[Bioperl-l] Bio::LocatableSeq warning

Mark A. Jensen maj at fortinbras.us
Wed Dec 17 13:41:30 EST 2008

Yes- my bad- if the sequence name contains a range, then clustalw does use this 
range for the length; if it does not, it counts as Roy says-
I agree; This is prob an AlignIO bug by now, eh?
----- Original Message ----- 
From: "Roy Chaudhuri" <roy.chaudhuri at gmail.com>
To: "Sendu Bala" <bix at sendu.me.uk>
Cc: "bioperl-l" <bioperl-l at lists.open-bio.org>
Sent: Wednesday, December 17, 2008 1:05 PM
Subject: Re: [Bioperl-l] Bio::LocatableSeq warning

> 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().
>> ---------------------------------------------------
>> 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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