def runAssembler(snpRate, typeOfGen, detail, parameterRobot):
#N, G, L, p,K,snpRate, typeOfGen, detail = 100, 100, 10000, 0.01,30,0.001, 'r', "1000"
motherGen, reads, noisyReads = dataGen.generateData(
typeOfGen, detail, parameterRobot)
motherGen, reads, noisyReads = logging.rawDataLoad(
parameterRobot.defaultFolder + "UnitTest", parameterRobot.G,
parameterRobot.N, parameterRobot.L, "dn")
f1 = cluster.groupIndelNoisyKmers(noisyReads, parameterRobot)
G1, startList, f1 = graphForm.getSeqGraph(f1, noisyReads, parameterRobot)
f2, G2 = branchClear.clearResidual(f1, G1, parameterRobot)
G3 = bridgeResolve.resolveRepeats(f2, G2, parameterRobot)
G4 = alignmentBridge.MSAresolve(f2, G3, noisyReads, snpRate,
parameterRobot)
#G4 = G3
recovSeq = eulerCycle.findEC(G4)
recovGen = readAns.reportRecovSeq(recovSeq, f2, noisyReads, parameterRobot)
numMistakes, success = compare.subAlignCompare(recovGen, motherGen,
parameterRobot)
#numMistakes, success = 0 , 0
return numMistakes, success
# Target of the new code : Fast Assemble and assembly in optimal amount of information
#t0 = time.time()
#N, G, L, p,snpRate, typeOfGen, detail = 1000, 10000,200, 0.015, 0.001 ,'m', "500-300-50"
#runAssembler(N, G, L, p,snpRate, typeOfGen, detail)
#print "Time (sec) :", time.time() - t0
def ECUnitTest(Nin,G, Lin, foldername = "", bridgingDepth = 20, msaWidth = 20 ):
dummyParameters = logging.parameterObj()
dummyParameters.bridgingDepth = bridgingDepth
dummyParameters.msaWidth = msaWidth
dummyParameters.N, dummyParameters.G, dummyParameters.L, dummyParameters.p = Nin, G,Lin, 0.015
dummyParameters.indel = True
dummyParameters.defaultFolder = foldername
dummyParameters.threshold = 5
dummyParameters.liid = 48
snpRate, typeOfGen, detail = 0.001 ,'m', "500-200-50"
G,N,L = dummyParameters.G, dummyParameters.N, dummyParameters.L,
motherGen, reads, noisyReads = logging.rawDataLoad(foldername+"UnitTest",G,N,L, "dn")
f2= logging.fmapfusedLoad(foldername+'clusteredGroup2.csv')
G2 = logging.loadGraph(foldername+'basicMapping.csv', foldername+'seqMapping.txt', 'simple')
checkCondensingBasic(G2, [G2[0]], "simple")
G3 = bridgeResolve.resolveRepeats(f2,G2,dummyParameters)
checkCondensingBasic(G3, [G3[0]], "MB")
G4 = alignmentBridge.MSAresolve(f2, G3, noisyReads, snpRate,dummyParameters)
#G4 = G3
#checkCondensingBasic(G4, [G4[0]], "MB")
recovSeq = eulerCycle.findEC(G4)
recovGen = readAns.reportRecovSeq(recovSeq, f2, noisyReads,dummyParameters)
numMistakes, success = compare.subAlignCompare(recovGen, motherGen,dummyParameters)
return numMistakes, success
def runAssembler(snpRate, typeOfGen, detail,parameterRobot):
#N, G, L, p,K,snpRate, typeOfGen, detail = 100, 100, 10000, 0.01,30,0.001, 'r', "1000"
motherGen, reads, noisyReads = dataGen.generateData(typeOfGen, detail,parameterRobot)
motherGen, reads, noisyReads = logging.rawDataLoad(parameterRobot.defaultFolder+"UnitTest",parameterRobot.G,parameterRobot.N,parameterRobot.L, "dn")
f1 = cluster.groupIndelNoisyKmers(noisyReads,parameterRobot)
G1,startList, f1 = graphForm.getSeqGraph(f1,noisyReads, parameterRobot)
f2, G2 = branchClear.clearResidual(f1, G1,parameterRobot)
G3 = bridgeResolve.resolveRepeats(f2, G2,parameterRobot)
G4 = alignmentBridge.MSAresolve(f2, G3, noisyReads, snpRate,parameterRobot )
#G4 = G3
recovSeq = eulerCycle.findEC(G4)
recovGen = readAns.reportRecovSeq(recovSeq, f2, noisyReads,parameterRobot)
numMistakes, success = compare.subAlignCompare(recovGen, motherGen,parameterRobot)
