On Wed, Feb 24, 2010 at 11:19, Bruno Santos <bacmsan...@gmail.com> wrote:
> It seems that the python 2.6.4 has a more efficient implementation of the
> lists. It runs faster on this version and slower on 2.5.4 on the same
> machine with debian. A lot faster in fact.
> I was trying to change my headche for the last couple of weeks. But you
> migth give me a lot more optimizations that I can pick. I am trying to
> optimize the following function
> def hypergeometric(self,lindex,rindex):
> """
> loc.hypergeometric(lindex,rindex)
> Performs the hypergeometric test for the loci between lindex and
> rindex.
> Returns the minimum p-Value
> """
> aASense = self.aASCounts[lindex*nSize:(rindex+1)*nSize]
> #Create the subarray to test
> aLoci =
> numpy.hstack([self.aSCounts[lindex*nSize:(rindex+1)*nSize],aASense[::-1]])
> #Get the values to test
> length = len(aLoci)
> lsPhasedValues = set([aLoci[i] for i in xrange(length) if i%nSize==0
> and aLoci[i]>0])
> m = length/nSize
> n = (length-1)-(length/nSize-1)
> #Create an array to store the Pvalues
> lsPvalues = []
> append = lsPvalues.append
> #Calculate matches in Phased and non Phased position
> for r in lsPhasedValues:
> #Initiate number of matches to 0
> q = sum([1 for j in xrange(length) if j%nSize==0 and
> aLoci[j]>=r])
> k = sum([1 for j in xrange(length) if aLoci[j]>=r])
> key = '%i,%i,%i,%i'%(q-1,m,n,k)
> try:append(dtPhyper[key])
> except KeyError:
> value = self.lphyper(q-1, m, n, k)
> append(value)
> dtPhyper[key]=value
> return min(lsPvalues)
> Is there any efficient way to test the array simultaneous for two different
> conditions?
j = np.arange(length)
j_nSize_mask = ((j % nSize) == 0)
lsPhasedValues = (j_nSize_mask & (aLoci >= 0)).sum()
...
bigALoci = (aLoci >= r)
q = (j_nSize_mask & bigALoci).sum()
k = bigALoci.sum()
Another way to do it:
j_nSize = np.arange(0, length, nSize)
lsPhasedValues = (aLoci[j_nSize] >= 0).sum()
...
q = (aLoci[j_nSize] >= r).sum()
k = (aLoci >= r).sum()
--
Robert Kern
"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
-- Umberto Eco
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