<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div apple-content-edited="true" class="">Glad to hear it Chris
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<br class=""><div><blockquote type="cite" class=""><div class="">On 16 Feb 2016, at 15:55, Christian Cole (Staff) <<a href="mailto:C.Cole@dundee.ac.uk" class="">C.Cole@dundee.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class="">Hi Andy,</div>
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<div class="">Many thanks. I must have got the ports mixed up at some point. Swapping them over and updating to release 83 seems to have sorted it.</div>
<div class="">Cheers,</div>
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<div class="">Chris</div>
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<span style="font-weight:bold" class="">From: </span><<a href="mailto:dev-bounces@ensembl.org" class="">dev-bounces@ensembl.org</a>> on behalf of Andrew Yates <<a href="mailto:ayates@ebi.ac.uk" class="">ayates@ebi.ac.uk</a>><br class="">
<span style="font-weight:bold" class="">Reply-To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org" class="">dev@ensembl.org</a>><br class="">
<span style="font-weight:bold" class="">Date: </span>Tuesday, 16 February 2016 13:08<br class="">
<span style="font-weight:bold" class="">To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org" class="">dev@ensembl.org</a>><br class="">
<span style="font-weight:bold" class="">Subject: </span>Re: [ensembl-dev] How to check which Human genome build?<br class="">
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Hi Chris,
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<div class="">The patched current and last GRCh37 databases are only available on port 3337. Using port 3306 sends you to the database that was used on the live site i.e. anything from release 76 onwards this will be GRCh38. Should you wish to fix your API
version to the last archive release of GRCh37 you can use API version 75 and port number 3306.</div>
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<div class="">You can use the code snippet to see how the API can report what the default assembly version is for a database:</div>
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<div class="">#!/usr/bin/env perl</div>
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<div class="">use strict;</div>
<div class="">use warnings;</div>
<div class="">use Bio::EnsEMBL::Registry;</div>
<div class="">my $port = @ARGV ? $ARGV[0] : 3306; # switch port from the command line</div>
<div class="">Bio::EnsEMBL::Registry->load_registry_from_db(</div>
<div class=""> -HOST => '<a href="http://ensembldb.ensembl.org/" class="">ensembldb.ensembl.org</a>', -PORT => $port, -USER => 'anonymous'</div>
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<div class="">warn Bio::EnsEMBL::Registry->get_adaptor('human', 'core', 'genomecontainer')->get_version();</div>
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<div class="">Here's the output from my command line just now:</div>
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<div class="">ayates@ayatesmba-2:~/Code/ensembl/ensembl (release/83=)$ perl ping_version.pl</div>
<div class="">GRCh38 at ping_version.pl line 11.</div>
<div class="">ayates@ayatesmba-2:~/Code/ensembl/ensembl (release/83=)$ perl ping_version.pl 3337</div>
<div class="">GRCh37 at ping_version.pl line 11.</div>
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<div class="">Hope this helps & any problems please get back in touch</div>
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<div class="">Andy</div>
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------------<br class="">
Andrew Yates - Genomics Technology Infrastructure Team Leader<br class="">
The European Bioinformatics Institute (EMBL-EBI)<br class="">
Wellcome Genome Campus<br class="">
Hinxton, Cambridge<br class="">
CB10 1SD, United Kingdom<br class="">
Tel: +44-(0)1223-492538<br class="">
Fax: +44-(0)1223-494468<br class="">
Skype: andy.yates.ebi</div>
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<a href="http://www.ebi.ac.uk/" class="">http://www.ebi.ac.uk/</a><br class="">
<a href="http://www.ensembl.org/" class="">http://www.ensembl.org/</a></div>
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<div class="">On 16 Feb 2016, at 12:23, Christian Cole (Staff) <<a href="mailto:C.Cole@dundee.ac.uk" class="">C.Cole@dundee.ac.uk</a>> wrote:</div>
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<div class="">Hi,</div>
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<div class="">I've just noticed that the GRCh37 perl API connection is only maintained for the current and previous release. Connecting to the GRCh37 port of 3306 on any other releases gives you GRCh38 data with no warning.</div>
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<div class="">How do I find out explicitly which human genome build I'm using without assuming the port connection gives me what I want?</div>
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<div class="">Also, would it be possible to report a warning that although I'm connecting to port 3306 via an older release, the data is still GRCh38?</div>
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<div class="">Many thanks,</div>
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<div class="">Chris</div>
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<div style="font-family: Calibri, sans-serif; font-size: 14px;" class=""><span style="font-family: Cochin; -webkit-text-stroke-color: rgb(0, 0, 0); -webkit-text-stroke-width: initial;" class="">Dr Christian Cole</span></div>
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