Vincent Davis wrote:
True, the "all you want is a mapping" is not quite true. I actually
plan to plot frequency (the number of times an observed sub sequence
overlaps a value in the De Bruijn sequence) The way the sub sequences
overlap is important to me and I don't see a way go from base-k (or
On Fri, Jan 24, 2014 at 2:23 AM, Peter Otten <__pete...@web.de> wrote:
> Then, how do you think Python /knows/ that it has to repeat the code 10
> times on my "slow" and 100 times on your "fast" machine? It runs the bench
> once, then 10, then 100, then 1000 times -- until there's a run that takes
On Fri, Jan 24, 2014 at 2:29 AM, Gregory Ewing
wrote:
> If all you want is a mapping between a sequence of
> length n and compact representation of it, there's
> a much simpler way: just convert it to a base-k
> integer, where k is the size of the alphabet.
>
> The resulting integer won't be any l
Vincent Davis wrote:
I plan to use the sequence as an index to count occurrences of sequences
of length n.
If all you want is a mapping between a sequence of
length n and compact representation of it, there's
a much simpler way: just convert it to a base-k
integer, where k is the size of the al
Vincent Davis wrote:
> Excellent Peter!
> I have a question, the times reported don't make sense to me, for example
> $ python3 -m timeit -s 'from debruijn_compat import debruijn_bytes as d'
> 'd(4, 8)'
> 100 loops, best of 3: 10.2 msec per loop
> This took ~4 secs (stop watch) which is much more
Vincent Davis Wrote in message:
>
I didn't really study the code, and the fact that there's a
nested function could mess it up. But if it were a
straightforward function with exactly one append, , then
replacing the append with a yield would produce the string one
character at a time.
-
On Thu, Jan 23, 2014 at 3:15 PM, Peter Otten <__pete...@web.de> wrote:
> $ python -m timeit -s 'from debruijn_compat import debruijn as d' 'd(4, 8)'
> 10 loops, best of 3: 53.5 msec per loop
> $ python -m timeit -s 'from debruijn_compat import debruijn_bytes as d'
> 'd(4, 8)'
> 10 loops, best of 3
Vincent Davis wrote:
> On Thu, Jan 23, 2014 at 2:36 PM, Mark Lawrence
> wrote:
>
>> FTR string.maketrans is gone from Python 3.2+. Quoting from
>> http://docs.python.org/dev/whatsnew/3.2.html#porting-to-python-3-2 "The
>> previously deprecated string.maketrans() function has been removed in
>> f
On Thu, Jan 23, 2014 at 2:36 PM, Mark Lawrence wrote:
> FTR string.maketrans is gone from Python 3.2+. Quoting from
> http://docs.python.org/dev/whatsnew/3.2.html#porting-to-python-3-2 "The
> previously deprecated string.maketrans() function has been removed in favor
> of the static methods bytes
On 23/01/2014 20:10, Peter Otten wrote:
Vincent Davis wrote:
On Thu, Jan 23, 2014 at 12:02 PM, Peter Otten <__pete...@web.de> wrote:
I just noted that the first Python loop can be eliminated:
Oops, I forgot to paste
import string
def chars(a, b):
return "".join(map(chr, range(a, b)))
Vincent Davis wrote:
> On Thu, Jan 23, 2014 at 12:02 PM, Peter Otten <__pete...@web.de> wrote:
>>
>> I just noted that the first Python loop can be eliminated:
Oops, I forgot to paste
import string
def chars(a, b):
return "".join(map(chr, range(a, b)))
_mapping = string.maketrans(chars(0, 1
On Thu, Jan 23, 2014 at 12:02 PM, Peter Otten <__pete...@web.de> wrote:
>
> I just noted that the first Python loop can be eliminated:
>
> def debruijn(k, n):
> a = k * n * bytearray([0])
> sequence = bytearray()
> extend = sequence.extend # factor out method lookup
> def db(t, p):
On 1/23/14, 10:18 AM, Dave Angel wrote:
> (something about your message seems to make it unquotable)
Not sure why the message was not quotable. I sent it using gmail.
On 1/23/14, 10:18 AM, Dave Angel wrote:
> 64gig is 4^18, so you can forget about holding a string of size 4^50
I guess I will hav
Peter Otten wrote:
> You could change de_bruijn_1() to use `bytearray`s instead of `list`s:
>
> # Python 2
> def debruijn(k, n):
> a = k * n * bytearray([0])
> sequence = bytearray()
> append = sequence.append # factor out method lookup
> def db(t, p,):
> if t > n:
>
Vincent Davis wrote:
> For reference, Wikipedia entry for De Bruijn sequence
> http://en.wikipedia.org/wiki/De_Bruijn_sequence
>
> At the above link is a python algorithm for generating De Brujin
> sequences. It works fine but outputs a list of integers [0, 0, 0, 1, 0, 1,
> 1, 1] and I would pref
On Thu, Jan 23, 2014 at 10:18 AM, Dave Angel wrote:
> If memory size is your issue, why not make the function a
> generator, by replacing the append with a yield?
>
One more thought on the generator. I have an idea for how to use the
generator but I still need 1, chucks of size n de_brujin(k
For reference, Wikipedia entry for De Bruijn sequence
http://en.wikipedia.org/wiki/De_Bruijn_sequence
At the above link is a python algorithm for generating De Brujin sequences.
It works fine but outputs a list of integers [0, 0, 0, 1, 0, 1, 1, 1] and I
would prefer a string '00010111'. This can b
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