<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello everyone,<div>I have been trying to extract conservation score for single base pair using compare API and following code block. </div><div>I was wondering if anyone confirm if <span style="color: rgb(81, 87, 189); font-family: Monaco; font-size: 11px; ">MethodLinkSpeciesSet </span>is the right way to extract conservation score. </div><div><br></div><div>Is there any way to double check these scores via Biomart. ? </div><div><br></div><div>Thanks,</div><div>Mamun</div><div>==================================================================================================================================</div><div><br></div><div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(81, 87, 189); "><span style="color: #000000">my </span><span style="color: #4f7272">$</span><span style="color: #000000">registry = </span>"Bio::EnsEMBL::Registry"<span style="color: #000000">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span style="color: #4f7272">$</span>registry->load_registry_from_db(</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(81, 87, 189); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #b05691">-</span><span style="color: #000000">host =</span><span style="color: #b05691">></span><span style="color: #000000"> </span>"<a href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a>"<span style="color: #000000">,</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(81, 87, 189); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span><span style="color: #b05691">-</span><span style="color: #000000">user =</span><span style="color: #b05691">></span><span style="color: #000000"> </span>"anonymous"<span style="color: #000000">,</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span><span style="color: #b05691">-</span>port =<span style="color: #b05691">></span> <span style="color: #011892">5306</span> );</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; ">my <span style="color: #4f7272">$</span>mlss_adaptor = <span style="color: #4f7272">$</span>registry->get_adaptor(<span style="color: #5157bd">"Multi"</span>, <span style="color: #5157bd">"compara"</span>, <span style="color: #5157bd">"MethodLinkSpeciesSet"</span>);</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; ">my <span style="color: #4f7272">$</span>mlss = <span style="color: #4f7272">$</span>mlss_adaptor->fetch_by_method_link_type_species_set_name(<span style="color: #5157bd">"GERP_CONSERVATION_SCORE"</span>, <span style="color: #5157bd">"mammals"</span>);</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 143, 98); ">#create slice</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; ">my <span style="color: #4f7272">$</span>slice_adaptor = <span style="color: #4f7272">$</span>registry->get_adaptor(<span style="color: #4f7272">$</span>species, <span style="color: #5157bd">'core'</span>, <span style="color: #5157bd">'Slice'</span>);</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; ">my <span style="color: #4f7272">$</span>slice = <span style="color: #4f7272">$</span>slice_adaptor->fetch_by_region(<span style="color: #5157bd">'toplevel'</span>, <span style="color: #4f7272">$</span>seq_region, <span style="color: #4f7272">$</span>seq_region_start, <span style="color: #4f7272">$</span>seq_region_end);</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 143, 98); ">#get conservation score adaptor</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; ">my <span style="color: #4f7272">$</span>cs_adaptor = <span style="color: #4f7272">$</span>registry->get_adaptor(<span style="color: #5157bd">"Multi"</span>, <span style="color: #5157bd">'compara'</span>, <span style="color: #5157bd">'ConservationScore'</span>);<span class="Apple-tab-span" style="white-space:pre"> </span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; ">my <span style="color: #4f7272">$</span>display_size = <span style="color: #4f7272">$</span>slice->end <span style="color: #b05691">-</span> <span style="color: #4f7272">$</span>slice->start <span style="color: #b05691">+</span> <span style="color: #011892">1</span>; </div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(78, 143, 98); ">## Get score array </div><div style="margin: 0px; font-size: 11px; font-family: Monaco; ">my <span style="color: #4f7272">$</span>scores = <span style="color: #4f7272">$</span>cs_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice(<span style="color: #4f7272">$</span>method_linked_species_Set, <span style="color: #4f7272">$</span>slice, <span style="color: #4f7272">$</span>display_size);</div></div><div><br></div><div>==================================================================================================================================</div></body></html>