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

[Olivier armant (ITG)]

dear Taylor,

Thanx for your fast answer. Her is the content of the input file:

ENSDART00000000004
ENSDART00000000005
ENSDART00000138183
ENSDART00000000019
ENSDART00000124452

And her is the output after calling the scripts:

Can't call method "seq" on an undefined value at get3UTR.pl line 50.
ENSDART00000000004GTGGGATTTGAACTCCTTGTAATTAACTATGATGGCAGCGCATACCTAGAGACTGCTGGATGGCCATTTCCTGTCTGCGGAGCTGCATGGAGTCGATCAGGTCATAGATGATGGCCATGGACCACATGGGTGACGGGTACCAGGATTTGACATTTCCGTCTTTTCCAACCAGCAGCATGGAAAAGTACTCGGGGCTGATCTGGAAGTAGTTTCTGATGTCTCTTACTAGAGTGGCAGAGATACCCTCACGCTCCACCGTTGCACTACCTGAAGTGGGTGTTGAAAAAAGGTGCGTAAGCATAAACAACAAATGCTGGATGTACATTAAACTGAGCTCTTTGTGCACCACAAATGACTTATTGGGGATTTAATTAATGAAATGCTGAACTCATATAATTATTATATTAGTTATACGAGTTATTTGGTTCAAAATGCAGTCATATTGAGGGTTTTTACTATTTAAAATGACATTTTAAAACAATTTAATGAGTGTTTCATTTCCATGATTCCAAAGCGGAATTTTTAGCTGAAATCTTTAAAATCTGAGGAACTAATTATAAGTAGGGAAGGGCAGCCTATATGTCATTACGTTACTATTGAGGGTCAACATGTGGAGATTGTAAACAGTTTTAAGTATCTGGGAATTATTTTAGAAAGTGGCTTAAATTTTGGTGAACACGCAGACTGTATCTATAAGAAAGCAACACAAAGACTCTTTTTAAACAATGAAATAGTTTTAATGTTATTAAGGGTATTCTGAGAAAGGTTTAATCTGGTTGAAAGTATTATCTCCTATAATATTTCTTGCTGGTGTGAAAATCTTGGAGCTAGAGGCAAGTATAAACATGCAAAGATGGTTAATATGGCTAGTAAGATCATAATGGACCCCCAGAAGTAGCTTGTGGAACTGTATACAAACCAGACCAGATGGAAAGCCTCACAGATAGTTCAGGACTCAACTCATCCTCTTTATTATGAGTTTGAAAATCTTCCTTCTGTTAGATGATACAGAGTACCCACAGCAAATTCAAATATTTTTAAGAAATCTTTGATACCGTCTGCTATTACCTTACTGAATAAATGACGGTGAAGTTTT

Olivier

On Apr 9, 2013, at 11:41 AM, Kieron Taylor wrote:

> 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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> 
> 
> 
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