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

[Giuseppe G.]

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

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