Hi Wim,
The use of ambiguous nucleotides requires you to use the AmbiguityDNACompoundSet
when you create your DNASequence, which means any:
new DNASequence(<yourString>)
changes to:
new DNASequence(<yourString>, AmbiguityDNACompoundSet.getDNACompoundSet())
I hope that helps,
Mark
On 3/28/2011 9:46 AM, Wim De Smet wrote:
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
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