[Seqinr-forum] Bug in kaks()

[Darren Obbard]

Hi,

there's a bug in kaks().

using the test case:

 >seq1
AAAGGGCCCTTT
 >seq2
AAAGGGCCCTT-

e.g.:

 > temp_align
$nb
[1] 2

$nam
[1] "seq1" "seq2"

$seq
[1] "AAAGGGCCCTTT" "AAAGGGCCCTT-"

$com
[1] NA

attr(,"class")
[1] "alignment"

I get

 > kaks(temp_align)
Error in kaks(temp_align) : Nombre de nt non multiple de trois.

This must be in the c, since its not in the R.

clearly both sequences have a multiple of 3 nts,

 > nchar(temp_align$seq[1])
[1] 12

And this isn't picked up by the test in the function

So it must be that the underlying C has a problem with (out-of-frame?) gaps.

However, the documentation says "Codons with gaps are not used for 
computations", which rather suggests that it will at least fail 
helpfully when there are gaps. If this is intended as a 'feature' then 
there should be some warning in the manual.


-- 

Darren Obbard
Institute of Evolutionary Biology
Room 123, Ash 2, Ashworth Labs
Kings Buildings
University of Edinburgh, UK
darren.obbard at ed.ac.uk
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http://www.biology.ed.ac.uk/research/groups/obbard/

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