[ensembl-dev] ensembl API get 3'UTR sequence from gene list

[Kieron Taylor]

Dear Olivier,

Perhaps you can send us the first five identifiers you are reading in 
from 'gene_test.txt'? It would also be useful if you can provide any 
errors or warnings that appear during the running of your script.

The mailing list will probably reject any attachment, so please include 
the data in-line. This will help us a great deal in determining the 
nature of your problem.

-- 
Kieron Taylor PhD.
Ensembl Core team
EBI

On 09/04/2013 10:07, Olivier armant wrote:
> Dear Ensembl API support,
>
> I want to get back the 3'UTR sequence from an array of genes defined
by their stable id. The script I am using is below. I only get back the
first hit and then get stuck. Could you please explain me why this does
not work?
>
> Cordially
>
> Olivier A
>
> #!/usr/bin/perl
> use strict;
> use warnings;
> use lib "/data/shared/src/Perl_API/ensembl_70/modules";
> use Bio::SeqIO;
> use Bio::EnsEMBL::SeqFeature;
> use Bio::EnsEMBL::Registry;
> use Bio::EnsEMBL::DBSQL::GeneAdaptor;
> #use Bio::EnsEMBL::DBSQL::ExonAdaptor;
> use Bio::EnsEMBL::Transcript;
> #use Data::Dumper;
>
> my $registry = 'Bio::EnsEMBL::Registry';
> $registry->load_registry_from_db(
>     -host => 'ensembldb.ensembl.org', # alternatively 'useastdb.ensembl.org'
>     -user => 'anonymous'
> );
> my $specie = 'Danio rerio';
> my $transcript_adaptor= $registry->get_adaptor($specie,'Core','Transcript') or die "ERROR 1 $!\n";
> my $geneinput= 'gene_test.txt';
> open (FILE, "$geneinput");
> my @data= <FILE>;
> close FILE;
> foreach my $line ( @data)  # stdin as ensembl gene identifier
> {
> $line=~s/ //g;
> $line=~s/\t//g;
> $line=~s/\n//g;
> my $transcript = $transcript_adaptor->fetch_by_stable_id($line);
> my $name = $transcript->display_id;
> my $n3UTR = $transcript->three_prime_utr;
> my $n3UTRseq = $n3UTR->seq();
> print "$name$n3UTRseq";
> }
> exit;
>
>
> Olivier ARMANT PhD.
>
> Institute of Toxicology and Genetics
> KIT Campus Nord
> Hermann-von-Helmholtz-Platz 1
> D-76344 Eggenstein-Leopoldshafen
> Germany
>
> tel: +49-721-608-26774
> fax: +49-721-608-23354
>
>
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