def dynamicAsking(G3, f2):
searchDepth = 5
var = "start none"
while len(var) > 0 :
command = var.split()
if command[0] == "printlist":
myNodeIndex = int(command[1])
myNode = []
for eachnode in G3:
if eachnode.nodeIndex == myNodeIndex:
myNode = eachnode
print "nodeIndex, nodeIndexList : ", myNode.nodeIndex, myNode.nodeIndexList
elif command[0] == "printstart":
myNodeIndex = int(command[1])
frankingdepth = int(command[2])
myNode = []
for eachnode in G3:
if eachnode.nodeIndex == myNodeIndex:
myNode = eachnode
frankinginList = myNode.nodeIndexList[frankingdepth: frankingdepth+searchDepth ]
inList = bridgeResolve.findRangeList(frankinginList, f2 )
print "inList : ", inList
elif command[0] == "printend":
myNodeIndex = int(command[1])
frankingdepth = int(command[2])
myNode = []
for eachnode in G3:
if eachnode.nodeIndex == myNodeIndex:
myNode = eachnode
frankingoutList = myNode.nodeIndexList[-frankingdepth- searchDepth: -frankingdepth ]
outList = bridgeResolve.findRangeList(frankingoutList, f2 )
print "outList : ", outList
var = raw_input("Enter Operations: ")
def dynamicAsking(G3, f2):
searchDepth = 5
var = "start none"
while len(var) > 0:
command = var.split()
if command[0] == "printlist":
myNodeIndex = int(command[1])
myNode = []
for eachnode in G3:
if eachnode.nodeIndex == myNodeIndex:
myNode = eachnode
print "nodeIndex, nodeIndexList : ", myNode.nodeIndex, myNode.nodeIndexList
elif command[0] == "printstart":
myNodeIndex = int(command[1])
frankingdepth = int(command[2])
myNode = []
for eachnode in G3:
if eachnode.nodeIndex == myNodeIndex:
myNode = eachnode
frankinginList = myNode.nodeIndexList[frankingdepth:frankingdepth +
searchDepth]
inList = bridgeResolve.findRangeList(frankinginList, f2)
print "inList : ", inList
elif command[0] == "printend":
myNodeIndex = int(command[1])
frankingdepth = int(command[2])
myNode = []
for eachnode in G3:
if eachnode.nodeIndex == myNodeIndex:
myNode = eachnode
frankingoutList = myNode.nodeIndexList[-frankingdepth -
searchDepth:-frankingdepth]
outList = bridgeResolve.findRangeList(frankingoutList, f2)
print "outList : ", outList
var = raw_input("Enter Operations: ")
def formToProcessList(f2, noisyReads, currentNode, indelRobot, flankinglen):
print "formToProcessList"
print "NodeDetail : ", currentNode.nodeIndex, len(currentNode.nodeIndexList) , len(currentNode.listOfPrevNodes), len(currentNode.listOfNextNodes)
searchDepth = 5
in1IndexList, in2IndexList, out1IndexList, out2IndexList, commonIndexList = [] ,[],[],[],[]
for prevNode, i in zip( currentNode.listOfPrevNodes, range(2)):
#print prevNode
edgeWt = prevNode[1]
KmerIndex = prevNode[0].nodeIndexList[-(edgeWt +1)]
if edgeWt+1+flankinglen <= len(prevNode[0].nodeIndexList):
frankingin = prevNode[0].nodeIndexList[-(edgeWt+1+flankinglen)]
readList = bridgeResolve.findRangeList(prevNode[0].nodeIndexList[-(edgeWt+1+flankinglen+searchDepth):-(edgeWt+1+flankinglen)], f2 )
elif len(prevNode[0].listOfPrevNodes) > 0:
edgeWt2 = prevNode[0].listOfPrevNodes[0][1]
maxlen = len(prevNode[0].listOfPrevNodes[0][0].nodeIndexList)
frankingin = prevNode[0].listOfPrevNodes[0][0].nodeIndexList[-min(edgeWt2 + 1 + edgeWt+flankinglen -len(prevNode[0].nodeIndexList),maxlen)]
readList = bridgeResolve.findRangeList(prevNode[0].listOfPrevNodes[0][0].nodeIndexList[-min(edgeWt2 + 1 + edgeWt+flankinglen -len(prevNode[0].nodeIndexList)+ searchDepth,maxlen):-min(edgeWt2 + 1 + edgeWt+flankinglen -len(prevNode[0].nodeIndexList),maxlen)], f2 )
else:
frankingin= prevNode[0].nodeIndexList[0]
