAL PRINT ERROR 3_</div>
<div class=""><br class="">
</div>
<div class="">_START SCRIPT_</div>
<div class="">
<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 $inputfile = $ARGV[0];</font></div>
<div class=""><font face="Courier New" class="">my $outputfile = $ARGV[1];</font></div>
<div class=""><font face="Courier New" class="">my $r_limit = $ARGV[2];</font></div>
<div class=""><font face="Courier New" class="">my $start_run = time();</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">open (IN, "<$inputfile");</font></div>
<div class=""><font face="Courier New" class="">open (OUT, ">$outputfile");</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</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=""><span class="Apple-tab-span" style="white-space:pre"></span>-host => '<a href="http://ensembldb.ensembl.org/" class="">ensembldb.ensembl.org</a>',</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>-user => 'anonymous'</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=""># Connect to the databases:</font></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 $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 class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">my $ld_population = $pop_adaptor->fetch_by_name('1000GENOMES:phase_3:CEU');</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""># Loop through all SNPs available and find SNPs in LD</font></div>
<div class=""><font face="Courier New" class="">while(<IN>) {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>chomp;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $variation_name = $_;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my $variation = $variation_adaptor->fetch_by_name($variation_name);</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>my @var_features;</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>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=""><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 '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=""><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=""><span class="Apple-tab-span" style="white-space:pre"></span>foreach my $vf (@var_features) {</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 = $vf->seq_region_name;</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span>print OUT "$region\t$rsid\t$start\n";</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>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>my $r2 = $ld_hash->{r2};</font></div>
<div class=""><font face="Courier New" class=""> <span class="Apple-tab-span" style="white-space:pre">
</span>if ($r2 >= $r_limit) {</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->{variation1}->variation_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 $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> <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 = $ld_hash->{variation2}->start;</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>if ($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$variation_name2\t$start2\tr2=$r2\n";</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>} else {</font></div>
<div class=""><font face="Courier New" class=""><span class="Apple-tab-span" style="white-space:pre"></span> <span class="Apple-tab-span" style="white-space:pre">
</span>print OUT "$pos1\t$variation_name1\t$start1\tr2=$r2\n"; <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> <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>}</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 class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class=""><font face="Courier New" class="">print "done\n";</font></div>
<div class=""><font face="Courier New" class="">close OUT;</font></div>
<div class=""><font face="Courier New" class="">close IN;</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="">_END SCRIPT_</div>
<div class=""></div>
</div>
<span id="cid:CFFB1F71736F084E8092E90438D36AC0@mail.uio.no" class=""><Asthma3.txt></span>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class=""></div>
</div>
<span id="cid:467CBEF65605BA41809A2D2CFB5C9132@mail.uio.no" class=""><out_0_Asthma3.txt></span>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class=""></div>
</div>
<span id="cid:61A71FECA8CAB748A9023D31619E7822@mail.uio.no" class=""><Atopicdermatitis3.txt></span>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class=""></div>
</div>
<span id="cid:97C8324587AC0342B422386ABDA05D45@mail.uio.no" class=""><out_0_Atopicdermatitis3.txt></span>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class=""></div>
</div>
<span id="cid:C8C5920518ED5A49B249EDE354F72E34@mail.uio.no" class=""><Ulcerativecolitis3.txt></span>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class=""></div>
</div>
<span id="cid:3DC7574AE16E424EA029B59295719977@mail.uio.no" class=""><Ulcerativecolitis5.txt></span>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class=""></div>
</div>
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</blockquote>
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</blockquote>
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