def clusterUnitTest():
typeLen = 30
readLen = 40
copyLen = 10
p = 0.01
noisyReads = np.zeros(typeLen * copyLen * 2 * readLen,
dtype=np.int8).reshape(typeLen * copyLen,
2 * readLen)
rawReads = np.zeros(typeLen * readLen,
dtype=np.int8).reshape(typeLen, readLen)
for typeindex in range(typeLen):
for eachbaseindex in range(readLen):
rawReads[typeindex][eachbaseindex] = random.randint(1, 4)
for index in range(copyLen):
startindex = index * typeLen
endindex = (index + 1) * typeLen
tempNoisyReads = dataGen.addIndelNoise(rawReads, p)
for j in range(startindex, endindex):
noisyReads[j][0:len(tempNoisyReads[j -
startindex])] = tempNoisyReads[
j - startindex][:]
logging.rawDataSave("clusterReadsUnitTest", "", "", noisyReads, 'n')
def clusterUnitTest():
typeLen = 30
readLen = 40
copyLen = 10
p = 0.01
noisyReads = np.zeros(typeLen*copyLen*2*readLen, dtype = np.int8).reshape(typeLen*copyLen,2*readLen)
rawReads = np.zeros(typeLen*readLen, dtype = np.int8).reshape(typeLen, readLen)
for typeindex in range(typeLen):
for eachbaseindex in range(readLen):
rawReads[typeindex][eachbaseindex] = random.randint(1,4)
for index in range(copyLen):
startindex = index* typeLen
endindex = (index +1 )*typeLen
tempNoisyReads = dataGen.addIndelNoise(rawReads, p)
for j in range(startindex, endindex):
noisyReads[j][0:len(tempNoisyReads[j-startindex])] = tempNoisyReads[j-startindex][:]
logging.rawDataSave("clusterReadsUnitTest", "", "", noisyReads, 'n')
def generateData( typeOfGen,detail, parameterRobot):
N, G, L,p = parameterRobot.N, parameterRobot.G, parameterRobot.L,parameterRobot.p
motherGen = np.zeros(G, dtype = np.int8 )
reads = np.zeros(N*L, dtype = np.int8).reshape(N,L)
noisyReads = np.zeros(N*L, dtype = np.int8).reshape(N,L)
detailArr = detail.split('-')
for index in range(G):
motherGen[index] = random.randint(1,4)
if typeOfGen == 'r' :
longestRepeatlength = int(detailArr[0])
repeatLoc1 = random.randint(0, G-2*longestRepeatlength)
repeatLoc2 = random.randint(repeatLoc1 +longestRepeatlength ,G-longestRepeatlength )
print "repeatLoc1, repeatLoc2, detail", repeatLoc1, repeatLoc2, detail
for eachindex in range(repeatLoc2, repeatLoc2 + longestRepeatlength):
motherGen[eachindex] = motherGen[eachindex - repeatLoc2 + repeatLoc1]
elif typeOfGen == 'i':
lrepeat = int(detailArr[0])
linter = int(detailArr[1])
repeatLoc1 = random.randint(0 , G- 2*lrepeat -2*linter )
intrepeatLoc1 = random.randint(repeatLoc1 + lrepeat ,G- lrepeat -2*linter )
repeatLoc2 = random.randint(intrepeatLoc1 + linter , G- lrepeat - linter )
intrepeatLoc2 = random.randint(repeatLoc2 + lrepeat, G-linter)
for eachindex in range(repeatLoc2, repeatLoc2+ lrepeat):
motherGen[eachindex] = motherGen[eachindex - repeatLoc2 + repeatLoc1]
for eachindex in range(intrepeatLoc2, intrepeatLoc2+ linter):
motherGen[eachindex] = motherGen[eachindex -intrepeatLoc2 + intrepeatLoc1 ]
print "repeatLoc1,repeatLoc2,intrepeatLoc1,intrepeatLoc2, lrepeat,linter",repeatLoc1,repeatLoc2,intrepeatLoc1,intrepeatLoc2, lrepeat,linter
elif typeOfGen == 't' :
ltriple = int(detailArr[0])
repeatLoc1 = random.randint(0, G-3*ltriple)
repeatLoc2 = random.randint(repeatLoc1+ ltriple, G- 2*ltriple)
repeatLoc3 = random.randint(repeatLoc2+ ltriple, G- ltriple)
for eachindex in range(repeatLoc2, repeatLoc2 + ltriple):
motherGen[eachindex] = motherGen[eachindex -repeatLoc2 + repeatLoc1 ]
