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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">That’s great. I’ll update the code for all future genomes we process then.
<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">Simon.<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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<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>Thibaut Hourlier<br>
<b>Sent:</b> 22 January 2019 09:22<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>
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<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">The fix should work for all species which have chromosomes.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The toplevel coordinate system returns all sequences which are not part of a bigger sequence. This means chromosomes, unplaced scaffolds and unlocalised scaffolds.<o:p></o:p></p>
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<p class="MsoNormal">The chromosome coordinate system return only the chromosomes.<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 cow, if you use chromosome (karyotype), you will have 30 sequences whereas if you use toplevel you will have 2211 sequences as the assembly has some unplaced scaffolds.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Previously we were storing the assemblies using the contig - scaffold - chromosome coordinate systems. For many new assemblies the contigs are close to the chromosome size, so to load the assemblies in our databases more easily, we load
the whole sequence instead of loading the contigs.<o:p></o:p></p>
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<p class="MsoNormal">Chromosome 1 in cow has been submitted as 1 sequence<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hope this help<o:p></o:p></p>
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<p class="MsoNormal">Thibaut<o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On 21 Jan 2019, at 17:09, Simon Andrews <<a href="mailto:simon.andrews@babraham.ac.uk">simon.andrews@babraham.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks for the reply - that’s really helpful and I think gives me a work round for now.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">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?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Simonb</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dev
<<a href="mailto:dev-bounces@ensembl.org"><span style="color:purple">dev-bounces@ensembl.org</span></a>><span class="apple-converted-space"> </span><b>On Behalf Of<span class="apple-converted-space"> </span></b>Kostas Billis<br>
<b>Sent:</b><span class="apple-converted-space"> </span>21 January 2019 14:52<br>
<b>To:</b><span class="apple-converted-space"> </span>Ensembl developers list <<a href="mailto:dev@ensembl.org"><span style="color:purple">dev@ensembl.org</span></a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ensembl-dev] No chromosomes in API for latest bos taurus</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<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>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On 21 Jan 2019, at 13:36, Simon Andrews <<a href="mailto:simon.andrews@babraham.ac.uk"><span style="color:purple">simon.andrews@babraham.ac.uk</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<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.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></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.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></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.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thanks</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Simon.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">#!/usr/bin/perl</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">use warnings;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">use strict;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">use Bio::EnsEMBL::Registry;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">my $registry = 'Bio::EnsEMBL::Registry';</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">$registry->load_registry_from_db(</span><o:p></o:p></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>',</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> -user => 'anonymous'</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> );</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></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");</span><o:p></o:p></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("mus musculus","Core");</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">warn "Genome is ", $db_adapter->species(), "\n";</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">my @chr_slices = @{$db_adapter -> get_adaptor('slice') -> fetch_all('chromosome',undef,0,1)};</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></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";</span><o:p></o:p></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
Charity No. 1053902.</span></i><o:p></o:p></p>
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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"><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" style="text-autospace:none"><o:p></o:p><o:p></o:p><span style="font-size:8.0pt;
font-family:"Arial","sans-serif";color:#1F497D">The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT
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mso-themeshade:191">Registered Charity No. 1053902.</span></i><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p></o:p></span></p>
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and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute.
</span><span style="font-size:8.0pt;
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mso-themeshade:191">Full conditions at:
</span><a href="http://www.babraham.ac.uk/terms"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";
color:#365F91;mso-themecolor:accent1;mso-themeshade:191">www.babraham.ac.uk</span></a><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#365F91;
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