Hi Benoit, Thank you very much for your answer. I ran the query on v46 and it seems to work fine.
Thanks, Matthias -----Original Message----- From: Benoit Ballester [mailto:[EMAIL PROTECTED] Sent: Saturday, November 17, 2007 10:10 AM To: Wahl, Matthias Cc: [email protected] Subject: Re: [mart-dev] Multiple genomic alignments Hi Mathias, Could you try to run your query on v46 ? I think I have spotted something odd in v47, but I need some time to investigate. Meanwhile please try on v46, and get back to me if you see the same error on v46. Regards, Benoit Wahl, Matthias wrote: > Hi all , > > I am using Biomart to retrieve pairwise or multiple genome alignments. > The following query: > > my $query = > BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default' ); > > $query->addFilter("mmus_dnafrag_start", ["1"]); > $query->addFilter("mmus_chro", ["1"]); > $query->addFilter("mmus_dnafrag_end", ["10000000"]); > $query->addAttribute("pairwise_genomic_alignments"); > Works for pairwise genomic alignments > $query->setDataset("compara_mart_blastznet_hsap_mmus"); > $query->addAttribute("pairwise_genomic_alignments"); > but not for multiple genomic alignments > $query->setDataset("compara_mart_gerp_10species"); > $query->addAttribute("multiple_genomic_alignments"); > > The line $query->addFilter("mmus_chro", ["1"]); results in the error > message > Filter 'mmus_chro' not found in dataset default.compara_mart_gerp_10species > > How can I set the chromosome so that I do not get alignments for the > specified regions on all chromosomes? > > Thank you very much! > > Matthias > > > 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/_ > -- Benoit Ballester, PhD Ensembl Team European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, United Kingdom
