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Sorry forgot to paste error:<br>
<br>
Processing Cached Registry:
/share/apps/local/biomart-perl/conf/cachedRegistries/martURLLocation_ensembl_76_hg38.xml.cached<br>
<br>
Attribute 'external_gene_id' not found in dataset
default.hsapiens_gene_ensembl<br>
<br>
Trace begun at
/share/apps/local/biomart-perl/lib/BioMart/Registry.pm line 490<br>
BioMart::Registry::getAttribute('BioMart::Registry=HASH(0x12746720)',
'hsapiens_gene_ensembl', 'external_gene_id', 'default', 'default')
called at /share/apps/local/biomart-perl/lib/BioMart/Query.pm line
1243<br>
BioMart::Query::addAttribute('BioMart::Query=HASH(0x2af76807f600)',
'external_gene_id') called at local.pl line 892<br>
<br>
I've tried with both Biomart 0.6 and 0,7 versions without luck on
Ensembl 76.<br>
<br>
<div class="moz-cite-prefix">On 24/09/14 13:13, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote cite="mid:5422A756.2030401@sistemasgenomicos.com"
type="cite">
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
Dear Thomas,<br>
<br>
I'm experiencing an error when querying to BioMart Ensembl 76
registry for both clean/cached.<br>
Using older Mart Registry to ensembl 75 registry archive works
for both clean/cached.<br>
<br>
my $action='clean';<br>
<blockquote>
<blockquote> my $initializer =
BioMart::Initializer->new('registryFile'=>$confFile,
'action'=>$action);<br>
my $registry = $initializer->getRegistry;<br>
<br>
my $query =
BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');<br>
<br>
$query->setDataset("hsapiens_gene_ensembl");<br>
if ( length($gene_name)==15 &&
substr($gene_name,0,4) eq "ENSG" ) {
$query->addFilter("ensembl_gene_id", @{$gene}); }<br>
else { $query->addFilter("hgnc_symbol", @{$gene});
}<br>
if ($query_type eq "gene_info"){<br>
#$query->addFilter("biotype",
["protein_coding"]);<br>
$query->addAttribute("ensembl_gene_id");<br>
$query->addAttribute("ensembl_transcript_id");<br>
$query->addAttribute("chromosome_name");<br>
<b>$query->addAttribute("external_gene_id");</b><br>
}<br>
</blockquote>
</blockquote>
Was this removed in Ensembl 76? Is there any documentation about
BioMart available queries per Ensembl release?<br>
<br>
Thank you and sorry for spam, I never had this issues when
changing Ensembl previously.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<br>
<div class="moz-cite-prefix">On 23/09/14 15:10, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote cite="mid:5421714A.7050200@sistemasgenomicos.com"
type="cite">
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
Dear Thomas,<br>
<br>
Ok I didn't understand correctly, now I do.<br>
As you say biomart website registry is still showing ensembl 75.<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 23/09/14 14:01, Thomas Maurel
wrote:<br>
</div>
<blockquote
cite="mid:F1A87ED1-E57D-4289-8CCD-2965E6FAAC28@ebi.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Dear Guillermo,
<div><br>
</div>
<div>The <a moz-do-not-send="true" href="http://biomart.org">biomart.org</a>
website seems to be very slow at the moment and I am afraid
the website is still displaying our release 75 marts on hg19
(GRCh37). According to the <a moz-do-not-send="true"
href="http://biomart.org">biomart.org</a> mart registry
page: <a moz-do-not-send="true"
href="http://www.biomart.org/biomart/martservice?type=registry">http://www.biomart.org/biomart/martservice?type=registry</a>, port
'80' is still valid.</div>
<div>If you want to use hg38 (GRCh38), the best way would be
to point your mart XML config to the <a
moz-do-not-send="true" href="http://ensembl.org">ensembl.org</a>
website in order to access our release 76 mart databases on
hg38 (GRCh38).</div>
<div>You can follow the previous instruction but just change
the mart registry URL page to get the mart release 76
registry informations:</div>
<div><br>
</div>
<div>
<blockquote type="cite">
<div text="#000066" bgcolor="#FFFFFF">
<blockquote
cite="mid:4B2EFDEF-33F9-4F59-8B37-30795F2DA7CA@ebi.ac.uk"
type="cite">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 </div>
</blockquote>
</div>
</blockquote>
<div text="#000066" bgcolor="#FFFFFF">
<div>Ensembl website on release 76 (hg38): <a
moz-do-not-send="true"
href="http://www.ensembl.org/biomart/martservice?type=registry">http://www.ensembl.org/biomart/martservice?type=registry</a></div>
</div>
<blockquote type="cite">
<div text="#000066" bgcolor="#FFFFFF">
<blockquote
cite="mid:4B2EFDEF-33F9-4F59-8B37-30795F2DA7CA@ebi.ac.uk"
type="cite">
<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><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>
</div>
</blockquote>
</div>
</blockquote>
</div>
<div><br>
</div>
<div>I am afraid $action=clean is quite resource consuming but
you will only need to run your script with this setting when
you change the registry information.</div>
<div><br>
</div>
<div>Hope this helps,</div>
<div>Best regards,</div>
<div>Thomas</div>
<div>
<div>
<div>On 23 Sep 2014, at 12:43, 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">
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
<div text="#000066" bgcolor="#FFFFFF"> 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 moz-do-not-send="true" 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">
<meta http-equiv="content-type"
content="text/html; 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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after-white-space; "><span
class="Apple-style-span"
style="border-collapse:
separate; font-family:
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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>
</div>
</span></div>
</span></div>
</span></div>
</span> </div>
<br>
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style="border-collapse: separate; color:
rgb(0, 0, 0); font-family: Helvetica;
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-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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