Hello, I installed the biomart following the steps described in
http://www.biomart.org/download.html
I need to run the code i show at the end of this mail, in a .pl flie,
from the command line (prompt) and i get the error:
###########
Can't locate BioMart/Initializer.pm in @INC (@INC contains:
/home/arubio/Ensembl/bioperl-1.2.3 /home/arubio/Ensembl/ensembl/modules
/home/arubio /Ensembl/ensembl-compara/modules
/home/arubio/Ensembl/ensembl-variation/modules
/home/arubio/Ensembl/ensembl-functgenomics/modules
/home/arubio/Biomart/biomart-rc6 /usr/local/lib64/perl5
/usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at
bio.pl line 5.
BEGIN failed--compilation aborted at bio.pl line 5.
###########
I have include "PERL5LIB=${PERL5LIB}:${HOME}/Biomart/biomart-rc6" in
bashrc file.
What can i do?
thanks
bio.pl->>>>
# An example script demonstrating the use of BioMart API.
# This perl API representation is only available for configuration
versions >= 0.5
use strict;
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $confFile = "PATH TO YOUR REGISTRY FILE UNDER biomart-perl/conf/.
For Biomart Central Registry navigate to
http://www.biomart.org/biomart/martservice?type=registry";;
#
# NB: change action to 'clean' if you wish to start a fresh
configuration
# and to 'cached' if you want to skip configuration step on subsequent
runs from the same registry
#
my $action='cached';
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile,
'action'=>$action);
my $registry = $initializer->getRegistry;
my $query =
BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');
$query->setDataset("hsapiens_gene_ensembl");
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("ensembl_transcript_id");
$query->addAttribute("atlas_celltype");
$query->addAttribute("atlas_diseasestate");
$query->addAttribute("atlas_organismpart");
$query->formatter("TSV");
my $query_runner = BioMart::QueryRunner->new();
############################## GET COUNT ############################
# $query->count(1);
# $query_runner->execute($query);
# print $query_runner->getCount();
#####################################################################
############################## GET RESULTS ##########################
# to obtain unique rows only
# $query_runner->uniqueRowsOnly(1);
$query_runner->execute($query);
$query_runner->printHeader();
$query_runner->printResults();
$query_runner->printFooter();
#####################################################################
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