Hi,
using the following code
Sequence seq = sequences.nextSequence(); SeqIOTools.writeGenpept(System.out,seq);
I tried to write out a sequence in Genpept format. The sequence was
previoulsy parsed in from a Genpept (NCBI protein) - format file.
(http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=13568390)
Biojava 1.4pre1 gives me some output, but is missing all features. I then tried
Biojava1.3, with even worse results:
Exception in thread "main" org.biojava.bio.symbol.IllegalSymbolException:
Symbol ARG not found in alphabet DNA
at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:278)
...
I had a brief look at the biojava-sourcecode. It seems to me that Genpept format files are not really expected to stand on their own? I.e. protein - sequences are only handled correct if part of a Genbank (nucleotide) file?
That would explain why I get an IllegalSymbolException - a DNA sequence is expected where in the Genpept format the AA sequence is. Strangely enough the file is parsed in correctly ... .
Or is there something I am missing?
Thanks in advance!
Christian
_______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
