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Dear Thomas,<br>
<br>
My BioMart perl script is using the following mart XML config file:<br>
<br>
<pre><?xml version="1.0" encoding="UTF-8"?>
</pre>
<pre><!DOCTYPE MartRegistry>
</pre>
<pre><MartRegistry>
</pre>
<pre> <MartURLLocation
</pre>
<pre> name = "ensembl"
</pre>
<pre> displayName = "ensembl"
</pre>
<pre> host = "<a class="moz-txt-link-abbreviated" href="http://www.biomart.org">www.biomart.org</a>"
</pre>
<pre> port = "80"
</pre>
<pre> visible = "1"
</pre>
<pre> default = ""
</pre>
<pre> includeDatasets = "hsapiens_gene_ensembl"
</pre>
<pre> martUser = ""
</pre>
<pre> />
</pre>
<pre></MartRegistry>
</pre>
However, I'm getting BioMart queries from hg19 and not hg38. Does
the default port '80' still working on hg19? how can I specify I
would like to use hg38 biomart service.<br>
<br>
On the other hand, it's always useful to know how to query older
Ensembl versions with Biomart. However using $action=clean with conf
file of ensembl 75 archive it's leading me to massive amounts of RAM
consumption in my Perl script.<br>
<br>
Thanks.<br>
<br>
Best regards,<br>
Guillermo.<br>
<div class="moz-cite-prefix">On 19/09/14 15:48, Thomas Maurel wrote:<br>
</div>
<blockquote
cite="mid:4B2EFDEF-33F9-4F59-8B37-30795F2DA7CA@ebi.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Dear Guillermo,
<div><br>
</div>
<div>If you are using:</div>
<div>1) the biomart-perl/scripts/webExample.pl script and an xml
file</div>
<div>You can change the path to the biomart website in the
following line:</div>
<blockquote style="margin: 0 0 0 40px; border: none; padding:
0px;">
<div>my $path="<a moz-do-not-send="true"
href="http://www.biomart.org/biomart/martservice?">http://www.biomart.org/biomart/martservice?</a>";</div>
</blockquote>
<div>With the path to our Ensembl release 75 archive:</div>
<blockquote style="margin: 0 0 0 40px; border: none; padding:
0px;">
<div>my $path="<a moz-do-not-send="true"
href="http://feb2014.archive.ensembl.org/biomart/martservice?">http://feb2014.archive.ensembl.org/biomart/martservice?</a>";</div>
</blockquote>
<div><br>
</div>
2) A BioMart perl script
<div>a) You first need to edit your configuration file in
"biomart-perl/conf/martURLLocation.xml" and paste the content of
the mart registry page for the Ensembl release 75 archive
website: <a moz-do-not-send="true"
href="http://feb2014.archive.ensembl.org/biomart/martservice?type=registry">http://feb2014.archive.ensembl.org/biomart/martservice?type=registry</a></div>
<div>b) Then edit your script and make sure that "my $confFile"
variable is looking at the martURLLocation.xml configuration
file in biomart-perl/conf</div>
<div>c) Finally, make sure to update the following line in your
script:</div>
<div><br>
</div>
<div>my $action='cached';</div>
<div>
<div><br>
</div>
<div>with:</div>
<div><br>
</div>
<div>my $action='clean';</div>
<div>
<div>
<div><br>
</div>
<div>The first run of your script on Ensembl 75 might be a
bit slow as BioMart will cache some data from the BioMart
website.</div>
<div>Once you have run your script with the action variable
set to "clean", you can set the variable to "cached"
again.</div>
<div><br>
</div>
<div>Hope this helps,</div>
<div>Best regards,</div>
<div>Thomas</div>
<div>On 19 Sep 2014, at 13:28, Guillermo Marco Puche <<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
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charset=windows-1252">
<div bgcolor="#FFFFFF" text="#000066"> Dear developers,<br>
<br>
I would like to know how to specify BioMart Perl code to
query against older Ensembl version (ie:75) and not
latest (I believe used by default).<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
</div>
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</blockquote>
</div>
<br>
<div>
<span class="Apple-style-span" style="border-collapse:
separate; border-spacing: 0px;">
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space; -webkit-line-break: after-white-space; "><span
class="Apple-style-span" style="border-collapse:
separate; color: rgb(0, 0, 0); font-family: Helvetica;
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<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space; "><span
class="Apple-style-span" style="border-collapse:
separate; color: rgb(0, 0, 0); font-family:
Helvetica; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing:
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border-spacing: 0px;
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-webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space; -webkit-line-break:
after-white-space; "><span
class="Apple-style-span"
style="border-collapse: separate; color:
rgb(0, 0, 0); font-family: Helvetica;
font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: 2; text-indent:
0px; text-transform: none; white-space:
normal; widows: 2; word-spacing: 0px;
border-spacing: 0px;
-webkit-text-decorations-in-effect: none;
-webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; ">
<div>--</div>
<div>Thomas Maurel<br>
Bioinformatician - Ensembl Production Team<br>
European Bioinformatics Institute
(EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Trust Genome Campus<br>
Hinxton<br>
Cambridge CB10 1SD<br>
United Kingdom</div>
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</span></div>
</span></div>
</span>
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