[ensembl-dev] Bio::LocatableSeq::end warning message

[Andy Yates]

Hi Giuseppe,

I've just gone & run the following query in an attempt to replicate your issue:

use strict;
use warnings;
use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
  -HOST => 'mysql.ebi.ac.uk',-PORT => 4157, -USER => 'anonymous',
  -DB_VERSION => 61
);
my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor('pan_homology', 'compara'); 
my $ha = $dba->get_HomologyAdaptor();
my $ma = $dba->get_MemberAdaptor();
my $stable_id = 'ESTEXT_FGENESH1_KG.C_4000003';
my $member = $ma->fetch_by_source_stable_id('ENSEMBLGENE', $stable_id);
my $homologies = $ha->fetch_all_by_Member($member);
foreach my $h (@{$homologies}) {
  my $sa = $h->get_SimpleAlign();
  warn $sa->overall_percentage_identity();
}

However the issue did not reappear. Can you confirm if the above script works on your setup or elaborate a bit more on the problem you're seeing.

Andy

On 8 Mar 2011, at 12:23, Giuseppe G. wrote:

> Hi,
> 
> I'm on version 61 and using the pan taxonomic database. Have you seen this kind of warning before:
> 
> 
> --------------------- WARNING ---------------------
> MSG: In sequence ESTEXT_FGENESH1_KG.C_4000003 residue count gives end value 353.
> Overriding value [354] with value 353 for Bio::LocatableSeq::end().
> MSMYGFEALNFNVDGGYLEAIVRGYRSGLLTSADYNNLCQCETLDDIKMHLGATDYGPYLANEPSPLHTATIVEKCTQKLVDEYNHMLTQATEPLSTFLEYITYGHMIDNVVLIVTGTLHERDVHELLEKCHPLGMFDSIASLAV---AQNMRELYRLVLVDTPLAPYFSECITSED----------LDDMNIEIMRNTLYKAYLEDFYRFCQKLGGATSTIMCDLLAFEADRRAVNITINSIGTELTR---DDRRKLYSKFGILYPYGHEELAACDDFDAVRGAMEKYPPYQAIFSKLS-FGES--------------QMLDKAFYEEEVKRLILSFEQQFHYAVFFAYMRLREQETRNLMWISECVAQNQKSRIHDGIVMTF----
> ---------------------------------------------------
> 
> I've just seen it so not sure what part of the code it comes from. I see the warning refers to Bio::LocatableSeq. The only bioperl method I'm using in this code is overall_percentage_identity() from Simple Align. I use it to get an OPI value for the homologous sequences as follows:
> 
> my $pairwise_alignment_from_multiple = $homology->get_SimpleAlign;
> 
> $opi = $pairwise_alignment_from_multiple->overall_percentage_identity;
> 
> The warnings are not there when version is < 60. Any ideas?
> 
> Best,
> Giuseppe
> 
> -- 
> 
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-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/