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
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
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
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
