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

Giuseppe G. G.Gallone at sms.ed.ac.uk
Tue Mar 8 16:27:05 GMT 2011


Hi Hans,

thanks for your reply. Out of curiosity, what was the nature of the 
problem you had found? Did you stop using 1.6.1 since that due to 
further complications? I haven't had any problems at all using 
1.6.1/Ensembl API for the past year but I might consider downgrading if 
more serious incompatibilities are found.

Best,
G.

On 08/03/11 16:14, Hans-Rudolf Hotz wrote:
>  > 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.
>>>>
>>>> _______________________________________________
>>>> Dev mailing list
>>>> Dev at ensembl.org
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>>>
>>
>

-- 

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Scotland, with registration number SC005336.




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