>>>>> "dion" == dion whitehead <[EMAIL PROTECTED]> writes:
dion> Hello, I am having a frustrating time with attempting to
dion> read in rna sequences. They contain the 'N' symbol which is
dion> a standard ambiguity symbol, but the code trips up on this
dion> every time, saying its not a recognized symbol in the
dion> alphabet. Do I have to specify it myself?
I got bitten by this too, when porting some of the code. If you look
in biojava-live/resources/org/biojava/bio/symbol/AlphabetManager.xml
you will see that the default RNA alphabet contains only
agcu-~. i.e. no ambiguity symbols at all.
I haven't tested this, but you could hack your AlphabetManager.xml to
include
<ambiguityMapping token="n">
<symbolref name="guanine" />
<symbolref name="adenine" />
<symbolref name="cytosine" />
<symbolref name="uracil" />
</ambiguityMapping>
as in the DNA alphabet. Not sure if this is the best solution - I'm
sure someone will say if it's not.
Keith
--
- Keith James <[EMAIL PROTECTED]> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -
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