Hi Syed,
the genes have been there a couple of 10^6 years. So they can wait a
few days. Thanks for your help. The query runs fine on the Biomart
Portal. However, if I take the perl code generated from that query and
run it local, I don't have any luck. I attach the code I am running
and the content of the Registry file. I'm sure I'm missing something
(as usual).
Best, Josef
------------------------------------------------------
#!/usr/bin/perl -w
use lib '/users/JA/biomart-perl/lib';
use strict;
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $confFile = (grep { m/biomart-perl\/lib+$/ } @INC)[0]."/../conf/
WebRegistry.xml";
my $action='clean';
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile,
'action'=>$action);
my $registry = $initializer->getRegistry;
my $query = BioMart::Query->new('registry'=>
$registry,'virtualSchemaName'=>'default');
$query->setDataset("mmusculus_gene_ensembl");
$query->addFilter("upstream_flank", ["200"]);
$query->addFilter("mgi_symbol", ["Nfkbie"]);
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("ensembl_transcript_id");
$query->addAttribute("cdna");
$query->formatter("FASTA");
my $query_runner = BioMart::QueryRunner->new();
$query_runner->execute($query);
$query_runner->printHeader();
$query_runner->printResults();
$query_runner->printFooter();
----------------------------------------------------------------
Content of registry file (WebRegistry.xml)
<MartRegistry>
<MartURLLocation database="ensembl_mart_57" default="1"
displayName="ENSEMBL GENES 57 (SANGER UK)" host="www.biomart.org"
includeDatasets="mmusculus_gene_ensembl" martUser="" name="ensembl"
path="/biomart/martservice" port="80" serverVirtualSchema="default"
visible="1" />
<MartURLLocation database="sequence_mart_57" default="0"
displayName="ENSEMBL SEQUENCE 57 (SANGER UK)" host="www.biomart.org"
includeDatasets="mmusculus_genomic_sequence" martUser=""
name="sequence" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="0" />
</MartRegistry>
On Mar 18, 2010, at 12:06 AM, Syed Haider wrote:
Hi Josef,
apologies for the delay in reply,
have you tried the same query on the web interface on Biomart
Central Portal (www.biomart.org) ? what happens there, i see the
query works just fine there. please let us know if that works for you.
Best,
Syed
