Hi my name is Andrew Evans and I work at a lab at Vanderbilt University and we're trying to use Biomart to query databases for gene data. However, I have been unable to run the queries effectively and I was hoping you could help.
I want to be able to query the Biomart Central portal without using the Web Interface manually. I have been able to generate queries in Perl and XML format via the Martview at biomart.org. When I try to run this perl script: # 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 = "http://www.biomart.org/biomart/martservice?type=registry";; # # 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='clean'; 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("refseq_dna", ["NM_016894","NM_177410","NM_145506","NM_001114662","NM_001159649","NM_026500","NM_178052","NM_001111316","NM_011210","NM_001039511","NM_001039512","NM_054102","NM_172843","NM_022329","NM_138314","NM_178071","NM_001113391","NM_001160262"]); $query->addAttribute("ensembl_gene_id"); $query->addAttribute("ensembl_transcript_id"); $query->addAttribute("external_gene_id"); $query->addAttribute("name_1006"); $query->addAttribute("go_cellular_component__dm_name_1006"); $query->addAttribute("go_molecular_function__dm_name_1006"); $query->addAttribute("refseq_dna"); $query->addAttribute("refseq_peptide"); $query->formatter("TSV"); 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(); ##################################################################### I get this message: Can't locate BioMart/Initializer.pm in @INC (@INC contains: /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at query.pl line 4. BEGIN failed--compilation aborted at query.pl line 4. When i try to run wget -O results.txt ' http://www.biomart.org/biomart/martservice?query=Query.xml using query.xml i created from Martview this is the results.txt: Query ERROR: caught BioMart::Exception: non-BioMart die(): File does not exist: Query.xml at /srv/biomart_server/ biomart.org/biomart-perl/lib/BioMart/Query.pm line 1935 When I try to run the Webexample.pl from the scripts directory using the xml I got from martview (saved as query.xml) the terminal window says: Usage: perl webExample.pl Query.xml and there is no results.txt file. Not sure If maybe I installed the Biomart-Perl API wrong or if I am not configuring my perl or xml files correctly. Any help would be greatly appreciated. Thanks Andrew Evans
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