Hi Syed, Thank you again for all your help. Since I somehow could not connect to martdb.ensembl.org this morning, I took the registry I previously used and removed everything not necessary for the script (only kept ensembl_mart_46 and compara_mart_pairwise_ga_46). Now everything works fine and the script finishes in seconds.
Thanks, Matthias -----Original Message----- From: Syed Haider [mailto:[EMAIL PROTECTED] Sent: Saturday, August 25, 2007 6:11 PM To: Wahl, Matthias Cc: [email protected] Subject: RE: [mart-dev] Biomart - pairwise_genomic_alignments Hi Matthias, finally nailed this down, there is a potential bug in internal batching system when you use MartURLLocation registry configuration. we will be fixing this soon. If you are not behind firewall, you may try using MartDBLocation form of registry connection params instead or you may use XML format of query against our web-service. for example, you may replace the <MartURLLocation..../> for the said query to <MartDBLocation databaseType="mysql" host="martdb.ensembl.org" database="sequence_mart_46" name="ensembl" displayName="ENSEMBL 46 GENE (SANGER)" port="3316" schema="sequence_mart_46" user="anonymous" password="" visible="1" default="1" martUser="" includeDatasets="" /> <MartDBLocation databaseType="mysql" host="martdb.ensembl.org" database="compara_mart_pairwise_ga_46" name="compara_mart_pairwise_ga_46" displayName="ENSEMBL 46 PAIRWISE ALIGNMENTS (SANGER)" port="3316" schema="compara_mart_pairwise_ga_46" user="anonymous" password="" visible="1" default="0" martUser="" includeDatasets="" /> cheers syed On Sat, 2007-08-25 at 16:28 -0500, Wahl, Matthias wrote: > 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'=>'de > > > faul > > > > > 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/ > > > > > > > > > > >
