<div dir="ltr">Ok ... thanks Magali.<div><br></div><div>I believe the latest VEP now supports an --assembly flag to allow it to annotate against a specific assembly.</div><div>Can we not have the same flag on the registry ? </div><div>How does VEP do it?</div><div>This would be incredibly useful because I would not have to create new scripts to support a different assembly.<br></div><div><br></div><div>I could just download all the tables and just tell the registry which one to use.</div><div><br></div><div>Please correct me if I am wrong but your proposed solution would mean I would have to bypass the registry completely and I would need to create each each adaptor from scratch and thus I would need to alter a lot of my scripts to support both assemblies.</div><div><br></div><div>"--assembly GRCh37" would be a much more preferable route.</div><div><br></div><div>Best regards,<br></div><div><br></div><div> Duarte</div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br> Duarte Miguel Paulo Molha <br></font><div><font style="background-color:rgb(255,255,255)" color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</font></div></div></div>
<br><div class="gmail_quote">On 27 April 2015 at 17:48, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Duarte,<br>
<br>
The mysql dumps for GRCh37 are available on the ftp site as well<br>
<a href="ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/" target="_blank">ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/</a><br>
<br>
I would recommend having only one copy of human for release 79.<br>
So if you are interested in the GRCh37 data, you can download the
database from <a href="ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/" target="_blank">ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/</a>
rather than <a href="ftp://ftp.ensembl.org/pub/release-79/mysql/" target="_blank">ftp://ftp.ensembl.org/pub/release-79/mysql/</a><br>
<br>
If you need both databases on the same server, you can access a
given database directly rather than using the registry.<br>
my $human_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(<br>
-HOST => 'localhost',<br>
-PORT => 3306,<br>
-USER => 'user',<br>
-DBNAME => 'homo_sapiens_core_79_37',<br>
-SPECIES => 'homo_sapiens',<br>
-GROUP => 'core'<br>
);<br>
<br>
<br>
Hope that helps,<br>
Magali<span class=""><br>
<br>
<div>On 27/04/2015 17:11, Duarte Molha
wrote:<br>
</div>
</span><blockquote type="cite">
<div dir="ltr"><span class="">Thanks Magali
<div><br>
</div>
<div>But I think you have not understtod my question.</div>
<div><br>
</div>
<div>Assume I want to download the databases to my local
computer and use the perl API 79 to query the latest 79_37
database instead of the default 79_38<font size="3">. </font></div>
<div><font size="3">Previously, I just had to download the mysql
tables corresponding to the api I was using to fetch the
data correctly, however, now you have broken that link
API->Underlying_assembly</font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3">So how do I tell my scripts what database to
query?</font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3">My local sql will all be under the same
port.</font></div>
<div><font size="3"><br>
</font></div>
</span><div><font size="3">Best regards</font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3">Duarte</font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3"><br>
</font></div>
</div>
<div class="gmail_extra"><span class=""><br clear="all">
<div>
<div><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br>
</font>
<div><font style="background-color:rgb(255,255,255)" color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
</div>
<br>
</span><div class="gmail_quote"><span class="">On 27 April 2015 at 17:01, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>
wrote:<br>
</span><div><div class="h5"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi Duarte,<br>
<br>
The archive 75 website is still based on the release 75
API.<br>
<br>
For the dedicated GRCh37 website though, we have used a
data freeze from release 75 and have since been updating
the website and underlying databases along with the main
release.<br>
The GRCh37 databases are available on our main MySQL
server on port 3337 (instead of the default 3306 which
will give you access to GRCh38 databases)<br>
<br>
<br>
Hope that helps,<br>
Magali
<div>
<div><br>
<br>
<div>On 27/04/2015 16:56, Duarte Molha wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<div dir="ltr">
<div>Dear developers</div>
<div><br>
</div>
<div>On your GRCh37 archive site you say this:</div>
<div><br>
</div>
<div>===========================</div>
<div><br>
</div>
<h2>About this archive</h2>
<p>This archive is based on Ensembl Release 75
data, and gives continuing access to human
assembly GRCh37, as well as all our other
release 75 species (data freeze March 2014) for
comparative purposes. Human variation and
regulation data has since been updated in March
2015.</p>
<p>The API and website will be updated in tandem
with the release of the main Ensembl website (<b>currently
version 79</b>), and we will also periodically
update this site with new data human, which will
be announced in this panel.</p>
<div><span>MySQL dumps of human databases on the
most recent schema version are available on
our</span><span> </span><a href="ftp://ftp.ensembl.org/pub/grch37/" target="_blank">FTP site</a><span>.</span></div>
<div><br>
</div>
<div>=========================</div>
<div><br>
</div>
<div>It was my understanding that an API version
was directly linked to a specific assembly. So I
thought that if I wanted to query the latest
GRCh37 assembly I would need to use the api v75
and if I wanted to use a local database, I would
download the corresponding sql tables for that
version.</div>
<div><br>
</div>
<div>However, according to this announcement, I
can now use the V79 api and query the old
assembly... How is this accomplished ?</div>
<div>What you I have to do on my scripts to make
sure I am querying the 37 version even though I
am using the latest API?</div>
<div><br>
</div>
<div>Sorry, I hope this is not a stupid question
but I am a bit confused.</div>
<div><br>
</div>
<div>Best regards</div>
<div><br>
</div>
<div>Duarte</div>
<div><br>
</div>
<div><br>
</div>
<br clear="all">
<div>
<div><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br>
</font>
<div><font style="background-color:rgb(255,255,255)" color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
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</div>
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