#numMistakes, success = 0 , 0
return numMistakes, success
# Target of the new code : Fast Assemble and assembly in optimal amount of information
#t0 = time.time()
#N, G, L, p,snpRate, typeOfGen, detail = 1000, 10000,200, 0.015, 0.001 ,'m', "500-300-50"
#runAssembler(N, G, L, p,snpRate, typeOfGen, detail)
#print "Time (sec) :", time.time() - t0
def resolveRepeatsUnitTest(foldername= ""):
var = raw_input("Enter something: ")
print "you entered ", var
f2= logging.fmapfusedLoad(foldername+'clusteredGroup2.csv')
G2 = logging.loadGraph(foldername+'basicMapping.csv', foldername+'seqMapping.txt', 'simple')
checkCondensingBasic(G2, [G2[0]], "simple")
dummyParameters = logging.parameterObj()
dummyParameters.bridgingDepth = 10
G3 = bridgeResolve.resolveRepeats(f2,G2,dummyParameters)
checkCondensingBasic(G3, [G3[0]], "MB")
def resolveRepeatsUnitTest(foldername=""):
var = raw_input("Enter something: ")
print "you entered ", var
f2 = logging.fmapfusedLoad(foldername + 'clusteredGroup2.csv')
G2 = logging.loadGraph(foldername + 'basicMapping.csv',
foldername + 'seqMapping.txt', 'simple')
checkCondensingBasic(G2, [G2[0]], "simple")
dummyParameters = logging.parameterObj()
dummyParameters.bridgingDepth = 10
G3 = bridgeResolve.resolveRepeats(f2, G2, dummyParameters)
checkCondensingBasic(G3, [G3[0]], "MB")
def MSAResolverEpeatUnitTest(Nin, Lin, foldername = ""):
f2= logging.fmapfusedLoad('clusteredGroup2.csv')
G2 = logging.loadGraph(foldername+'basicMapping.csv', foldername+'seqMapping.txt', 'simple')
#checkCondensingBasic(G2, [G2[0]], "simple")
dummyParameters = logging.parameterObj()
dummyParameters.bridgingDepth = 5
dummyParameters.msaWidth = 20
G3 = bridgeResolve.resolveRepeats(f2,G2,dummyParameters)
#checkCondensingBasic(G3, [G3[0]], "MB")
N, G, L, p,snpRate, typeOfGen, detail = Nin, 10000,Lin, 0.015, 0.001 ,'m', "500-300-50"
motherGen, reads, noisyReads = logging.rawDataLoad(foldername+"UnitTest",G,N,L,"dn")
alignmentBridge.MSAresolve(f2, G3, noisyReads, snpRate,dummyParameters)
def MSAResolverEpeatUnitTest(Nin, Lin, foldername=""):
f2 = logging.fmapfusedLoad('clusteredGroup2.csv')
G2 = logging.loadGraph(foldername + 'basicMapping.csv',
foldername + 'seqMapping.txt', 'simple')
#checkCondensingBasic(G2, [G2[0]], "simple")
dummyParameters = logging.parameterObj()
dummyParameters.bridgingDepth = 5
dummyParameters.msaWidth = 20
G3 = bridgeResolve.resolveRepeats(f2, G2, dummyParameters)
#checkCondensingBasic(G3, [G3[0]], "MB")
N, G, L, p, snpRate, typeOfGen, detail = Nin, 10000, Lin, 0.015, 0.001, 'm', "500-300-50"
motherGen, reads, noisyReads = logging.rawDataLoad(foldername + "UnitTest",
G, N, L, "dn")
alignmentBridge.MSAresolve(f2, G3, noisyReads, snpRate, dummyParameters)
def ECUnitTest(Nin, G, Lin, foldername="", bridgingDepth=20, msaWidth=20):
dummyParameters = logging.parameterObj()
dummyParameters.bridgingDepth = bridgingDepth
dummyParameters.msaWidth = msaWidth
dummyParameters.N, dummyParameters.G, dummyParameters.L, dummyParameters.p = Nin, G, Lin, 0.015
dummyParameters.indel = True
dummyParameters.defaultFolder = foldername
dummyParameters.threshold = 5
dummyParameters.liid = 48
snpRate, typeOfGen, detail = 0.001, 'm', "500-200-50"
G, N, L = dummyParameters.G, dummyParameters.N, dummyParameters.L,
motherGen, reads, noisyReads = logging.rawDataLoad(foldername + "UnitTest",
G, N, L, "dn")
f2 = logging.fmapfusedLoad(foldername + 'clusteredGroup2.csv')
G2 = logging.loadGraph(foldername + 'basicMapping.csv',
