In deed, I retrieve the whole results. I guess I will have to wait a little longer.
Thank you very much! Matthias -----Original Message----- From: Syed Haider [mailto:[EMAIL PROTECTED] Sent: Fri 8/24/2007 6:37 PM To: Wahl, Matthias Cc: [email protected] Subject: RE: [mart-dev] Biomart - pairwise_genomic_alignments Hi Matthias Are you retrieving the whole results set or just a subset (using some filters) ? The results you see on EnsMart are first 10 results only. cheers syed On Fri, 2007-08-24 at 16:22 -0500, Wahl, Matthias wrote: > 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/ > >
