Beispiel #1
0
def testImpute(snpData, Ls):
    """
	Function that slides the window(s) and calculates accuracy of imputation
	on all called values.
	"""

    global corrects
    global count

    L = max(Ls)
    vectors = snpData.vectors
    snps = snpData.snps
    numSNPs = len(snps)

    print "Running imputation window test with %d window sizes..." % len(Ls),

    count = 0
    corrects = zeros(len(Ls))

    vectorLength = len(vectors.values()[0])

    vectorQueue = CircularQueue(Ls, vectorLength)
    acc = zeros((len(Ls), vectorLength), uint16)
    # Initialize queue
    for i in xrange(L):
        snpVector = vectors[snps[i]]
        vectorQueue.queue[i] = snpVector
        for j in xrange(len(Ls)):
            if i < Ls[j]:
                add(acc[j], snpVector, acc[j])

                # Begin impute
    for i in xrange(numSNPs):
        if i + L < numSNPs:
            vectorQueue.enqueue(vectors[snps[i + L]])
        else:
            vectorQueue.enqueue(zeros(vectorLength, uint16))

        mid = vectorQueue.getMid()
        snp = snps[i]

        for j in xrange(len(Ls)):
            top, bottom = vectorQueue.getEnds(j)
            add(acc[j], top, acc[j])
            subtract(acc[j], bottom, acc[j])
            imputeSNPT(snpData, i, acc[j] - mid, snp, j)

    print "Done"

    return count, corrects
Beispiel #2
0
def testImpute(snpData, Ls):
    '''
    Function that slides the window(s) and calculates accuracy of imputation
    on all called values.
    '''

    global corrects
    global count

    L = max(Ls)
    vectors = snpData.vectors
    snps = snpData.snps
    numSNPs = len(snps)

    print 'Running imputation window test with %d window sizes...' % len(Ls),

    count = 0
    corrects = zeros(len(Ls))

    vectorLength = len(vectors.values()[0])

    vectorQueue = CircularQueue(Ls, vectorLength)
    acc = zeros((len(Ls), vectorLength), uint16)
    # Initialize queue
    for i in xrange(L):
        snpVector = vectors[snps[i]]
        vectorQueue.queue[i] = snpVector
        for j in xrange(len(Ls)):
            if i < Ls[j]:
                add(acc[j], snpVector, acc[j])

    # Begin impute
    for i in xrange(numSNPs):
        if i + L < numSNPs:
            vectorQueue.enqueue(vectors[snps[i + L]])
        else:
            vectorQueue.enqueue(zeros(vectorLength, uint16))

        mid = vectorQueue.getMid()
        snp = snps[i]

        for j in xrange(len(Ls)):
            top, bottom = vectorQueue.getEnds(j)
            add(acc[j], top, acc[j])
            subtract(acc[j], bottom, acc[j])
            imputeSNPT(snpData, i, acc[j] - mid, snp, j)

    print 'Done'

    return count, corrects
Beispiel #3
0
def impute(snpData, L):
    """
	Function that slides the window and calls other functions to do the actual imputation.
	"""

    global count

    snpData.changes = dict()
    count = 0
    snps = snpData.snps
    vectors = snpData.vectors
    numSNPs = len(snps)

    sys.stderr.write("Imputing with window size " + str(L) + "...")

    vectorLength = len(vectors.values()[0])
    vectorQueue = CircularQueue([L], vectorLength)
    acc = zeros(vectorLength, uint16)

    # Initialize queue
    for i in xrange(L):
        snpVector = vectors[snps[i]]
        vectorQueue.queue[i] = snpVector
        add(acc, snpVector, acc)

        # Begin impute
    for i in xrange(numSNPs):

        if i + L < numSNPs:
            snpVector = vectors[snps[i + L]]
            vectorQueue.enqueue(snpVector)
        else:
            vectorQueue.enqueue(zeros(vectorLength, uint16))

        top, bottom = vectorQueue.getEnds(0)
        add(acc, top, acc)
        subtract(acc, bottom, acc)
        snp = snps[i]
        if "?" in snp:
            imputeSNP(snpData, i, acc, snp)

    sys.stderr.write("Done.\n")
    return count
Beispiel #4
0
def impute(snpData, L):
    '''
    Function that slides the window and calls other functions to do the actual imputation.
    '''

    global count

    snpData.changes = dict()
    count = 0
    snps = snpData.snps
    vectors = snpData.vectors
    numSNPs = len(snps)

    print "Imputing with window size " + str(L) + "...",

    vectorLength = len(vectors.values()[0])
    vectorQueue = CircularQueue([L], vectorLength)
    acc = zeros(vectorLength, uint16)

    # Initialize queue
    for i in xrange(L):
        snpVector = vectors[snps[i]]
        vectorQueue.queue[i] = snpVector
        add(acc, snpVector, acc)

    # Begin impute
    for i in xrange(numSNPs):

        if i + L < numSNPs:
            snpVector = vectors[snps[i + L]]
            vectorQueue.enqueue(snpVector)
        else:
            vectorQueue.enqueue(zeros(vectorLength, uint16))

        top, bottom = vectorQueue.getEnds(0)
        add(acc, top, acc)
        subtract(acc, bottom, acc)
        snp = snps[i]
        if '?' in snp:
            imputeSNP(snpData, i, acc, snp)

    print "Done"
    return count
class TicketCounterSimulation:
    def __init__(self, numAgents, numMinutes, betweenTime, serviceTime):
        self._arriveprob = 1.0 / betweenTime
        self._serviceTime = serviceTime
        self._numMinutes = numMinutes
        self.served = 0

        self._passengers = CircularQueue()
        self._Agents = [None] * numAgents
        for i in range(numAgents):
            self._Agents = TicketAgent(i + 1)

        self._totalWaitTime = 0
        self._numPassengers = 0

    def run(self):
        for curTime in range(self._numMinutes):
            self._handleArrival(curTime)
            self._handleBeginService(curTime)
            self._handleEndService(curTime)
        self.printResult()

    def printResult(self):
        numServed = self._numPassengers - len(self._passengers)
        avgwait = float(self._totalWaitTime) / numServed
        print("")
        print("Number of passengers served()")
        print("Number of passengers remaining in line")
        print("The average wait time was")

    # Handle Customer Arrival
    def _handleArrival(self, curTime):
        prob = randint(0.0, 1.0)
        if 0.0 <= prob and prob <= self._arriveprob:
            person = Passenger(self._numPassengers + 1, curTime)
            self._passengers.enqueue(person)
            self._numPassengers += 1
            print("Time Passenger")

    # Begin Customer Service
    def _handleBeginService(self, curTime):
        i = 0
        while i < len(self._Agents):
            if self._Agents[i].isFree() and not self._passengers.isEmpty(
            ) and curTime != self._numMinutes:
                passenger = self._passengers.dequeue()
                self.served += 1
                stoptime = curTime + self._serviceTime
                self._Agents[i].starService(passenger, stoptime)
                self._totalWaitTime += (curTime - passenger.timeArrivaed())
                print("Time Agent started serving")

    # End Customer Service
    def _handleEndService(self, curTime):
        i = 0
        while i < len(self._Agents):
            if self._Agents[i].isFinished(curTime):
                passenger = self._Agents[i].stopService()
                print(":Time Agent stoped serving")

            i += 1