[Bioperl-l] Bio::LocatableSeq warning

Sendu Bala bix at sendu.me.uk
Wed Dec 17 12:13:09 EST 2008

I've just committed a test alignment file to bioperl-run t/data, and 
Bio::LocatableSeq spurts up a warning about it:

perl -MBio::AlignIO -e '$ai = Bio::AlignIO->new(-file => 
"t/data/pal2nal.aln"); $aln = $ai->next_aln;'

--------------------- WARNING ---------------------
MSG: In sequence pseudogene residue count gives end value 183.
Overriding value [178] with value 183 for Bio::LocatableSeq::end().

Is there simply something wrong with the alignment file (quite 
possible), and this warning means something?

Or is this just normal behaviour now for valid alignment files? What is 
this warning supposed to mean to the user? What should I do about it? 
Why do I need to see it?

More information about the Bioperl-l mailing list