[ensembl-dev] GRCh37 Protein sequence has asterisks

[Alessandro Vullo]

Hi Luke,

thanks for reporting this, we're currently investigating the issue.

best,

Alessandro

On 04/12/17 15:57, Luke Goodsell wrote:
> Hi,
> 
> I’ve been trying to retrieve some GRCh37 protein sequences with code 
> similar to that below and have found some proteins that have corrupted 
> sequences, including asterisks. Please can you tell me how to get the 
> correct protein sequences?
> 
> #!/usr/bin/env perl
> 
> usestrict;
> 
> usewarnings;
> 
> useBio::EnsEMBL::Registry;
> 
> useGetopt::Long qw(GetOptionsFromArray);
> 
> my$registry = 'Bio::EnsEMBL::Registry';
> 
> $registry->load_registry_from_db(
> 
> -host => 'ensembldb.ensembl.org',
> 
> -user => 'anonymous',
> 
> -port => '3337'
> 
> );
> 
> my$transcript_adaptor = $registry->get_adaptor( 'Human', 
> 'otherfeatures', 'Transcript');
> 
> foreachmy$transcript_id ("NM_002426.4") {
> 
> foreachmy$transcript (@{ 
> $transcript_adaptor->fetch_all_versions_by_stable_id($transcript_id) }) {
> 
> my$protein = $transcript->translation();
> 
> defined($protein) ornext;
> 
> print">". $protein->stable_id() . "\n";
> 
> print$protein->seq() . "\n";
> 
> }
> 
> }
> 
> Kind regards,
> 
> Luke
> 
> This e-mail message contains confidential information intended only for 
> the use of the individual or entity to which it is addressed. If you are 
> not the intended recipient, please do not disseminate, distribute or 
> copy this communication, by e-mail or otherwise. Instead, please notify 
> us immediately by return e-mail and then delete and discard all copies 
> of the e-mail. We have taken all reasonable precautions to check this 
> e-mail and any attachments for viruses, but we cannot accept any 
> liability for any damage sustained as a result of any virus, worm or 
> other malicious software. Achilles Therapeutics Limited (10167668) is 
> registered in England and Wales. The registered office is at 215 Euston 
> Road, London, NW1 2BE, UK.
> 
> 
> _______________________________________________
> 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/
> 


-- 
Alessandro Vullo, PhD
Software Engineer, Ensembl
European Bioinformatics Institute (EMBL-EBI)
http://www.ebi.ac.uk
http://www.ensembl.org