for eachindex in range(repeatLoc3, repeatLoc3 + ltriple):
motherGen[eachindex] = motherGen[eachindex - repeatLoc3 + repeatLoc1]
print "repeatLoc1, repeatLoc2, repeatLoc3, ltriple", repeatLoc1, repeatLoc2, repeatLoc3, ltriple
elif typeOfGen == 'd' :
filename = detailArr[0]
truncatestart = int(detailArr[1])
truncateend = int(detailArr[2])
f = open(filename , 'r')
line = f.readline()
motherStr = ""
print "Genome Detail ", line
while(len(line) > 0):
line= f.readline()
motherStr = motherStr + line[0:-1]
print "genomeLen", len(motherStr)
G = truncateend - truncatestart
print "G:", G
motherGen = np.zeros(G, dtype = np.int8)
for eachindex in range(truncatestart, truncateend):
if motherStr[eachindex] == 'A':
motherGen[eachindex- truncatestart] = 1
elif motherStr[eachindex] == 'C':
motherGen[eachindex- truncatestart] = 2
elif motherStr[eachindex] == 'G':
motherGen[eachindex- truncatestart] = 3
elif motherStr[eachindex] == 'T':
motherGen[eachindex- truncatestart] = 4
f.close()
elif typeOfGen == 'm':
lrepeat = int(detailArr[0])
lsnp = int(detailArr[1])
lint = int(detailArr[2])
randLoc1 = random.randint(0, G - 2*lrepeat - 2*lsnp - 2*lint)
randLocSnp1 = random.randint(randLoc1+ lrepeat, G - lrepeat - 2*lsnp - 2*lint)
randLocint1 = random.randint(randLocSnp1 + lsnp , G - lrepeat - lsnp - 2*lint)
randLoc2 = random.randint(randLocint1 + lint, G - lrepeat - lsnp - lint)
randLocSnp2 = random.randint(randLoc2 + lrepeat, G - lsnp - lint)
randLocint2 = random.randint(randLocSnp2 + lsnp, G - lint)
for eachindex in range(randLoc2, randLoc2+ lrepeat):
motherGen[eachindex] = motherGen[eachindex - randLoc2 + randLoc1]
for eachindex in range(randLocSnp2, randLocSnp2+ lsnp):
motherGen[eachindex] = motherGen[eachindex - randLocSnp2 + randLocSnp1]
for eachindex in range(randLocint2, randLocint2 + lint):
motherGen[eachindex] = motherGen[eachindex - randLocint2 + randLocint1]
#print eachindex, eachindex - randLocint2 + randLocint1
#print motherGen[randLocint1:randLocint1+lint] == motherGen[randLocint2:randLocint2+lint]
# introduce 1 SNP on both sides
motherGen[randLocSnp2 + lsnp/4] = motherGen[randLocSnp2 + lsnp/4] + 1
if motherGen[randLocSnp2 + lsnp/4] == 5 :
motherGen[randLocSnp2 + lsnp/4] = 1
motherGen[randLocSnp2 + lsnp*3/4] = motherGen[randLocSnp2 + lsnp*3/4] + 1
if motherGen[randLocSnp2 + lsnp*3/4] == 5:
motherGen[randLocSnp2 + lsnp*3/4] = 1
print "randLocSnp1 + lsnp/4, randLocSnp2 + lsnp/4",randLocSnp1 + lsnp/4, randLocSnp2 + lsnp/4
print motherGen[randLocSnp1 + lsnp/4], motherGen[randLocSnp2 + lsnp/4]
print "randLocSnp1 + 3*lsnp/4, randLocSnp2 + 3*lsnp/4",randLocSnp1 + 3*lsnp/4, randLocSnp2 + 3*lsnp/4
print motherGen[randLocSnp1 + 3*lsnp/4], motherGen[randLocSnp2 + 3*lsnp/4]
# motherGen[randLocSnp2 + lsnp/2] = motherGen[randLocSnp2 + lsnp/2] + 1
# if motherGen[randLocSnp2 + lsnp/2] == 5 :
# motherGen[randLocSnp2 + lsnp/2] = 1
# print motherGen[randLocSnp1 + lsnp/2], motherGen[randLocSnp2 + lsnp/2]
elif typeOfGen == 'a':
print "Tandem Repeat"
ltandem1 = int(detailArr[0])
lcopyNum1 = int(detailArr[1])
ltandem2 = int(detailArr[2])
lcopyNum2 = int(detailArr[3])
lrepeat1 = ltandem1*lcopyNum1
lrepeat2 = ltandem2*lcopyNum2
randLoc1 = random.randint(0, G - lrepeat1 - lrepeat2)
randLoc2 = random.randint(randLoc1 + lrepeat1, G - lrepeat2)
