<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi, </div><div class=""><br class=""></div><div class="">I am trying to get the EPO mammals coordinates of this regions in hg38 chr1:1287672-1287836</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div class=""><div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: "Andale Mono"; color: rgb(39, 214, 16); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">The API version used is 111</span></div><div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: "Andale Mono"; color: rgb(39, 214, 16); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">chr1<span class="Apple-tab-span" style="white-space: pre;"> </span>1287672<span class="Apple-tab-span" style="white-space: pre;"> </span>1287836<span class="Apple-tab-span" style="white-space: pre;"> </span>ENST00000325425.12_cds_7_0_chr1_1287673_f</span></div><div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: "Andale Mono"; color: rgb(39, 214, 16); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>$VAR1 = undef;</span></div><div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: "Andale Mono"; color: rgb(39, 214, 16); background-color: rgba(0, 0, 0, 0.9);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">Can't call method "seq_region_name" on an undefined value at wgaEnsemblEPO.pl line 103, <FH> line 1.</span></div></div><div class=""><br class=""></div><div class=""><br class=""></div></div><div class=""><br class=""></div><div class="">When using the Ensembl compara API, following the <a href="https://www.ensembl.org/info/docs/api/compara/compara_tutorial.html" class="">https://www.ensembl.org/info/docs/api/compara/compara_tutorial.html</a> as example, I fetch the GAB from the human query slice, then restricting the $gab, then I get undef when trying to get the Slice from the genomic align.</div><div class=""><br class=""></div><div class="">The API doc for get_Slice says :</div><div class=""><a href="https://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1Locus.html#afbe22a62da57178280ca67b06eda9d5c" class="">https://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1Locus.html#afbe22a62da57178280ca67b06eda9d5c</a> </div><div class=""><pre style="font-family: "Courier New", Courier, monospace; margin-top: 0px; margin-bottom: 16px; line-height: 16px; font-variant-ligatures: normal; orphans: 2; widows: 2; text-decoration-thickness: initial;" class=""> Exceptions : return -undef- if slice cannot be created (this is likely to
happen if the <a class="elRef" doxygen="ensembl.tag:../core-api//" href="https://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Registry.html" style="color: rgb(61, 87, 140); text-decoration: none;">Registry</a> is misconfigured)</pre><div class="">Well, I am using the classic public registry in my script :</div></div><div class=""><div class="">$registry->load_registry_from_db(</div><div class=""> -host => '<a href="http://ensembldb.ensembl.org" class="">ensembldb.ensembl.org</a>',</div><div class=""> -user => 'anonymous'</div><div class="">);</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Is there something else I am missing somewhere ?</div><div class="">I am not sending the script here, as my email will get blocked like last time. </div><div class=""><br class=""></div><div class="">Thanks for the feedback, </div><div class=""><br class=""></div><div class="">Cheers, </div><div class=""><br class=""></div><div class="">Ben</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">
<meta charset="UTF-8" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">--<br class="">Benoît Ballester, PhD<br class="">Aix Marseille Univ, INSERM, TAGC, Marseille, France</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class="">+33 4 91 82 87 28<br class="">(1st) <a href="mailto:benoit.ballester@inserm.fr" class="">benoit.ballester@inserm.fr</a><br class="">(2nd) <a href="mailto:benoit.ballester@univ-amu.fr" class="">benoit.ballester@univ-amu.fr</a> </div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">ReMap2022:<span class="Apple-converted-space"> </span><a href="http://remap.univ-amu.fr/" class="">http://remap.univ-amu.fr/</a><br class=""><br class=""></div></div></div></div></div>
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