def computeSimilarity(dataArray):
start = time()
sampleIDList = dataArray[8]
n = len(sampleIDList)
matrix = np.zeros((n,n))
for i in range(n):
for j in range(i,n):
#Total ratio computation
common,in1,in2,_,_,_,_,_ = compute(dataArray[7],[sampleIDList[i]],[sampleIDList[j]])
commonA = countAssignmentsInCommon(common,[sampleIDList[i]],[sampleIDList[j]])
numberA1 = countAssignments(in1,[sampleIDList[i]])
numberA2 = countAssignments(in2,[sampleIDList[j]])
tratio = totalRatio(commonA,numberA1,numberA2)
#Pattern ratio computation
commonPatternsList = enumerateCommonPatterns(dataArray[7],[sampleIDList[i]],[sampleIDList[j]])
specificPatternsList1 = enumerateSpecificPatterns(dataArray[7],[sampleIDList[i]],[sampleIDList[j]])
specificPatternsList2 = enumerateSpecificPatterns(dataArray[7],[sampleIDList[i]],[sampleIDList[j]])
pRatio = patternRatio(commonPatternsList,specificPatternsList1,specificPatternsList2)
#Diversity coefficient
dRatio1,_ = computeDiversityCoefficient(dataArray[5],[sampleIDList[i]],dataArray)
dRatio2,_ = computeDiversityCoefficient(dataArray[5],[sampleIDList[j]],dataArray)
subdRatio = abs(dRatio1 - dRatio2)
if subdRatio:
s = sumOpInf(pRatio,tratio) - subdRatio
else:
s = sumOpInf(pRatio,tratio)
matrix[i][j] = s
matrix[j][i] = s
end = time()
print "TIME:",(end-start)
return matrix
def diversityAct(dataArray):
sampleNameList,metadata,interval1,interval2 = createSampleNameList(dataArray)
#@dataArray[5] = n is the number of nodes in the taxonomic tree
coefficient,sample = computeDiversityCoefficient(dataArray[5],sampleNameList,dataArray)
print "\nMicrobial Diversity coefficient is: " + str(coefficient)
print "[If you have obtained -inf, it could mean the taxonomic tree is actually empty.]\n"
answer = raw_input("Save the results? Y/N\n")
if (answer == "Y"):
data = "Microbial Diversity Results ****\n for lists " + str(sampleNameList) + "\n"
if metadata:
data += "selected on metadata: " + str(metadata) + "with extreme values: " + str(interval1) + " (lower bounds) and " + str(interval2) + " (upper bounds) \n"
data += "\nMicrobial Diversity coefficient is: " + str(coefficient) +"\n\nEND OF FILE ****"
writeFile(data,"","text")
elif not (answer == "N"):
print "/!\ You should answer 'Y' or 'N'!"
answer = raw_input("Do you want to display the pie chart of the assignments to the taxonomic tree in the selected samples? Y/N\n")
if (answer == "Y"):
plotPieChart([sample1[0] for sample1 in sample],[sample1[1] for sample1 in sample],"Assignments to the taxonomic tree in " + str(sampleNameList[:3]))
elif not (answer == "N"):
print "/!\ You should answer 'Y' or 'N'!"
