Hi Syed, Thank you very much for your effort. But when I use the filters below, it runs forever (still running). I installed the biomart-perl this Fri from CVS (release-0_6) and am using the registry from http://www.biomart.org/biomart/martservice?type=registry.
Matthias -----Original Message----- From: Syed Haider [mailto:[EMAIL PROTECTED] Sent: Sat 8/25/2007 3:58 PM To: Wahl, Matthias Cc: [email protected] Subject: RE: [mart-dev] Biomart - pairwise_genomic_alignments Hi Matthias I am slightly lost now... The following query does work on my end and finishes in couple of seconds. $query->setDataset("compara_mart_blastznet_hsap_mmus"); $query->addFilter("hsap_dnafrag_end", ["10000000"]); $query->addFilter("hsap_chro", ["1"]); $query->addFilter("hsap_dnafrag_start", ["9990000"]); $query->addAttribute("pairwise_genomic_alignments"); however with out any filters, I just started it and now waiting for the results to finish. I expect it to take substantial time given I am not using any filters. Please let me know if there is something I am missing. I will keep you posted about performance on my end. cheers syed On Sat, 2007-08-25 at 13:48 -0500, Wahl, Matthias wrote: > Hy Syed, > > I thought I am filtering for human chromosome 1, bases 9990000 to 10000000 by > adding the following: > > > > $query->addFilter("hsap_dnafrag_end", ["10000000"]); > > $query->addFilter("hsap_chro", ["1"]); > > $query->addFilter("hsap_dnafrag_start", ["9990000"]); > > Thanks, > > Matthias > > > -----Original Message----- > From: Syed Haider [mailto:[EMAIL PROTECTED] > Sent: Sat 8/25/2007 2:19 PM > To: Wahl, Matthias > Cc: [email protected] > Subject: RE: [mart-dev] Biomart - pairwise_genomic_alignments > > Hi Matthias, > could you confirm if thats your query > > $query->setDataset("compara_mart_blastznet_hsap_mmus"); > $query->addAttribute("pairwise_genomic_alignments"); > > and no filters at all ? > > cheers > syed > > > On Sat, 2007-08-25 at 11:03 -0500, Wahl, Matthias wrote: > > Hi Syed, > > > > I am still struggling with getting the pairwise genomic alignments > > between mouse and human. > > > > I changed my query in order to get only a short stretch starting with > > only 10000 bases of the human chromosome: > > > > $query->setDataset("compara_mart_blastznet_hsap_mmus"); > > $query->addFilter("hsap_dnafrag_end", ["10000000"]); > > $query->addFilter("hsap_chro", ["1"]); > > $query->addFilter("hsap_dnafrag_start", ["9990000"]); > > $query->addAttribute("pairwise_genomic_alignments"); > > > > The same query takes me a few seconds on EnsMart (the whole results), > > but with my script it even did not even finish after over night. > > > > Thanks, > > > > Matthias > > > > -----Original Message----- > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > Sent: Friday, August 24, 2007 6:38 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/ > > > > > >
