> -----Original Message----- > From: Cook, Malcolm [mailto:[email protected]] > Sent: Thursday, April 29, 2010 4:06 PM > To: Junjun Zhang; '[email protected]' > Subject: RE: BioMart::Exception::Configuration', 'Attribute > \'gene_exon_intron\' not found in dataset default > > Hi JunJun, > > Perfect. Excellent. All Fixed. Thanks.
No problem, glad to hear it works. > > Oh, and, as I refreshed by cache, during the refresh, I got > multiple warnings, like this: > Warning: Too many Options for filter [ chromosome_name ] > possible rendering problems for Martview OK > > Any worries here? No, no worries, it should be safe for you running perl api. Cheers, Junjun > > Again, thanks > > Malcolm Cook > Stowers Institute for Medical Research - Bioinformatics > Kansas City, Missouri USA > > > -----Original Message----- > From: Junjun Zhang [mailto:[email protected]] > Sent: Thursday, April 29, 2010 12:35 AM > To: Cook, Malcolm; '[email protected]' > Subject: RE: BioMart::Exception::Configuration', 'Attribute > \'gene_exon_intron\' not found in dataset default > > Hi Malcolm, > > You will need to include one more mart in your registry as following: > > includeMarts = "msd,uniprot,ensembl,sequence" > > This should work. > > Cheers, > Junjun > > > > -----Original Message----- > > From: Cook, Malcolm [mailto:[email protected]] > > Sent: Wednesday, April 28, 2010 5:02 PM > > To: Junjun Zhang; '[email protected]' > > Subject: RE: BioMart::Exception::Configuration', 'Attribute > > \'gene_exon_intron\' not found in dataset default > > > > Hi Junjun, > > > > Sure. It is very small: > > > > <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE MartRegistry> > > <MartRegistry> > > > > <RegistryURLPointer > > name = "central_server" > > host = "www.biomart.org" > > port = "80" > > path = "" > > includeMarts = "msd,uniprot,ensembl" > > /> > > </MartRegistry> > > > > > > > > -----Original Message----- > > From: Junjun Zhang [mailto:[email protected]] > > Sent: Wednesday, April 28, 2010 3:33 PM > > To: Cook, Malcolm; '[email protected]' > > Subject: RE: BioMart::Exception::Configuration', 'Attribute > > \'gene_exon_intron\' not found in dataset default > > > > Hi Malcolm, > > > > We need more information from you in order to find out the cause of > > the problem. > > > > Could you send me the registry file you used in the perl API code? > > It's specified in the line like this: > > > > my $initializer = > > BioMart::Initializer->new('registryFile'=>$confFile, > > 'action'=>$action); > > > > Cheers, > > Junjun > > > > > > > > > -----Original Message----- > > > From: [email protected] > > > [mailto:[email protected]] On Behalf Of Cook, Malcolm > > > Sent: Tuesday, April 27, 2010 10:01 AM > > > To: '[email protected]' > > > Subject: [mart-dev] BioMart::Exception::Configuration', > > > 'Attribute \'gene_exon_intron\' not found in dataset default > > > > > > Does anyone know how to work-around this exception > > > > > > at > > > /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.8/Exception/Cl > > > ass.pm line 269 > > > > > > Exception::Class::Base::throw('BioMart::Exception::Configurati > > > on', 'Attribute \'gene_exon_intron\' not found in dataset > > > default.m...') called at > > > /n/site/inst/shared/bioinfo/ensembl/biomart-perl/release-0_7/l > > > ib//BioMart/Registry.pm line 490 > > > > > > > > > I'm querying with perl api (/ensembl/biomart-perl/release-0_7 > > > ) using code exported from biomart/ensembl from dec2008 > > > > > > Below is a URL to the query, which works interactively, > followed by > > > (slightly editted) perl code exported upon clicking the > > "perl" button > > > > > > Thanks for your help.... > > > > > > --Malcolm Cook > > > > > > > > > > > > http://dec2008.archive.ensembl.org/biomart/martview/f26d676eaf > > > a1feaf994ca31a18fcadf0/f26d676eafa1feaf994ca31a18fcadf0/f26d67 > > > 6eafa1feaf994ca31a18fcadf0?VIRTUALSCHEMANAME=default&ATTRIBUTE > > S=mmusculus_gene_ensembl.default.sequences.ensembl_gene_id|mmu > > sculus_gene_ensembl.default.sequences.gene_exon_int> > > ron|mmusculus_gene_ensembl.default.sequences.chromosome_name|m > > > musculus_gene_ensembl.default.sequences.strand|mmusculus_gene_ > > > ensembl.default.sequences.start_position|mmusculus_gene_ensemb > > > l.default.sequences.end_position&FILTERS=mmusculus_gene_ensemb > > > l.default.filters.ensembl_gene_id."ENSMUSG00000083773,ENSMUSG0 > > > 0000081262,ENSMUSG00000082711"&VISIBLEPANEL=filterpanel > > > > > > > > > > > > > > > > > > #!/bin/env perl > > > > > > > > > # An example script demonstrating the use of BioMart API. > > > # This perl API representation is only available for > configuration > > > versions >= 0.5 use strict; use BioMart::Initializer; use > > > BioMart::Query; use BioMart::QueryRunner; > > > > > > my $confFile = #"PATH TO YOUR REGISTRY FILE UNDER > > biomart-perl/conf/. > > > For Biomart Central Registry navigate to # > > > "http://www.biomart.org/biomart/martservice?type=registry"; > > > > > > "/n/site/inst/shared/bioinfo/ensembl/biomart-perl/release-0_7/ > > > conf/registryURLPointer.xml" > > > ; > > > # > > > # NB: change action to 'clean' if you wish to start a fresh > > > configuration # and to 'cached' if you want to skip > > configuration step > > > on subsequent runs from the same registry # > > > > > > my $action='cached'; > > > my $initializer = > > > BioMart::Initializer->new('registryFile'=>$confFile, > > > 'action'=>$action); my $registry = $initializer->getRegistry; > > > > > > my $query = > > > BioMart::Query->new('registry'=>$registry,'virtualSchemaName'= > > > >'default'); > > > $query->setDataset("mmusculus_gene_ensembl"); > > > $query->addFilter("ensembl_gene_id", > > > ["ENSMUSG00000083773","ENSMUSG00000081262","ENSMUSG00000082711"]); > > > $query->addAttribute("ensembl_gene_id"); > > > $query->addAttribute("gene_exon_intron"); > > > $query->addAttribute("chromosome_name"); > > > $query->addAttribute("strand"); > > > $query->addAttribute("start_position"); > > > $query->addAttribute("end_position"); > > > > > > $query->formatter("FASTA"); > > > > > > my $query_runner = BioMart::QueryRunner->new(); > > > > > > $query_runner->execute($query); > > > $query_runner->printResults(); > > >
