[Bioperl-l] Distance between non-overlapping sequences in DNAStatistics
Chris Fields
cjfields at illinois.edu
Mon Jan 25 05:35:06 UTC 2010
Just a quick question for those using DNAStatistics. I just fixed a bug in Bio::Align::DNAStatistics that failed with a div by zero error (bug 2901) on this data:
>seq1
GGTACCAGCAGGTGGGCCGCCTACTGCGCACGCGCGGGTTTGCGGGCAGCCGC
>seq2
GGTACCAGCTGGTGGGCCGCCTACTGCGCACGCGCGGGTTTGCGGGCAGCCGC
>seq3
GGTACCAGCAGGTGGTCCGCCTA------------------------------
>seq4
--------------------------CGCACGCGCGTGTTTGCGGGCAGCCGC
Since seq3 and seq4 don't overlap, the distance can't be calculated. In our case, I replace the score with 'NA' as a placeholder, but I'm worried about downstream app breakage. Anyone have an objection to using 'NA' here, or know of ways this may lead to problems elsewhere?
chris
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