On Fri, Jan 24, 2014 at 12:26 AM, Vincent Davis wrote:

I happen to be working with De Bruijn sequences. Is there any interest in this being part of numpy/scipy?

https://gist.github.com/vincentdavis/8588879

That looks like an old copy of GPL code from Sage: http://git.sagemath.org/sage.git/tree/src/sage/combinat/debruijn_sequence.py... Besides the licensing issue, it doesn't really belong in scipy and certainly not in numpy imho. Ralf

Vincent Davis

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Sage sites "The algorithm used is from Frank Ruskey’s “Combinatorial Generation”." It looks like Frank Ruskey's orginal publication on the algorithm was Joe Sawada and Frank Ruskey, "An Efficient Algorithm for Generating Necklaces with Fixed Density", SIAM Journal of Computing 29:671-684, 1999. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.2.5237&rep=rep1&type=pdf If you take a look at this page http://www.theory.csc.uvic.ca/~cos/inf/neck/NecklaceInfo.html You can get a C or Pascal program, the License in the attached program is. /**************************************************************************** * C program to generate necklaces, Lyndon words, and De Bruijn * * sequences. The algorithm is CAT and is described in the book * * "Combinatorial Generation." This program, was obtained from the * * (Combinatorial) Object Server, COS, at http://www.theory.csc.uvic.ca/ * * The inputs are n, the length of the string, k, the arity of the * * string, and density, the maximum number of non-0's in the string. * * The De Bruijn option doesn't make sense unless density >= n. * * The program can be modified, translated to other languages, etc., * * so long as proper acknowledgement is given (author and source). * * Programmer: Frank Ruskey (1994), translated to C by Joe Sawada * *****************************************************************************/ Vincent Davis 720-301-3003 On Sat, Feb 1, 2014 at 8:57 AM, Peter Cock wrote:

On Sat, Feb 1, 2014 at 3:40 PM, Ralf Gommers

wrote:

...

On Fri, Jan 24, 2014 at 12:26 AM, Vincent Davis <

vincent@vincentdavis.net>

...

wrote:

...

I happen to be working with De Bruijn sequences. Is there any interest

in

...

this being part of numpy/scipy?

https://gist.github.com/vincentdavis/8588879

That looks like an old copy of GPL code from Sage:

http://git.sagemath.org/sage.git/tree/src/sage/combinat/debruijn_sequence.py...

...

Besides the licensing issue, it doesn't really belong in scipy and

certainly

...

not in numpy imho.

Ralf

If it is GPL code that would be a problem, but in terms of scope it might fit under Biopython given how much De Bruijn graphs are used in current sequence analysis.

Regards,

Peter