[Biojava-dev] SymbolTokenizer for Meme class

[mark.schreiber at novartis.com]

Probably depends on which type of sequence you ran meme on. If it was DNA 
use the DNATools.getDNA() if protein use ProteinTools.getAlphabet()

Let us know if this still doesn't work.

Would be good if you could tell us the version of biojava and paste in 
some of the meme file.

- Mark





Rainer Pudimat <rpudimat at informatik.uni-jena.de>
Sent by: biojava-dev-bounces at portal.open-bio.org
07/11/2005 07:41 PM
Please respond to rpudimat

 
        To:     biojava-dev at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] SymbolTokenizer for Meme class


Hello,

once again, I try to use the Meme class for reading ASCII results of the 
meme software. However, I don't know which SymbolTokenizer should be 
used in the arguments of Meme constructor.
I tried to use

SymbolTokenization st = new CharacterTokenization(DNATools.getDNA(),true);

An exception was thrown:
"This tokenization doesn't contain character: 'A'."

So, which one to use instead?

Thank you,
Bye,
Rainer.


-- 
Rainer Pudimat

Bioinformatics
Institute for Computer Science
Friedrich-Schiller-University
Ernst-Abbe-Platz 2 /Room 3427
D - 07743 - Jena

Phone: +49 3641 946 456
Web: http://www.bio.inf.uni-jena.de/~rpudimat/
_______________________________________________
biojava-dev mailing list
biojava-dev at biojava.org
http://biojava.org/mailman/listinfo/biojava-dev