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

[Giuseppe G.]

Hi Andy,

thanks for your reply. On my machine your script produces the warnings. 
The following one does as well:

----------------------
my $ID = 'PF13_0197a';
my $organism = 'Plasmodium falciparum';
my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_multiple_dbs(
{
      -host       => 'ensembldb.ensembl.org',
      -user       => 'anonymous',
      -verbose    => 1,
     },
{
      -host    => 'mysql.ebi.ac.uk',
      -user    => 'anonymous',
      -port    => 4157,
      -verbose => 1,
     }
);

my $member_adaptor = $registry->get_adaptor('pan_homology', 
'compara', 'Member');
my $homology_adaptor = $registry->get_adaptor('pan_homology', 
'compara', 'Homology');

my $member = $member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE', $ID);
my $homologies = $homology_adaptor->fetch_all_by_Member($member);
foreach my $h (@{$homologies}) {
   my $sa = $h->get_SimpleAlign();
   warn $sa->overall_percentage_identity();
}
----------------------------------------------

I'm wondering if it might depend on the fact that I don't have the 
recommended Bioperl installation on this machine? (running the 1.6.1 
currently)

Best,
Giuseppe


On 08/03/11 15:00, Andy Yates wrote:
> 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
>>
>> --
>>
>> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
>>
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>

-- 

The University of Edinburgh is a charitable body, registered in 
Scotland, with registration number SC005336.