Hi Syed, Thank you very much for the quick answer. I removed the three lines and the program is executing, however it runs forever (it is running more than one hour now without finishing), but the same query over the EnsMart web page is done in a few seconds.
Thanks, Matthias -----Original Message----- From: Syed Haider [mailto:[EMAIL PROTECTED] Sent: Friday, August 24, 2007 2:36 PM To: Wahl, Matthias Cc: [email protected] Subject: Re: [mart-dev] Biomart - pairwise_genomic_alignments 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'=>'defaul > t'); > > > $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/ >
