[Bioperl-l] Problem parsing clustalw format ni AlignIO

Catherine Letondal letondal at pasteur.fr
Thu Feb 15 15:23:55 EST 2007


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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: protal2dna
Type: application/octet-stream
Size: 11093 bytes
Desc: not available
Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20070215/42a0ba43/attachment.obj 
-------------- next part --------------

-------------- next part --------------
A non-text attachment was scrubbed...
Name: alig-protal2dna.dat
Type: application/octet-stream
Size: 12022 bytes
Desc: not available
Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20070215/42a0ba43/attachment-0001.obj 
-------------- next part --------------

-------------- next part --------------
A non-text attachment was scrubbed...
Name: dna-protal2dna.data
Type: application/octet-stream
Size: 7739 bytes
Desc: not available
Url : http://lists.open-bio.org/pipermail/bioperl-l/attachments/20070215/42a0ba43/attachment-0002.obj 


More information about the Bioperl-l mailing list