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

[Giuseppe G.]

Hi Andy,

thanks a lot.

Best,
Giuseppe

On 08/03/11 16:10, Andy Yates wrote:
> Hi Giuseppe,
>
> A quick investigation into that particular protein's sequence (ESTEXT_FGENESH1_KG.C_4000003) there is a final stop codon which should not be present in sequences stored in the compara schema. My guess is that an API (probably BioPerl) is trimming that stop which gives a sequence length of 363 rather than 364.
>
> As for the reason why this only appears in resources less than 61 is because this gene is from Physcomitrella patens which came into Ensembl Genomes in release 8.
>
> My gut feeling is that you can ignore the BioPerl message as it is only an warning&  your OPI value should be unaffected. I'll see what can be done about future releases
>
> Best regards,
>
> Andy
>
> On 8 Mar 2011, at 15:54, 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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>>>
>>
>> --
>>
>> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
>

-- 

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