for copyindex in range(lcopyNum1):
for eachindex in range(randLoc1+copyindex*ltandem1, randLoc1 + (copyindex+1) *ltandem1 ):
motherGen[eachindex]= motherGen[eachindex- copyindex*ltandem1]
for copyindex in range(lcopyNum2):
for eachindex in range(randLoc2+copyindex*ltandem2, randLoc2 + (copyindex+1) *ltandem2 ):
motherGen[eachindex]= motherGen[eachindex- copyindex*ltandem2]
print "randLoc1, randLoc2", randLoc1, randLoc2
else:
print "Error in Type "
indel = parameterRobot.indel
reads, noisyReads = readGen(N,L,p, motherGen, indel)
logging.rawDataSave(parameterRobot.defaultFolder+"UnitTest", motherGen, reads, noisyReads)
return motherGen, reads, noisyReads
def generateData(typeOfGen, detail, parameterRobot):
N, G, L, p = parameterRobot.N, parameterRobot.G, parameterRobot.L, parameterRobot.p
motherGen = np.zeros(G, dtype=np.int8)
reads = np.zeros(N * L, dtype=np.int8).reshape(N, L)
noisyReads = np.zeros(N * L, dtype=np.int8).reshape(N, L)
detailArr = detail.split('-')
for index in range(G):
motherGen[index] = random.randint(1, 4)
if typeOfGen == 'r':
longestRepeatlength = int(detailArr[0])
repeatLoc1 = random.randint(0, G - 2 * longestRepeatlength)
repeatLoc2 = random.randint(repeatLoc1 + longestRepeatlength,
G - longestRepeatlength)
print "repeatLoc1, repeatLoc2, detail", repeatLoc1, repeatLoc2, detail
for eachindex in range(repeatLoc2, repeatLoc2 + longestRepeatlength):
motherGen[eachindex] = motherGen[eachindex - repeatLoc2 +
repeatLoc1]
elif typeOfGen == 'i':
lrepeat = int(detailArr[0])
linter = int(detailArr[1])
repeatLoc1 = random.randint(0, G - 2 * lrepeat - 2 * linter)
intrepeatLoc1 = random.randint(repeatLoc1 + lrepeat,
G - lrepeat - 2 * linter)
repeatLoc2 = random.randint(intrepeatLoc1 + linter,
G - lrepeat - linter)
intrepeatLoc2 = random.randint(repeatLoc2 + lrepeat, G - linter)
for eachindex in range(repeatLoc2, repeatLoc2 + lrepeat):
motherGen[eachindex] = motherGen[eachindex - repeatLoc2 +
repeatLoc1]
for eachindex in range(intrepeatLoc2, intrepeatLoc2 + linter):
motherGen[eachindex] = motherGen[eachindex - intrepeatLoc2 +
intrepeatLoc1]
print "repeatLoc1,repeatLoc2,intrepeatLoc1,intrepeatLoc2, lrepeat,linter", repeatLoc1, repeatLoc2, intrepeatLoc1, intrepeatLoc2, lrepeat, linter
elif typeOfGen == 't':
ltriple = int(detailArr[0])
repeatLoc1 = random.randint(0, G - 3 * ltriple)
repeatLoc2 = random.randint(repeatLoc1 + ltriple, G - 2 * ltriple)
repeatLoc3 = random.randint(repeatLoc2 + ltriple, G - ltriple)
for eachindex in range(repeatLoc2, repeatLoc2 + ltriple):
motherGen[eachindex] = motherGen[eachindex - repeatLoc2 +
repeatLoc1]
for eachindex in range(repeatLoc3, repeatLoc3 + ltriple):
motherGen[eachindex] = motherGen[eachindex - repeatLoc3 +
repeatLoc1]
print "repeatLoc1, repeatLoc2, repeatLoc3, ltriple", repeatLoc1, repeatLoc2, repeatLoc3, ltriple
elif typeOfGen == 'd':
filename = detailArr[0]
truncatestart = int(detailArr[1])
truncateend = int(detailArr[2])
f = open(filename, 'r')
line = f.readline()
motherStr = ""
print "Genome Detail ", line
while (len(line) > 0):
line = f.readline()
motherStr = motherStr + line[0:-1]
print "genomeLen", len(motherStr)
G = truncateend - truncatestart
print "G:", G
motherGen = np.zeros(G, dtype=np.int8)
for eachindex in range(truncatestart, truncateend):
if motherStr[eachindex] == 'A':