foldername + 'seqMapping.txt', 'simple')
checkCondensingBasic(G2, [G2[0]], "simple")
G3 = bridgeResolve.resolveRepeats(f2, G2, dummyParameters)
checkCondensingBasic(G3, [G3[0]], "MB")
G4 = alignmentBridge.MSAresolve(f2, G3, noisyReads, snpRate,
dummyParameters)
#G4 = G3
#checkCondensingBasic(G4, [G4[0]], "MB")
recovSeq = eulerCycle.findEC(G4)
recovGen = readAns.reportRecovSeq(recovSeq, f2, noisyReads,
dummyParameters)
numMistakes, success = compare.subAlignCompare(recovGen, motherGen,
dummyParameters)
return numMistakes, success
def interactiveNodeRemoval(foldername, modeOfOpt = "skip"):
'''
delnode 1002
deledge 1004, 1028
addedge 1023 , 3434
'''
G2 = []
if modeOfOpt == "skip":
varList = ["start none", ""]
elif modeOfOpt == "desiredOpt":
varList = ["start none", "delnode 734288", "delnode 1716432", "fusenode 1438104", "fusenode 1166060" , "view", ""]
var = varList.pop(0)
while len(var) > 0 :
command = var.split()
if command[0] == "start":
print "Start"
G2 = logging.loadGraph(foldername+'basicMapping.csv', foldername+'seqMapping.txt', 'simple')
elif command[0] == "delnode":
print "To delete node"
currentNodeIndex = int(command[1])
print "currentNodeIndex", currentNodeIndex
for eachnode in G2:
if eachnode.nodeIndex == currentNodeIndex:
currentNode = eachnode
for eachitem in currentNode.listOfPrevNodes:
eachitem.listOfNextNodes.remove(currentNode)
currentNode.listOfPrevNodes = []
for eachitem in currentNode.listOfNextNodes:
eachitem.listOfPrevNodes.remove(currentNode)
currentNode.listOfNextNodes = []
currentNode.nodeIndexList = []
graphForm.condenseGraph(G2)
elif command[0] == "deledge":
node1 = int(command[1])
node2 = int(command[2])
startNode, endNode = [] , []
for eachnode in G2:
if eachnode.nodeIndex == node1:
startNode = eachnode
if eachnode.nodeIndex == node2:
endNode = eachnode
startNode.listOfNextNodes.remove(endNode)
endNode.listOfPrevNodes.remove(startNode)
print "To insert nodes"
elif command[0] == "addedge" :
node1 = int(command[1])
node2 = int(command[2])
startNode, endNode = [] , []
for eachnode in G2:
if eachnode.nodeIndex == node1:
startNode = eachnode
if eachnode.nodeIndex == node2:
endNode = eachnode
startNode.listOfNextNodes.append(endNode)
endNode.listOfPrevNodes.append(startNode)
elif command[0] == "fusenode":
myNodeIndex = int(command[1])
for eachnode in G2:
if eachnode.nodeIndex == myNodeIndex:
currentNode = eachnode
if len(currentNode.listOfPrevNodes) == 1:
prevNode = currentNode.listOfPrevNodes[0]
for eachnextnode in currentNode.listOfNextNodes:
eachnextnode.listOfPrevNodes.remove(currentNode)
eachnextnode.listOfPrevNodes.append(prevNode)
prevNode.listOfNextNodes.append(eachnextnode)
prevNode.listOfNextNodes.remove(currentNode)
currentNode.listOfNextNodes = []
currentNode.listOfPrevNodes =[]
currentNode.nodeIndexList = []
elif len(currentNode.listOfNextNodes) ==1 :
nextNode = currentNode.listOfNextNodes[0]
for eachprevnode in currentNode.listOfPrevNodes:
eachprevnode.listOfNextNodes.remove(currentNode)
eachprevnode.listOfNextNodes.append(nextNode)
nextNode.listOfPrevNodes.append(eachprevnode)
nextNode.listOfPrevNodes.remove(currentNode)
currentNode.listOfNextNodes = []
currentNode.listOfPrevNodes = []
currentNode.nodeIndexList = []
elif command[0] == "view":
G2 = graphForm.newCondensingStep(G2)
G2 = G2[0]
checkCondensingBasic(G2, [G2[0]], "simple")
#var = raw_input("Enter Operations: ")
var = varList.pop(0)
dummyParameters = logging.parameterObj()
dummyParameters.bridgingDepth = 20
