[Biojava-dev] Some problems with createDNASequence

[Thomas Down]

Hi William,


On 18 Nov 2004, at 07:11, William Stott wrote:
>
>  Sequence dna = DNATools.createDNASequence("atgctgB", "dna_1");
>
>  I expected an exception to be thrown (see attached Unit Test) as B is 
> not a valid character for a DNA sequence (atgc), but it wasn't.

B doesn't represent one of the four bases of DNA, but there's also a 
well-defined representation for ambiguous nucleotide sequences, in 
which B means "C, G, or T".  A complete list is at:

             http://www.hgu.mrc.ac.uk/Softdata/Misc/ambcode.html

Mostly you just see 'N' symbols nowadays, but there definitely is 
sequence in the databases which uses some of the others.  They're also 
commonly used when represented redundant sequence motifs, like 
transcription factor binding sites.

>  Do you publish the JUnit Tests for BioJava? Where can they be 
> obtained? Is there a more formal mechanism for  submitting defect 
> reports?

Yes, we do have a test suite -- if you download a full source 
distribution (or check it out of CVS), there's a tests/ tree containing 
the test suite.  The full suite can be run by typing "ant runtests".

          Thomas.