Hi Matthias
I have tested your code all you need to do is to remove the following
three lines which are only for retrieving count
$query->count(1);
$query_runner->execute($query);
print $query_runner->getCount();
Count, in case of Genomic sequence data has some problem, which we will
address soon. In addition, the two sections (one for count and one for
data retrievel are mutually exclusive - you can execute only one at a
time.)
hope this will get you going with your work for now.
cheers
syed
On Fri, 2007-08-24 at 12:43 -0500, Wahl, Matthias wrote:
> 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/
>
