Hello,
I am trying to retrieve a transcript sequence using the BioMart perl API, and I
am also interested in the 100bp flanking the transcript.
When I use the Ensembl BioMart web page, everything works fine. However, using
the perl code automatically generated by the online query (see below), flanks
can never be retrieved. Ensembl's HelpDesk redirected me to BioMart, where the
problem allegedly lies.
Can someone explain how to retrieve flanking regions?
Thank you,
Francesco Marass
###
# 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 = "ensembl.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("hsapiens_gene_ensembl");
$query->addFilter("downstream_flank", ["100"]);
$query->addFilter("upstream_flank", ["100"]);
$query->addFilter("ensembl_transcript_id", ["ENST00000478798"]);
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("ensembl_transcript_id");
$query->addAttribute("transcript_exon_intron");
$query->formatter("FASTA");
my $query_runner = BioMart::QueryRunner->new();
$query_runner->execute($query);
$query_runner->printHeader();
$query_runner->printResults();
$query_runner->printFooter();
###
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