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

[Giuseppe G.]

Dear Anne and Chris,

thank you for the clarification.

Best,
Giuseppe

On 08/03/11 16:55, 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
>
>
>
>
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-- 

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