def userNodeSelectionAct(dataArray):
print dataArray[1]
metadatum = sanitize(raw_input("Input the metadatum that will cluster the set of samples among those written above. [ e.g. " + dataArray[1][0] + " ]\n")).split(";")[0]
isInDatabase([metadatum],dataArray[1])
listnodes = dataArray[3].values()
nodesList = parseListNode(raw_input("Choose the group of nodes you want to consider exclusively. [ Read the taxonomic tree to help you: e.g. " + sanitizeNode(listnodes[-3]) + ";" + sanitizeNode(listnodes[1]) + ";" + sanitizeNode(listnodes[-1]) + " ]\n"))
isInDatabase(nodesList,listnodes)
numberSamples = len(dataArray[0])
numberStartingSamples = sanitize(raw_input("Knowing there is/are " + str(numberSamples) + " sample(s), how many samples do you want to create the training set?\n"))
x = integer.match(numberStartingSamples)
if not x or (x and int(numberStartingSamples) > numberSamples) :
print "\n/!\ ERROR: You should write down an integer inferior or equal to ",numberSamples,"."
raise ValueError
numberStartingSamples = int(numberStartingSamples)
assignedClasses,classes,valueSet = classifyIt(dataArray,metadatum,nodesList,numberStartingSamples)
numberClass = len(classes)
youdenJ = countYouden(assignedClasses,classes,numberStartingSamples)
interpretIt(youdenJ)
answer = raw_input("Do you want to plot the classes obtained as a pie chart? Y/N")
if answer == "Y":
labels = [ metadatum + " = " + str(value) for value in valueSet ]
percentagesAs = [ len(class1) for class1 in assignedClasses ]
percentages = [ len(class1) for class1 in classes ]
plotPieChart(labels,percentagesAs,"Assignments depending on " + str(nodesList) + " to class for metadatum " + metadatum)
plotPieChart(labels,percentages,"Real classes depending on " + str(nodesList) + " for metadatum " + metadatum)
elif not (answer == "N"):
print "\n Answer by Y or N!"
answer = raw_input("Do you want to save the results? Y/N")
if (answer == "Y"):
writeFile("Youden's J statistic for this classification is: " + str(youdenJ) + "\n","Assignments depending on " + listNodes(nodesList) + " to classes for metadatum " + metadatum)
elif not (answer == "N"):
print "\n Answer by Y or N!"
return assignedClasses,youdenJ
def userNodeSelectionAct(dataArray):
print dataArray[1]
metadatum = sanitize(
raw_input(
"Input the metadatum that will cluster the set of samples among those written above. [ e.g. "
+ dataArray[1][0] + " ]\n")).split(";")[0]
isInDatabase([metadatum], dataArray[1])
listnodes = dataArray[3].values()
nodesList = parseListNode(
raw_input(
"Choose the group of nodes you want to consider exclusively. [ Read the taxonomic tree to help you: e.g. "
+ sanitizeNode(listnodes[-3]) + ";" + sanitizeNode(listnodes[1]) +
";" + sanitizeNode(listnodes[-1]) + " ]\n"))
isInDatabase(nodesList, listnodes)
numberSamples = len(dataArray[0])
numberStartingSamples = sanitize(
raw_input(
"Knowing there is/are " + str(numberSamples) +
" sample(s), how many samples do you want to create the training set?\n"
))
x = integer.match(numberStartingSamples)
if not x or (x and int(numberStartingSamples) > numberSamples):
print "\n/!\ ERROR: You should write down an integer inferior or equal to ", numberSamples, "."