print "Loading fmap and graph "
f2= logging.fmapfusedLoad(foldername+'clusteredGroup2.csv')
G3 = bridgeResolve.resolveRepeats(f2,G2,dummyParameters)
assert(1==2)
G3 = G2
print "Done Loading the fmap and graph"
#checkCondensingBasic(G3, [G3[0]], "MB")
return G3,f2
def interactiveNodeRemoval(foldername, modeOfOpt="skip"):
'''
delnode 1002
deledge 1004, 1028
addedge 1023 , 3434
'''
G2 = []
if modeOfOpt == "skip":
varList = ["start none", ""]
elif modeOfOpt == "desiredOpt":
varList = [
"start none", "delnode 734288", "delnode 1716432",
"fusenode 1438104", "fusenode 1166060", "view", ""
]
var = varList.pop(0)
while len(var) > 0:
command = var.split()
if command[0] == "start":
print "Start"
G2 = logging.loadGraph(foldername + 'basicMapping.csv',
foldername + 'seqMapping.txt', 'simple')
elif command[0] == "delnode":
print "To delete node"
currentNodeIndex = int(command[1])
print "currentNodeIndex", currentNodeIndex
for eachnode in G2:
if eachnode.nodeIndex == currentNodeIndex:
currentNode = eachnode
for eachitem in currentNode.listOfPrevNodes:
eachitem.listOfNextNodes.remove(currentNode)
currentNode.listOfPrevNodes = []
for eachitem in currentNode.listOfNextNodes:
eachitem.listOfPrevNodes.remove(currentNode)
currentNode.listOfNextNodes = []
currentNode.nodeIndexList = []
graphForm.condenseGraph(G2)
elif command[0] == "deledge":
node1 = int(command[1])
node2 = int(command[2])
startNode, endNode = [], []
for eachnode in G2:
if eachnode.nodeIndex == node1:
startNode = eachnode
if eachnode.nodeIndex == node2:
endNode = eachnode
startNode.listOfNextNodes.remove(endNode)
endNode.listOfPrevNodes.remove(startNode)
print "To insert nodes"
elif command[0] == "addedge":
node1 = int(command[1])
node2 = int(command[2])
startNode, endNode = [], []
for eachnode in G2:
if eachnode.nodeIndex == node1:
startNode = eachnode
if eachnode.nodeIndex == node2:
endNode = eachnode
startNode.listOfNextNodes.append(endNode)
endNode.listOfPrevNodes.append(startNode)
elif command[0] == "fusenode":
myNodeIndex = int(command[1])
for eachnode in G2:
if eachnode.nodeIndex == myNodeIndex:
currentNode = eachnode
if len(currentNode.listOfPrevNodes) == 1:
prevNode = currentNode.listOfPrevNodes[0]
for eachnextnode in currentNode.listOfNextNodes:
eachnextnode.listOfPrevNodes.remove(currentNode)
eachnextnode.listOfPrevNodes.append(prevNode)
prevNode.listOfNextNodes.append(eachnextnode)
prevNode.listOfNextNodes.remove(currentNode)
currentNode.listOfNextNodes = []
currentNode.listOfPrevNodes = []
currentNode.nodeIndexList = []
elif len(currentNode.listOfNextNodes) == 1:
nextNode = currentNode.listOfNextNodes[0]
for eachprevnode in currentNode.listOfPrevNodes:
eachprevnode.listOfNextNodes.remove(currentNode)
eachprevnode.listOfNextNodes.append(nextNode)
nextNode.listOfPrevNodes.append(eachprevnode)
nextNode.listOfPrevNodes.remove(currentNode)
currentNode.listOfNextNodes = []
currentNode.listOfPrevNodes = []
currentNode.nodeIndexList = []
elif command[0] == "view":
G2 = graphForm.newCondensingStep(G2)
G2 = G2[0]
checkCondensingBasic(G2, [G2[0]], "simple")
#var = raw_input("Enter Operations: ")
var = varList.pop(0)
dummyParameters = logging.parameterObj()
dummyParameters.bridgingDepth = 20
print "Loading fmap and graph "
f2 = logging.fmapfusedLoad(foldername + 'clusteredGroup2.csv')
G3 = bridgeResolve.resolveRepeats(f2, G2, dummyParameters)
assert (1 == 2)
G3 = G2
print "Done Loading the fmap and graph"
#checkCondensingBasic(G3, [G3[0]], "MB")
return G3, f2