Hi (sorry if you get 2 copies, I sent this to -request by mistake)
Apologies if this has come up before, a quick search didn't turn anything up.
I'm attempting to do a pairwise alignment between two DNA sequences using biojava 3. When I try to construct a DNASequence from a string that contains an ambiguous base though (in this case 'y'), I get the following stacktrace.
Exception in thread "main" org.biojava3.core.exceptions.CompoundNotFoundError: Compound not found for: Cannot find compound for: y at org.biojava3.core.sequence.storage.ArrayListSequenceReader.setContents(ArrayListSequenceReader.java:196) at org.biojava3.core.sequence.template.AbstractSequence.<init>(AbstractSequence.java:88) at org.biojava3.core.sequence.DNASequence.<init>(DNASequence.java:64)
Should I attempt to mask them somehow? What's the best way to deal with these?
cheers Wim -- Wim De Smet http://www.straininfo.net/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
