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

[Kieron Taylor]

Dear Olivier,

The method three_prime_utr() is intended to return an undef in the event 
of there being no UTR. ENSDART00000000005 has no UTR, hence your script 
fails.

The example code supplied in the documentation for Transcript is as follows:

my $three_prime  = $transcrpt->three_prime_utr or warn "No three prime UTR";

You should adapt your script similarly,

Regards,

Kieron

On 09/04/2013 11:38, Olivier armant (ITG) wrote:
> 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.
> ENSDART00000000004GTGGGATTTGAACTCCTTGTAATTAACTATGATGGCAGCGCATACCTAGAGACTGCTGGATGGCCATTTCCTGTCTGCGGAGCTGCATGGAGTCGATCAGGTCATAGATGATGGCCATGGACCACATGGGTGACGGGTACCAGGATTTGACATTTCCGTCTTTTCCAACCAGCAGCATGGAAAAGTACTCGGGGCTGATCTGGAAGTAGTTTCTGATGTCTCTTACTAGAGTGGCAGAGATACCCTCACGCTCCACCGTTGCACTACCTGAAGTGGGTGTTGAAAAAAGGTGCGTAAGCATAAACAACAAATGCTGGATGTACATTAAACTGAGCTCTTTGTGCACCACAAATGACTTATTGGGGATTTAATTAATGAAATGCTGAACTCATATAATTATTATATTAGTTATACGAGTTATTTGGTTCAAAATGCAGTCATATTGAGGGTTTTTACTATTTAAAATGACATTTTAAAACAATTTAATGAGTGTTTCATTTCCATGATTCCAAAGCGGAATTTTTAGCTGAAATCTTTAAAATCTGAGGAACTAATTATAAGTAGGGAAGGGCAGCCTATATGTCATTACGTTACTATTGAGGGTCAACATGTGGAGATTGTAAACAGTTTTAAGTATCTGGGAATTATTTTAGAAAGTGGCTTAAATTTTGGTGAACACGCAGACTGTATCTATAAGAAAGCAACACAAAGACTCTTTTTAAACAATGAAATAGTTTTAATGTTATTAAGGGTATTCTGAGAAAGGTTTAATCTGGTTGAAAGTATTATCTCCTATAATATTTCTTGCTGGTGTGAAAATCTTGGAGCTAGAGGCAAGTATAAACATGCAAAGATGGTTAATATGGCTAGTAAGATCATAATGGACCCCCAGAAGTAGCTTGTGGAACTGTATACAAACCAGACCAGATGGAAAGCCTCACAGATAGTTCAGGACTCAACTCATCCTCTT
 TA
>   TTATGAGTTTGAAAATCTTCCTTCTGTTAGATGATACAGAGTACCCACAGCAAATTCAAATATTTTTAAGAAATCTTTGATACCGTCTGCTATTACCTTACTGAATAAATGACGGTGAAGTTTT
>
> 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
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>
>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>


-- 
Kieron Taylor PhD.
Ensembl Core team
EBI