[Bioperl-l] Problem parsing clustalw format ni AlignIO

Kevin Brown Kevin.M.Brown at asu.edu
Thu Feb 15 16:38:25 EST 2007


Did you try Bioperl 1.5.2 to see if updates to it might fix the issue?
IIRC 1.4 is nearly 2 years old now.  1.5.2 was released within the last
few months.

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Catherine Letondal
> Sent: Thursday, February 15, 2007 1:24 PM
> To: bioperl-l
> Cc: Catherine Letondal; Katja Schuerer
> Subject: [Bioperl-l] Problem parsing clustalw format ni AlignIO
> 
> Hi bioperlers,
> 
> I have a script called protal2dna
> (http://bioweb.pasteur.fr/seqanal/interfaces/protal2dna.html, 
> see attachment #1) that realign DNA sequences giving their 
> sequences + the corresponding protein alignment (sequences 
> have to be in the same order or named equivalently). We have 
> a parsing problem reported from the AlignIO class when users 
> enter some clustalw file (see attachment #2 for an example):
> 
> % protal2dna alig-protal2dna.dat dna-protal2dna.data no 
> alignment available in 'clustalw' format from file 
> 'alig-protal2dna.dat'
> %
> 
> I have tried with bioperl 1.4. I have looked in the archive 
> and in the BUGS, but found nothing?
> Is there any bug fix for this? I also provide the DNA 
> sequences file if you want to test.
> 
> Thanks a lot in advance,
> 
> --
> Catherine Letondal -- Institut Pasteur
> www.pasteur.fr/~letondal
> 
> 



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