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

[Anne Parker]

My understanding is that the Ensembl webcode is currently dependent on  
1.2.3 because of our geriatric BLAST interface, but the API is moving  
towards compatibility with 1.6.x.

Cheers

Anne


On 8 Mar 2011, at 16:26, Chris Fields wrote:

> (Speaking from the bioperl end)
>
> IIRC this was due to a logic issue in Bio::Range (which LocatableSeq  
> inherits) that had been around for a long time in bioperl and led to  
> silent bugs elsewhere in the code (not warning when bad start/end  
> was given).
>
> The last word I heard on the subject, the Ensembl folks will likely  
> tell you that they only support bioperl 1.2.3.  The bioperl devs are  
> more than happy to help push that up to the latest release if  
> possible, soon to be v1.6.2.
>
> chris
>
> On Mar 8, 2011, at 10:14 AM, 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
>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>
>>>
>>
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Anne Parker
Ensembl Web Production Manager
http://www.ensembl.org