motherGen[eachindex - truncatestart] = 1
elif motherStr[eachindex] == 'C':
motherGen[eachindex - truncatestart] = 2
elif motherStr[eachindex] == 'G':
motherGen[eachindex - truncatestart] = 3
elif motherStr[eachindex] == 'T':
motherGen[eachindex - truncatestart] = 4
f.close()
elif typeOfGen == 'm':
lrepeat = int(detailArr[0])
lsnp = int(detailArr[1])
lint = int(detailArr[2])
randLoc1 = random.randint(0, G - 2 * lrepeat - 2 * lsnp - 2 * lint)
randLocSnp1 = random.randint(randLoc1 + lrepeat,
G - lrepeat - 2 * lsnp - 2 * lint)
randLocint1 = random.randint(randLocSnp1 + lsnp,
G - lrepeat - lsnp - 2 * lint)
randLoc2 = random.randint(randLocint1 + lint,
G - lrepeat - lsnp - lint)
randLocSnp2 = random.randint(randLoc2 + lrepeat, G - lsnp - lint)
randLocint2 = random.randint(randLocSnp2 + lsnp, G - lint)
for eachindex in range(randLoc2, randLoc2 + lrepeat):
motherGen[eachindex] = motherGen[eachindex - randLoc2 + randLoc1]
for eachindex in range(randLocSnp2, randLocSnp2 + lsnp):
motherGen[eachindex] = motherGen[eachindex - randLocSnp2 +
randLocSnp1]
for eachindex in range(randLocint2, randLocint2 + lint):
motherGen[eachindex] = motherGen[eachindex - randLocint2 +
randLocint1]
#print eachindex, eachindex - randLocint2 + randLocint1
#print motherGen[randLocint1:randLocint1+lint] == motherGen[randLocint2:randLocint2+lint]
# introduce 1 SNP on both sides
motherGen[randLocSnp2 +
lsnp / 4] = motherGen[randLocSnp2 + lsnp / 4] + 1
if motherGen[randLocSnp2 + lsnp / 4] == 5:
motherGen[randLocSnp2 + lsnp / 4] = 1
motherGen[randLocSnp2 +
lsnp * 3 / 4] = motherGen[randLocSnp2 + lsnp * 3 / 4] + 1
if motherGen[randLocSnp2 + lsnp * 3 / 4] == 5:
motherGen[randLocSnp2 + lsnp * 3 / 4] = 1
print "randLocSnp1 + lsnp/4, randLocSnp2 + lsnp/4", randLocSnp1 + lsnp / 4, randLocSnp2 + lsnp / 4
print motherGen[randLocSnp1 + lsnp / 4], motherGen[randLocSnp2 +
lsnp / 4]
print "randLocSnp1 + 3*lsnp/4, randLocSnp2 + 3*lsnp/4", randLocSnp1 + 3 * lsnp / 4, randLocSnp2 + 3 * lsnp / 4
print motherGen[randLocSnp1 + 3 * lsnp / 4], motherGen[randLocSnp2 +
3 * lsnp / 4]
# motherGen[randLocSnp2 + lsnp/2] = motherGen[randLocSnp2 + lsnp/2] + 1
# if motherGen[randLocSnp2 + lsnp/2] == 5 :
# motherGen[randLocSnp2 + lsnp/2] = 1
# print motherGen[randLocSnp1 + lsnp/2], motherGen[randLocSnp2 + lsnp/2]
elif typeOfGen == 'a':
print "Tandem Repeat"
ltandem1 = int(detailArr[0])
lcopyNum1 = int(detailArr[1])
ltandem2 = int(detailArr[2])
lcopyNum2 = int(detailArr[3])
lrepeat1 = ltandem1 * lcopyNum1
lrepeat2 = ltandem2 * lcopyNum2
randLoc1 = random.randint(0, G - lrepeat1 - lrepeat2)
randLoc2 = random.randint(randLoc1 + lrepeat1, G - lrepeat2)
for copyindex in range(lcopyNum1):
for eachindex in range(randLoc1 + copyindex * ltandem1,
randLoc1 + (copyindex + 1) * ltandem1):
motherGen[eachindex] = motherGen[eachindex -
copyindex * ltandem1]
for copyindex in range(lcopyNum2):
for eachindex in range(randLoc2 + copyindex * ltandem2,
randLoc2 + (copyindex + 1) * ltandem2):
motherGen[eachindex] = motherGen[eachindex -
copyindex * ltandem2]
print "randLoc1, randLoc2", randLoc1, randLoc2
else:
print "Error in Type "
indel = parameterRobot.indel
reads, noisyReads = readGen(N, L, p, motherGen, indel)
logging.rawDataSave(parameterRobot.defaultFolder + "UnitTest", motherGen,
reads, noisyReads)
return motherGen, reads, noisyReads