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

[Hans-Rudolf Hotz]

Hi Giuseppe

> 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.

I don't think it is serious. I got the same result independent of the 
BioPerl version. Using, the current version, I just got the warning 
message about overriding the value.

Since, I don't like warnings, I have both BioPerl versions installed and 
I use the old one whenever I do ensembl stuff.

Regards, Hans


> 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
>>
>>
>>
>>

>>>>> --------------------- 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
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>>>>>
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>>>>
>>>
>>
>