readList = bridgeResolve.findRangeList(prevNode[0].nodeIndexList[0:min(searchDepth, len(prevNode[0].nodeIndexList))], f2 )
#readList = bridgeResolve.obtainReadNum(frankingin, f2)
if i == 0 :
for eachitem in readList:
in1IndexList.append(eachitem[0])
elif i == 1 :
for eachitem in readList:
in2IndexList.append(eachitem[0])
for nextNode, i in zip( currentNode.listOfNextNodes, range(2)):
#KmerIndex = nextNode[0].nodeIndex
edgeWt = nextNode[1]
KmerIndex = nextNode[0].nodeIndexList[edgeWt ]
if edgeWt+flankinglen < len(nextNode[0].nodeIndexList) :
frankingout = nextNode[0].nodeIndexList[edgeWt+flankinglen]
readList = bridgeResolve.findRangeList(nextNode[0].nodeIndexList[edgeWt+flankinglen:edgeWt+flankinglen+searchDepth], f2 )
elif len(nextNode[0].listOfNextNodes) > 0:
edgeWt2 = nextNode[0].listOfNextNodes[0][1]
maxlen = len(nextNode[0].listOfNextNodes[0][0].nodeIndexList)
frankingout = nextNode[0].listOfNextNodes[0][0].nodeIndexList[min(edgeWt2+edgeWt+flankinglen -len(nextNode[0].nodeIndexList), maxlen-1)]
readList = bridgeResolve.findRangeList(nextNode[0].listOfNextNodes[0][0].nodeIndexList[min(edgeWt2+edgeWt+flankinglen -len(nextNode[0].nodeIndexList), maxlen-1):min(edgeWt2+edgeWt+flankinglen -len(nextNode[0].nodeIndexList)+searchDepth, maxlen-1)], f2 )
else:
frankingout = nextNode[0].nodeIndexList[-1]
readList = bridgeResolve.findRangeList(nextNode[0].nodeIndexList[max(0, len(nextNode[0].nodeIndexList) - searchDepth):len(nextNode[0].nodeIndexList)], f2 )
#readList = bridgeResolve.obtainReadNum(frankingout, f2)
if i == 0 :
for eachitem in readList:
out1IndexList.append(eachitem[0])
elif i == 1 :
for eachitem in readList:
out2IndexList.append(eachitem[0])
lrep= len(currentNode.nodeIndexList)
Llong = indelRobot.Llong
liid = indelRobot.liid
print "lrep, Llong, liid", lrep, Llong, liid
anchorPoint1 , anchorPoint2 = max ( int(lrep* 0.3 ), liid) , min ( int(lrep *0.7) , lrep - liid)
print "anchorPoint1, anchorPoint2 ", anchorPoint1, anchorPoint2
readSet1 = bridgeResolve.findRangeList(currentNode.nodeIndexList[anchorPoint1:anchorPoint1+searchDepth], f2 )
print "readSet1", readSet1
readSet2 = bridgeResolve.findRangeList(currentNode.nodeIndexList[anchorPoint2: anchorPoint2 + searchDepth], f2)
print "readSet2", readSet2
combinedList = bridgeResolve.distinct(readSet1,"zero") + bridgeResolve.distinct(readSet2, "zero")
combinedList = sorted(combinedList)
for i in range(len(combinedList) -1 ):
if combinedList[i][0] == combinedList[i+1][0]:
commonIndexList.append(combinedList[i][0])
commonIndexList = bridgeResolve.distinct(commonIndexList)
toProcessList = [in1IndexList, in2IndexList, out1IndexList, out2IndexList, commonIndexList]
for eachitem in toProcessList:
print "len(eachitem)" , len(eachitem), eachitem
return toProcessList
def formToProcessList(f2, noisyReads, currentNode, indelRobot, flankinglen):
print "formToProcessList"
print "NodeDetail : ", currentNode.nodeIndex, len(
currentNode.nodeIndexList), len(currentNode.listOfPrevNodes), len(
currentNode.listOfNextNodes)
searchDepth = 5
in1IndexList, in2IndexList, out1IndexList, out2IndexList, commonIndexList = [] ,[],[],[],[]
for prevNode, i in zip(currentNode.listOfPrevNodes, range(2)):
#print prevNode
edgeWt = prevNode[1]
KmerIndex = prevNode[0].nodeIndexList[-(edgeWt + 1)]
if edgeWt + 1 + flankinglen <= len(prevNode[0].nodeIndexList):
frankingin = prevNode[0].nodeIndexList[-(edgeWt + 1 + flankinglen)]
readList = bridgeResolve.findRangeList(
