<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; "><div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;">Hello, </div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div bgcolor="#FFFFFF" text="#000000"><div class="moz-forward-container"><div><br></div><div>I submitted the inquiry (below) to Miguel Pignatelli and he suggested that I forward the question to you. Upon looking at our error messages, he suspects we're having an issue connecting with the database or else it may be a general API issue. I've attached the script that we are attempting to use.</div><div><br></div><div>Thank you for your assistance -</div><div>Mike Montague</div><table class="moz-email-headers-table" border="0" cellpadding="0" cellspacing="0" style="position: static; z-index: auto; "><tbody><tr><td>____________</td></tr></tbody></table><div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br>Michael J. Montague, Ph.D.<br>Post-Doctoral Research Associate<br>The Genome Institute, Washington University School of Medicine<br>4444 Forest Park Avenue, Campus Box 8501<br>St. Louis, MO 63108<br>T. 718.809.4093<br></div><div><br></div></span></span></div></div></div><div>Hello Miguel,</div></div><div><br></div><div>With the release of Cafe.v3, we intend to use your script to obtain data from Ensembl for input into Cafe. We are interested in gene expansion outliers for the cat lineage (ID 9685) relative to Carnivora (ID 33554).</div><div><br></div><div>We made a copy of get_expansions.pl (attached below) and added line 10 to call on the Ensembl API here at the Genome Institute. It seems to load fine (line 28).</div><div><br></div><blockquote style="margin: 0px 0px 0px 40px; border: none; padding: 0px; ">L10: <span style="font-family: Menlo; font-size: 11px; color: rgb(187, 44, 162); ">use</span><span style="font-family: Menlo; font-size: 11px; "> lib </span><span style="color: rgb(209, 47, 27); font-family: Menlo; font-size: 11px; ">'/gscmnt/sata206/techd/ensembl_api/v70/ensembl/modules'</span><span style="font-family: Menlo; font-size: 11px; ">;</span></blockquote><br>The human adapter loads fine (line 33) but we're wondering what it has to do with cat?</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br></div></div></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span style="font-family: Menlo; font-size: 11px; ">L33: </span><span style="font-family: Menlo; font-size: 11px; color: rgb(187, 44, 162); ">my </span><span style="font-family: Menlo; font-size: 11px; ">$human_gene_adaptor = $reg->get_adaptor(</span><span style="font-family: Menlo; font-size: 11px; color: rgb(209, 47, 27); ">"Homo sapiens"</span><span style="font-family: Menlo; font-size: 11px; ">, </span><span style="font-family: Menlo; font-size: 11px; color: rgb(209, 47, 27); ">"core"</span><span style="font-family: Menlo; font-size: 11px; ">, </span><span style="font-family: Menlo; font-size: 11px; color: rgb(209, 47, 27); ">"Gene"</span><span style="font-family: Menlo; font-size: 11px; ">);</span></div></div></div></blockquote><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">The problem is with line 35, which returns nothing so it crashes in lines 38, 39 and 40.</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><blockquote style="margin: 0px 0px 0px 40px; border: none; padding: 0px; "><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin: 0px; font-size: 11px; font-family: Menlo; "><div style="margin: 0px; ">L35: <span style="color: rgb(187, 44, 162); ">my</span> $comparaDBA = Bio::EnsEMBL::Registry->get_DBAdaptor(<span style="color: rgb(209, 47, 27); ">'Multi'</span>, <span style="color: rgb(209, 47, 27); ">'compara'</span>);</div><div style="margin: 0px; "><div style="margin: 0px; ">L38: <span style="color: #bb2ca2">my</span> $gene_member_adaptor = $comparaDBA->get_GeneMemberAdaptor;</div></div></div></div></div></blockquote><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "></div></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br></div>Error:<br><blockquote style="margin: 0px 0px 0px 40px; border: none; padding: 0px; "><div><br></div><div>test_get_expansions.pl 9685 > cat_expansions.txt</div><div><br></div><div>Can't call method "get_GeneMemberAdaptor" on an undefined value at /gscuser/mmontagu/bin/test_get_expansions.pl line 38.</div><div>cafe_output$ </div><div><br></div></blockquote>or<div><br></div><blockquote style="margin: 0px 0px 0px 40px; border: none; padding: 0px; "><div>perl ~/bin/test_get_expansions.pl 9685 > cat_expansions.txt</div><div><br></div><div>DBD::mysql::db selectall_arrayref failed: Can't read dir of '.' (errno: 24) at /gscmnt/sata206/techd/ensembl_api/v70/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1600.</div><div><br></div><div>-------------------- WARNING ----------------------</div><div>MSG: Homo sapiens is not a valid species name (check DB and API version)</div><div>FILE: Bio/EnsEMBL/Registry.pm LINE: 1187</div><div>CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 972</div><div>Date (localtime) = Wed Jul 24 14:14:00 2013</div><div>Ensembl API version = 70</div><div>---------------------------------------------------</div><div><br></div><div>-------------------- EXCEPTION --------------------</div><div>MSG: Can not find internal name for species 'Homo sapiens'</div><div>STACK Bio::EnsEMBL::Registry::get_adaptor /gscmnt/sata206/techd/ensembl_api/v70/ensembl/modules/Bio/EnsEMBL/Registry.pm:974</div><div>STACK toplevel /gscuser/mmontagu/bin/test_get_expansions.pl:33</div><div>Date (localtime) = Wed Jul 24 14:14:00 2013</div><div>Ensembl API version = 70</div><div>---------------------------------------------------</div></blockquote><div><br>Mainly, we were wondering if the inputs for lines 33 and 35 are correct for cat? </div></div></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div style="margin: 0px; font-size: 11px; font-family: Menlo; "><br></div></div></div></div></blockquote><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Or alternatively, are we calling on an incorrect version of the API? Or, perhaps were overlooking something else altogether?<div><br></div><div></div></div></div></div></body></html>