[Biojava-l] RNATools possible bug

[Simon Foote]

I've found a slight problem with RNATools when transcribing/translating 
DNA to RNA to protein.

Not sure if its a bug or I did something wrong.  
I'm justing doing a simple RNATools.transcribe on a DNA symbol list.  

It throws the following error:

Exception in thread "main" 
org.biojava.bio.symbol.IllegalSymbolException: Token
`phe' does not appear as a named symbol in alphabet `PROTEIN-TERM'
        at 
org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.java:85)

I've traced the problem to a case issue between TranslatonTables.xml and 
AlphabetManager.xml

TranslationTables.xml is returning lower case amino acids while 
AlphabetManager.xml contains upper case amino acids.
Changing Line 373 in RNATools.java to:
               String to = te.getAttribute("to").toUpperCase();
fixes the problem.  But, I think changing TranslatonTables.xml to upper 
case amino acids is probably the correct fix.

Cheers,
Simon Foote

-- 
Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
[T] 613-991-4342  [F] 613-952-9092