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<p class="MsoNormal">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></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’ve put a test script at the bottom - if someone could take a look at this I’d be grateful.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Simon.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">#!/usr/bin/perl<o:p></o:p></p>
<p class="MsoNormal">use warnings;<o:p></o:p></p>
<p class="MsoNormal">use strict;<o:p></o:p></p>
<p class="MsoNormal">use Bio::EnsEMBL::Registry;<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">my $registry = 'Bio::EnsEMBL::Registry';<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">$registry->load_registry_from_db(<o:p></o:p></p>
<p class="MsoNormal"> -host => 'ensembldb.ensembl.org',<o:p></o:p></p>
<p class="MsoNormal"> -user => 'anonymous'<o:p></o:p></p>
<p class="MsoNormal"> );<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">my $db_adapter = $registry -> get_DBAdaptor("bos taurus","Core");<o:p></o:p></p>
<p class="MsoNormal">#my $db_adapter = $registry -> get_DBAdaptor("mus musculus","Core");<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">warn "Genome is ", $db_adapter->species(), "\n";<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">my @chr_slices = @{$db_adapter -> get_adaptor('slice') -> fetch_all('chromosome',undef,0,1)};<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">warn "Found ", scalar @chr_slices, " chromosomes for ", $db_adapter->species(), "\n";<o:p></o:p></p>
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