Plant Reactome BioMart Perl API script for Justin

biomart_perl_query_4Justin.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 = "../conf/martURLLocation.xml";
my $species = shift || "bnapus";

print STDERR "The other species is $species\n";


#
# 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='clean';
#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("osativa_eg_gene");
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("${species}_eg_homolog_ensembl_gene");
$query->addAttribute("${species}_eg_homolog_perc_id");
$query->addAttribute("${species}_eg_homolog_perc_id_r1");
$query->addAttribute("${species}_eg_homolog_orthology_confidence");

$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();
#####################################################################