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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