You may want to split your query into several queries with which one return fewer sequence entries. For example, you can fire one query for one chromosome. Junjun
On 11-07-15 10:43 AM, "pip pipster" <[email protected]> wrote: Thank you, adding the sequence mart fixed that issue. However, now I'm getting "Problems with the web server: 500 read timeout". I've tried it a few times and it normally stops at approx 5.8MB. Ideas? ________________________________ From: Junjun Zhang <[email protected]> To: "'[email protected]'" <[email protected]>; "'[email protected]'" <[email protected]> Sent: Thursday, July 14, 2011 6:03 PM Subject: Re: [BioMart Users] Problem getting cDNA data using Perl script In addition to ensembl gene mart, you will need to include ensembl sequence mart in your registry file. Please see http://www.biomart.org/biomart/martservice?type=registry for how to include sequence mart. Junjun Sent from my BBerry From: pip pipster [mailto:[email protected]] Sent: Thursday, July 14, 2011 05:41 PM To: [email protected] <[email protected]> Subject: [BioMart Users] Problem getting cDNA data using Perl script Hello - I'm having trouble getting cDNA sequences using the bioperl/biomart api's. Here is an example query that I'm building. It works fine until I add the "cdna" attribute. Once I add that attribute, I get the message, "Attribute 'cdna' not found in dataset default.hsapiens_gene_ensembl" Perhaps cDNA is in another mart? I used the Ensembl Biomart 'perl' button to generate the perl query. Perhaps cDNA isn't an attribute and should be handled another way instead? my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action); my $registry = $initializer->getRegistry; my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default'); $query->setDataset("hsapiens_gene_ensembl"); $query->addFilter("biotype", ["pseudogene"]); $query->addAttribute("ensembl_transcript_id"); $query->addAttribute("ensembl_gene_id"); $query->addAttribute("chromosome_name"); $query->addAttribute("strand"); $query->addAttribute("cdna"); $query->formatter("FASTA"); my $query_runner = BioMart::QueryRunner->new(); Here is my registryFile content. Does this look OK? <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE MartRegistry> <MartRegistry> <MartURLLocation database="ensembl_mart_63" default="1" displayName="Ensembl Genes 63" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" /> </MartRegistry> I also tried this mart as well and received the same cdna not found in dataset message: <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE MartRegistry> <MartRegistry> <MartURLLocation database="ensembl_mart_63" default="1" displayName="ENSEMBL GENES 63 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" /> </MartRegistry> Thank you.
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