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

[Hans-Rudolf Hotz]

 > 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)


Yes, this looks very similar to the BioPer 1.6.1 versus BioPerl 1.2.3 
issue in the "getConstrainedElements.pl" example script (taken from: 
/ensembl-compara/scripts/examples/) I tried to report a while ago.


Regards, Hans




On 03/08/2011 04:54 PM, Giuseppe G. wrote:
> 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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>>
>