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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thanks for the reply - that’s really helpful and I think gives me a work round for now.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">We use this same script across a range of different species so I’d like to understand whether this is something we’d need to change
permanently in the script, or if it’s something perculiar to this assembly. Is there a different meaning for just using a “toplevel” coord system rather than a chromosome based one when the assembly appears to be chromosome based overall?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thanks<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Simonb<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Dev <dev-bounces@ensembl.org>
<b>On Behalf Of </b>Kostas Billis<br>
<b>Sent:</b> 21 January 2019 14:52<br>
<b>To:</b> Ensembl developers list <dev@ensembl.org><br>
<b>Subject:</b> Re: [ensembl-dev] No chromosomes in API for latest bos taurus<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Simon, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I think your script looks good. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">+-----------------+------------+------------------+------------+------+--------------------------------+<o:p></o:p></p>
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<p class="MsoNormal">| coord_system_id | species_id | name | version | rank | attrib |<o:p></o:p></p>
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<p class="MsoNormal">+-----------------+------------+------------------+------------+------+--------------------------------+<o:p></o:p></p>
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<p class="MsoNormal">| 1 | 1 | primary_assembly | ARS-UCD1.2 | 1 | default_version,sequence_level |<o:p></o:p></p>
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<p class="MsoNormal">+-----------------+------------+------------------+------------+------+--------------------------------+<o:p></o:p></p>
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<p class="MsoNormal">1 row in set (0.00 sec)<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">You can get all top-level sequences. For example, <o:p></o:p></p>
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<p class="MsoNormal">Instead of: <span style="font-family:"Calibri",sans-serif">my @chr_slices = @{$db_adapter -> get_adaptor('slice') -> fetch_all('chromosome',undef,0,1)}</span><o:p></o:p></p>
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<p class="MsoNormal">Try: my @chr_slices = @{$db_adapter -> get_adaptor('slice') -> fetch_all('toplevel',undef,0,1)};<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">A way to get the chromosomes is via karyotype attribute. For example: <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">my @karyo_slices = @{$db_adapter->get_SliceAdaptor->fetch_all_karyotype()};<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">foreach my $karyo (@karyo_slices) {<o:p></o:p></p>
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<p class="MsoNormal"> print "FOUND " , $karyo->name, "\n"<o:p></o:p></p>
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<p class="MsoNormal">}<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">warn "Found ", "kary " , scalar(@karyo_slices) , " and ", scalar @chr_slices, " chromosomes for ", $db_adapter->species(), "\n";<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Please let me know if this works for you. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanks, <o:p></o:p></p>
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<p class="MsoNormal">Kostas <o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 21 Jan 2019, at 13:36, Simon Andrews <<a href="mailto:simon.andrews@babraham.ac.uk">simon.andrews@babraham.ac.uk</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">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></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">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></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">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></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thanks<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Simon.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">#!/usr/bin/perl<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">use warnings;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">use strict;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">use Bio::EnsEMBL::Registry;<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">my $registry = 'Bio::EnsEMBL::Registry';<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">$registry->load_registry_from_db(<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> -host => '<a href="http://ensembldb.ensembl.org/"><span style="color:#954F72">ensembldb.ensembl.org</span></a>',<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> -user => 'anonymous'<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> );<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">my $db_adapter = $registry -> get_DBAdaptor("bos taurus","Core");<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">#my $db_adapter = $registry -> get_DBAdaptor("mus musculus","Core");<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">warn "Genome is ", $db_adapter->species(), "\n";<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">my @chr_slices = @{$db_adapter -> get_adaptor('slice') -> fetch_all('chromosome',undef,0,1)};<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">warn "Found ", scalar @chr_slices, " chromosomes for ", $db_adapter->species(), "\n";<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Arial",sans-serif;color:#1F497D">The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT<span class="apple-converted-space"> </span></span><i><span style="font-size:8.0pt;font-family:"Arial",sans-serif;color:#365F91">Registered
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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<p class="MsoNormal"><o:p> </o:p></p>
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