<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="">Hi Simon, <div class=""><br class=""></div><div class=""><br class=""></div><div class="">I think your script looks good. </div><div class=""><br class=""></div><div class="">For new cow annotation, we used a different loading system and we store the top-level sequences (primary assembly) in seq_region, for this reason coord_system table has only one entry - the primary assembly.</div><div class=""><br class=""></div><div class="">+-----------------+------------+------------------+------------+------+--------------------------------+</div><div class="">| coord_system_id | species_id | name | version | rank | attrib |</div><div class="">+-----------------+------------+------------------+------------+------+--------------------------------+</div><div class="">| 1 | 1 | primary_assembly | ARS-UCD1.2 | 1 | default_version,sequence_level |</div><div class="">+-----------------+------------+------------------+------------+------+--------------------------------+</div><div class="">1 row in set (0.00 sec)</div><div class=""> </div><div class=""><br class=""></div><div class="">You can get all top-level sequences. For example, </div><div class="">Instead of: <span style="font-family: Calibri, sans-serif;" class="">my @chr_slices = @{$db_adapter -> get_adaptor('slice') -> fetch_all('chromosome',undef,0,1)}</span></div><div class="">Try: my @chr_slices = @{$db_adapter -> get_adaptor('slice') -> fetch_all('toplevel',undef,0,1)};</div><div class=""><br class=""></div><div class="">A way to get the chromosomes is via karyotype attribute. For example: </div><div class=""><div class=""><br class=""></div><div class="">my @karyo_slices = @{$db_adapter->get_SliceAdaptor->fetch_all_karyotype()};</div><div class=""><br class=""></div><div class="">foreach my $karyo (@karyo_slices) {</div><div class=""> print "FOUND " , $karyo->name, "\n"</div><div class="">}</div><div class=""><br class=""></div><div class="">warn "Found ", "kary " , scalar(@karyo_slices) , " and ", scalar @chr_slices, " chromosomes for ", $db_adapter->species(), "\n";</div></div><div class=""><br class=""></div><div class=""><div><br class=""></div><div><br class=""></div><div><br class=""></div><div>Please let me know if this works for you. </div><div><br class=""></div><div><br class=""></div><div>Thanks, </div><div>Kostas </div><div><br class=""><blockquote type="cite" class=""><div class="">On 21 Jan 2019, at 13:36, Simon Andrews <<a href="mailto:simon.andrews@babraham.ac.uk" class="">simon.andrews@babraham.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Something odd is happening in the API for the latest bos Taurus release. When I try to get chromosome adapters I can’t find any.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">This worked OK for the previous build and still works OK for other species in the current release. The web site still shows it as a chromosome based assembly so I’m guessing something is wrong somewhere.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I’ve put a test script at the bottom - if someone could take a look at this I’d be grateful.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Simon.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">#!/usr/bin/perl<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">use warnings;<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">use strict;<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">use Bio::EnsEMBL::Registry;<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">my $registry = 'Bio::EnsEMBL::Registry';<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">$registry->load_registry_from_db(<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> -host => '<a href="http://ensembldb.ensembl.org/" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">ensembldb.ensembl.org</a>',<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> -user => 'anonymous'<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> );<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">my $db_adapter = $registry -> get_DBAdaptor("bos taurus","Core");<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">#my $db_adapter = $registry -> get_DBAdaptor("mus musculus","Core");<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">warn "Genome is ", $db_adapter->species(), "\n";<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">my @chr_slices = @{$db_adapter -> get_adaptor('slice') -> fetch_all('chromosome',undef,0,1)};<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">warn "Found ", scalar @chr_slices, " chromosomes for ", $db_adapter->species(), "\n";<o:p class=""></o:p></div></div><div style="margin: 0cm 0cm 0.0001pt; 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