[mart-dev] Biomart - pairwise_genomic_alignments

[Wahl, Matthias]

Hi All,

I am trying to retrieve pairwise genomic alignments from EnsMart using
the script below (taken from the web page), but all I get the following
error message:

Unimplemented method 'BioMart::Dataset::GenomicSequence::getCount'

Does anyone know what I am doing wrong? 
Thanks,

Matthias




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("compara_mart_blastznet_hsap_mmus");
        $query->addFilter("mmus_dnafrag_start", ["1"]);
        $query->addFilter("mmus_chro", ["1"]);
        $query->addFilter("mmus_dnafrag_end", ["10000000"]);
        $query->addAttribute("pairwise_genomic_alignments");

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

Matthias Wahl, PhD
Stowers Institute for Medical Research
1000 E. 50th Street
Kansas City, MO  64110
Phone:  816-926-4302
Fax: 816-926-2044
E-mail : [EMAIL PROTECTED]
http://www.stowers-institute.org/