raise ValueError
numberStartingSamples = int(numberStartingSamples)
assignedClasses, classes, valueSet = classifyIt(dataArray, metadatum,
nodesList,
numberStartingSamples)
numberClass = len(classes)
youdenJ = countYouden(assignedClasses, classes, numberStartingSamples)
interpretIt(youdenJ)
answer = raw_input(
"Do you want to plot the classes obtained as a pie chart? Y/N")
if answer == "Y":
labels = [metadatum + " = " + str(value) for value in valueSet]
percentagesAs = [len(class1) for class1 in assignedClasses]
percentages = [len(class1) for class1 in classes]
plotPieChart(
labels, percentagesAs, "Assignments depending on " +
str(nodesList) + " to class for metadatum " + metadatum)
plotPieChart(
labels, percentages, "Real classes depending on " +
str(nodesList) + " for metadatum " + metadatum)
elif not (answer == "N"):
print "\n Answer by Y or N!"
answer = raw_input("Do you want to save the results? Y/N")
if (answer == "Y"):
writeFile(
"Youden's J statistic for this classification is: " +
str(youdenJ) + "\n", "Assignments depending on " +
listNodes(nodesList) + " to classes for metadatum " + metadatum)
elif not (answer == "N"):
print "\n Answer by Y or N!"
return assignedClasses, youdenJ
def randomSubSamplingAct(dataArray):
print dataArray[1]
metadatum = sanitize(raw_input("Input the metadatum that will cluster the set of samples among those written above. [ e.g. " + dataArray[1][0] + " ]\n")).split(";")[0]
isInDatabase([metadatum],dataArray[1])
s = raw_input("Input the number s of random samplings.\n")
n = raw_input("Input the number n of nodes to select at each try.\n")
if not integer.match(s) or not integer.match(n):
print "\n/!\ ERROR: s and n must both be integers."
raise ValueError
numberSamples = len(dataArray[0])
numberStartingSamples = sanitize(raw_input("Knowing there is/are " + str(numberSamples) + "sample(s), how many samples do you want to create the training set? \n"))
x = integer.match(numberStartingSamples)
if not x or (x and int(numberStartingSamples) > numberSamples):
print "\n/!\ ERROR: You should write down an integer."
raise ValueError
numberStartingSamples = int(numberStartingSamples)
listnodes = dataArray[3].values()
s,n = int(s),int(n)
#Here the set of classes is a list of two lists containing the samples in C and not C
bestClassification = []
bestClassesList = []
#Worse value for this coefficient
currBestYouden = inf
nodesNumber = len(dataArray[3])
while s:
#Randomly draw n distinct nodes among the nodes in the taxonomic tree
nodesList = randomChoice(listnodes,n)
assignedClasses,classes,valueSet = classifyIt(dataArray,metadatum,nodesList,numberStartingSamples)
numberClass = len(classes)
youdenJ = countYouden(assignedClasses,classes,numberSamples)
res = numberClass - youdenJ
if min(res,currBestYouden) == res:
bestClassification = []
for i in nodesList:
bestClassification.append(i)
currBestYouden = res
bestClassesList = []
for i in assignedClasses:
bestClassesList.append(i)
s -= 1
interpretIt(numberClass - currBestYouden)
if answer == "Y":
percentagesAs = [ len(class1) for class1 in assignedClasses ]
labels = [ metadatum + " = " + str(value) for value in valueSet ]
percentages = [ len(class1) for class1 in classes ]
plotPieChart(labels,percentagesAs,"Assignments depending on " + listNodes(nodesList) + " to class for metadatum " + metadatum)
plotPieChart(labels,percentages,"Real classes depending on " + listNodes(nodesList) + " for metadatum " + metadatum)
answer = raw_input("Do you want to save the results? Y/N")
if (answer == "Y"):
writeFile("Best Youden's J statistic for this classification is: " + str(numberClass - currBestYouden) + "\nand most relevant list of nodes for this metadatum is:" + str(bestClassification),"Assignments to classes for metadatum " + metadatum)
elif not (answer == "N"):
print "\n Answer by Y or N!"
