[Bioperl-l] Bio::LocatableSeq warning

[Roy Chaudhuri]

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.

Roy.
--
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().
> ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND
> ---------------------------------------------------
> 
> 
> 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?
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