[Bioperl-l] Bio::LocatableSeq warning

Roy Chaudhuri roy.chaudhuri at gmail.com
Wed Dec 17 13:05:15 EST 2008

Depends what you mean by valid. Your file contains asterisks and digits, 
representing stop codons and frameshifts (using Genewise notation 
according to the Pal2Nal paper). Bio::AlignIO::clustalw ignores those by 
doing an s/[^A-Za-z]//g before calculating the sequence length. 
Bio::LocatableSeq notices the discrepancy and corrects the length while 
issuing a warning. Bio::AlignIO::clustalw would need to be fixed if you 
want it to parse files with non-letter residues correctly. I think 
ClustalW itself removes non-letter residues from the input data so will 
never output such files.

Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.

Sendu Bala wrote:
> 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?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list