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

Tue Mar 8 16:56:18 GMT 2011

I guess if the warning mentioned below is actually an error on the bioperl end let us know.  

cheers,

chris

On Mar 8, 2011, at 10:55 AM, Anne Parker wrote:

> 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.
>>>>>> 
>>>>>> _______________________________________________
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>>>>> 
>>>> 
>>> 
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> 
> Anne Parker
> Ensembl Web Production Manager
> http://www.ensembl.org
> 
> 
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a charity registered in England with number 1021457 and acompany registered in England with number 2742969, whose registeredoffice is 215 Euston Road, London, NW1 2BE.