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
Vincent Davis
On Fri, Jan 24, 2014 at 12:26 AM, Vincent Davis vincent@vincentdavis.netwrote:
I happen to be working with De Bruijn sequences. Is there any interest in this being part of numpy/scipy?
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
NumPyDiscussion mailing list NumPyDiscussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpydiscussion
On Sat, Feb 1, 2014 at 3:40 PM, Ralf Gommers ralf.gommers@gmail.com 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?
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
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 29:671684, 1999. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.2.5237&rep=rep1...
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 non0'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 7203013003
On Sat, Feb 1, 2014 at 8:57 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Sat, Feb 1, 2014 at 3:40 PM, Ralf Gommers ralf.gommers@gmail.com
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?
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
participants (3)

Peter Cock

Ralf Gommers

Vincent Davis