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
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