<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="">Hi,<div class=""><br class=""></div><div class="">I am using API version 88.</div><div class=""><br class=""></div><div class="">Compared to version 86, ensembl-funcgen/modules/Bio/EnsEMBL/Funcgen/DBSQL/ no longer contains SegmentationFeatureAdaptor.pm.</div><div class=""><br class=""></div><div class="">This is causing the API to complain/fail when I perform</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span class="sh_keyword" style="font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 1em; background-color: rgb(250, 250, 250); color: rgb(0, 102, 153); font-weight: bold;">my</span><span style="color: rgb(51, 51, 51); font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 13px; background-color: rgb(250, 250, 250);" class=""> </span><span class="sh_variable" style="font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 1em; background-color: rgb(250, 250, 250); color: rgb(170, 119, 0) !important;">$annotated_features</span><span style="color: rgb(51, 51, 51); font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 13px; background-color: rgb(250, 250, 250);" class=""> </span><span class="sh_symbol" style="font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 1em; background-color: rgb(250, 250, 250); color: rgb(127, 0, 85);">=</span><span style="color: rgb(51, 51, 51); font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 13px; background-color: rgb(250, 250, 250);" class=""> </span><span class="sh_variable" style="font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 1em; background-color: rgb(250, 250, 250); color: rgb(170, 119, 0) !important;">$current_annotated_feature_set</span><span class="sh_symbol" style="font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 1em; background-color: rgb(250, 250, 250); color: rgb(127, 0, 85);">-></span><span class="sh_function" style="font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 1em; background-color: rgb(250, 250, 250); color: rgb(255, 20, 147);">get_Features_by_Slice</span><span class="sh_symbol" style="font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 1em; background-color: rgb(250, 250, 250); color: rgb(127, 0, 85);">(</span><span class="sh_variable" style="font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 1em; background-color: rgb(250, 250, 250); color: rgb(170, 119, 0) !important;">$slice</span><span class="sh_symbol" style="font-family: Consolas, 'Bitstream Vera Sans Mono', 'Courier New', Courier, monospace; font-size: 1em; background-color: rgb(250, 250, 250); color: rgb(127, 0, 85);">);</span></div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>(as described on <a href="http://www.ensembl.org/info/docs/api/funcgen/regulation_tutorial.html" class="">http://www.ensembl.org/info/docs/api/funcgen/regulation_tutorial.html</a>)</div><div class=""><br class=""></div><div class="">The error is shown below.</div><div class=""><br class=""></div><div class="">Is there a revised call that should be used for version 88? Is there something else I’m doing wrong?</div><div class=""><br class=""></div><div class="">Thanks for any help.</div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""></div><div class="">Andrew<span class="Apple-tab-span" style="white-space:pre"> </span></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div class="">-------------------- WARNING ----------------------</div><div class="">MSG: 'Bio::EnsEMBL::Funcgen::DBSQL::SegmentationFeatureAdaptor' cannot be found.</div><div class="">Exception Can't locate Bio/EnsEMBL/Funcgen/DBSQL/SegmentationFeatureAdaptor.pm in @INC (you may need to install the Bio::EnsEMBL::Funcgen::DBSQL::SegmentationFeatureAdaptor module) (@INC contains: /home/andrew/gte/src_88/bioperl-live /home/andrew/gte/src_88/ensembl/modules /home/andrew/gte/src_88/ensembl-io/modules /home/andrew/gte/src_88/ensembl-compara/modules /home/andrew/gte/src_88/ensembl-variation/modules /home/andrew/gte/src_88/ensembl-funcgen/modules /home/andrew/gte/src_88/lib/perl/5.18.2/ /home/andrew/gte/src_88/share/perl/5.18.2/ /home/andrew/gte/src_88/lib/perl5/x86_64-linux-gnu-thread-multi/ /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at (eval 493) line 2.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">FILE: Bio/EnsEMBL/Registry.pm LINE: 1174</div><div class="">CALLED BY: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 989</div><div class="">Date (localtime) = Tue Apr 25 12:45:25 2017</div><div class="">Ensembl API version = 88</div><div class="">---------------------------------------------------</div><div class=""><br class=""></div><div class="">-------------------- WARNING ----------------------</div><div class="">MSG: Could not find SegmentationFeature adaptor in the registry for homo_sapiens funcgen</div><div class=""><br class=""></div><div class="">FILE: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 992</div><div class="">CALLED BY: EnsEMBL/Funcgen/FeatureSet.pm LINE: 256</div><div class="">Date (localtime) = Tue Apr 25 12:45:25 2017</div><div class="">Ensembl API version = 88</div><div class="">---------------------------------------------------</div><div class=""><br class=""></div><div class="">-------------------- EXCEPTION --------------------</div><div class="">MSG: Could not get adaptor SegmentationFeature for homo_sapiens funcgen</div><div class=""><br class=""></div><div class="">STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD /home/andrew/gte/src_88/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:996</div><div class="">STACK Bio::EnsEMBL::Funcgen::FeatureSet::get_FeatureAdaptor /home/andrew/gte/src_88/ensembl-funcgen/modules/Bio/EnsEMBL/Funcgen/FeatureSet.pm:256</div><div class="">STACK Bio::EnsEMBL::Funcgen::FeatureSet::get_Features_by_Slice /home/andrew/gte/src_88/ensembl-funcgen/modules/Bio/EnsEMBL/Funcgen/FeatureSet.pm:280</div></div><div class="">Etc.</div><div class=""><br class=""></div><div class=""><br class=""></div></body></html>