prevNode[0].nodeIndexList[-(edgeWt + 1 + flankinglen +
searchDepth):-(edgeWt + 1 +
flankinglen)], f2)
elif len(prevNode[0].listOfPrevNodes) > 0:
edgeWt2 = prevNode[0].listOfPrevNodes[0][1]
maxlen = len(prevNode[0].listOfPrevNodes[0][0].nodeIndexList)
frankingin = prevNode[0].listOfPrevNodes[0][0].nodeIndexList[-min(
edgeWt2 + 1 + edgeWt + flankinglen -
len(prevNode[0].nodeIndexList), maxlen)]
readList = bridgeResolve.findRangeList(
prevNode[0].listOfPrevNodes[0][0].nodeIndexList[-min(
edgeWt2 + 1 + edgeWt + flankinglen -
len(prevNode[0].nodeIndexList) + searchDepth, maxlen):-min(
edgeWt2 + 1 + edgeWt + flankinglen -
len(prevNode[0].nodeIndexList), maxlen)], f2)
else:
frankingin = prevNode[0].nodeIndexList[0]
readList = bridgeResolve.findRangeList(
prevNode[0].nodeIndexList[
0:min(searchDepth, len(prevNode[0].nodeIndexList))], f2)
#readList = bridgeResolve.obtainReadNum(frankingin, f2)
if i == 0:
for eachitem in readList:
in1IndexList.append(eachitem[0])
elif i == 1:
for eachitem in readList:
in2IndexList.append(eachitem[0])
for nextNode, i in zip(currentNode.listOfNextNodes, range(2)):
#KmerIndex = nextNode[0].nodeIndex
edgeWt = nextNode[1]
KmerIndex = nextNode[0].nodeIndexList[edgeWt]
if edgeWt + flankinglen < len(nextNode[0].nodeIndexList):
frankingout = nextNode[0].nodeIndexList[edgeWt + flankinglen]
readList = bridgeResolve.findRangeList(
nextNode[0].nodeIndexList[edgeWt + flankinglen:edgeWt +
flankinglen + searchDepth], f2)
elif len(nextNode[0].listOfNextNodes) > 0:
edgeWt2 = nextNode[0].listOfNextNodes[0][1]
maxlen = len(nextNode[0].listOfNextNodes[0][0].nodeIndexList)
frankingout = nextNode[0].listOfNextNodes[0][0].nodeIndexList[min(
edgeWt2 + edgeWt + flankinglen -
len(nextNode[0].nodeIndexList), maxlen - 1)]
readList = bridgeResolve.findRangeList(
nextNode[0].listOfNextNodes[0][0].nodeIndexList[min(
edgeWt2 + edgeWt + flankinglen -
len(nextNode[0].nodeIndexList), maxlen - 1):min(
edgeWt2 + edgeWt + flankinglen -
len(nextNode[0].nodeIndexList) + searchDepth, maxlen -
1)], f2)
else:
frankingout = nextNode[0].nodeIndexList[-1]
readList = bridgeResolve.findRangeList(
nextNode[0].
nodeIndexList[max(0,
len(nextNode[0].nodeIndexList) -
searchDepth):len(nextNode[0].nodeIndexList)],
f2)
#readList = bridgeResolve.obtainReadNum(frankingout, f2)
if i == 0:
for eachitem in readList:
out1IndexList.append(eachitem[0])
elif i == 1:
for eachitem in readList:
out2IndexList.append(eachitem[0])
lrep = len(currentNode.nodeIndexList)
Llong = indelRobot.Llong
liid = indelRobot.liid
print "lrep, Llong, liid", lrep, Llong, liid
anchorPoint1, anchorPoint2 = max(int(lrep * 0.3),
liid), min(int(lrep * 0.7), lrep - liid)
print "anchorPoint1, anchorPoint2 ", anchorPoint1, anchorPoint2
readSet1 = bridgeResolve.findRangeList(
currentNode.nodeIndexList[anchorPoint1:anchorPoint1 + searchDepth], f2)
print "readSet1", readSet1
readSet2 = bridgeResolve.findRangeList(
currentNode.nodeIndexList[anchorPoint2:anchorPoint2 + searchDepth], f2)
print "readSet2", readSet2
combinedList = bridgeResolve.distinct(
readSet1, "zero") + bridgeResolve.distinct(readSet2, "zero")
combinedList = sorted(combinedList)
for i in range(len(combinedList) - 1):
if combinedList[i][0] == combinedList[i + 1][0]:
commonIndexList.append(combinedList[i][0])
commonIndexList = bridgeResolve.distinct(commonIndexList)
toProcessList = [
in1IndexList, in2IndexList, out1IndexList, out2IndexList,
commonIndexList
]
for eachitem in toProcessList:
print "len(eachitem)", len(eachitem), eachitem
return toProcessList