return bestClassification,(numberClass - currBestYouden),bestClassesList
def plottingAct(dataArray):
creatingArrayOutput = creatingArray(dataArray)
if creatingArrayOutput[0] == "graph":
graphTypeInput,xArray,yArray,typeInput,valueInput1,valueInput2 = creatingArrayOutput
maxx,minix = getMaxMin(xArray)
maxy,miniy = getMaxMin(yArray)
if typeInput == "BB":
xLabel = "Group of bacteria 1"
yLabel = "Group of bacteria 2"
#typeInput == "BM"
else:
xLabel = "Group of bacteria"
yLabel = "Metadatum"
plotGraph(xArray,yArray,xLabel=xLabel,yLabel=yLabel,maxx=maxx+1,minx=minix-1,maxy=maxy+1,miny=miniy-1,title="Plotting of type " + typeInput + " with values " + str(valuesInput1[:3]) + "... and " + str(valuesInput2[:3]) + "...")
elif creatingArrayOutput[0] == "pie":
graphTypeInput,result,nodesGroup,sampleNameList,metadataList = creatingArrayOutput
plotPieChart(sampleNameList,result,"Assignments to the group of bacterias: " + str(nodesGroup) + " depending on samples")
else:
print "\n/!\ ERROR: [BUG] [actions/plottingAct] Unknown type of graph."
raise ValueError
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'!"
def randomSubSamplingAct(dataArray):
print dataArray[1]
metadatum = sanitize(
raw_input(
"Input the metadatum that will cluster the set of samples among those written above. [ e.g. "
+ dataArray[1][0] + " ]\n")).split(";")[0]
isInDatabase([metadatum], dataArray[1])
s = raw_input("Input the number s of random samplings.\n")
n = raw_input("Input the number n of nodes to select at each try.\n")
if not integer.match(s) or not integer.match(n):
print "\n/!\ ERROR: s and n must both be integers."
raise ValueError
numberSamples = len(dataArray[0])
numberStartingSamples = sanitize(
raw_input(
"Knowing there is/are " + str(numberSamples) +
"sample(s), how many samples do you want to create the training set? \n"
))
x = integer.match(numberStartingSamples)
if not x or (x and int(numberStartingSamples) > numberSamples):
print "\n/!\ ERROR: You should write down an integer."
raise ValueError
numberStartingSamples = int(numberStartingSamples)
listnodes = dataArray[3].values()
s, n = int(s), int(n)
#Here the set of classes is a list of two lists containing the samples in C and not C
bestClassification = []
bestClassesList = []
#Worse value for this coefficient
currBestYouden = inf
nodesNumber = len(dataArray[3])
while s:
#Randomly draw n distinct nodes among the nodes in the taxonomic tree
nodesList = randomChoice(listnodes, n)
assignedClasses, classes, valueSet = classifyIt(
dataArray, metadatum, nodesList, numberStartingSamples)
numberClass = len(classes)
youdenJ = countYouden(assignedClasses, classes, numberSamples)
res = numberClass - youdenJ
if min(res, currBestYouden) == res:
bestClassification = []
for i in nodesList:
bestClassification.append(i)
currBestYouden = res
bestClassesList = []
for i in assignedClasses:
bestClassesList.append(i)
s -= 1
interpretIt(numberClass - currBestYouden)
if answer == "Y":
percentagesAs = [len(class1) for class1 in assignedClasses]
labels = [metadatum + " = " + str(value) for value in valueSet]
percentages = [len(class1) for class1 in classes]
plotPieChart(
labels, percentagesAs, "Assignments depending on " +
listNodes(nodesList) + " to class for metadatum " + metadatum)
plotPieChart(
labels, percentages, "Real classes depending on " +
listNodes(nodesList) + " for metadatum " + metadatum)
answer = raw_input("Do you want to save the results? Y/N")
if (answer == "Y"):
writeFile(
"Best Youden's J statistic for this classification is: " +
str(numberClass - currBestYouden) +
"\nand most relevant list of nodes for this metadatum is:" +
str(bestClassification),
"Assignments to classes for metadatum " + metadatum)
elif not (answer == "N"):
print "\n Answer by Y or N!"
return bestClassification, (numberClass - currBestYouden), bestClassesList
