[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.
> 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  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
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