[Biojava-l] Phred Sequence

Schreiber, Mark mark.schreiber at agresearch.co.nz
Thu Mar 6 16:44:58 EST 2003

Hi -

I was trying to replicate this error to fix it but I can't (has someone
kindly fixed it for me??). The following code seems to work fine

    System.out.println("Testing n symbol");
    Symbol ambig = PhredTools.getPhredSymbol(DNATools.n(),
    System.out.println("Successfuly constructed "+ambig.getName());


Testing n symbol 
Successfuly constructed ([cytosine adenine thymine guanine] 12) 

Are you still having problems with this? Are you using BioJava live?

- Mark

> -----Original Message-----
> From: David Waring [mailto:dwaring at u.washington.edu] 
> Sent: Thursday, 20 February 2003 4:20 p.m.
> To: biojava
> Subject: [Biojava-l] Phred Sequence
> I am writing code to parse a .phd file and create a 
> PhredSequence. It is failing with an IllegalSymbolException 
> when I have an 'n' in the sequence. Do CrossProductAlphabets 
> only take AtomicSymbols?
> David
> Exception in thread "main" 
> org.biojava.bio.symbol.IllegalSymbolException:
> Token
> `([cytosine adenine guanine thymine] 2)' does not appear as a 
> named symbol in al phabet `PHRED'
>         at 
> org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.j
> ava:105)
>         at 
> org.biojava.bio.program.phred.PhredTools.getPhredSymbol(PhredTools.ja
> va:162)
> rethrown as org.biojava.utils.NestedError
>         at 
> org.biojava.bio.program.phred.PhredTools.getPhredSymbol(PhredTools.ja
> va:164)
>         at
> org.biojava.bio.program.phred.PhredTools.createPhred(PhredTools.java:
> 142)
>         at 
> edu.washington.genome.seqio.phd.PhredBuilder.makeSequence(PhredBuilde
> r.java:238)
>         at 
> org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:10
> 1)
>         at readPhd.main(readPhd.java:45)
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