def identifyRepeat(folderName, mummerLink, contigFilename, contigReadGraph,
repeatFilename, optionToRun):
'''
Input : Graph --- phaseStringGraph1
Output: repeat pairs { [ (1,2), (3,4) ] , [(5,6),(7,8)] }
Algorithm:
a) Reachability test on the graph to find the partners
b) Form Bipartite graph
c) Find connected component in the bipartite and define as repeat pairs
'''
# ## (a) reachability test to find partners
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
# G.reportEdge()
lenDicCC = IORobot.obtainLength(folderName,
contigFilename + "_Double.fasta")
adjacencyList = [[] for i in range(len(lenDicCC))]
N1 = len(lenDicCC)
# # Debug
# for i in range(14):
# debugGraphPath(i, 2, G, N1)
# # End Debug
for i in range(len(lenDicCC)):
adjacencyList[i] = abunGraphLib.findAllReachable(i, N1, G)
print "i, adjacencyList[i] : ", i, adjacencyList[i]
# ## (b) formation of bipartite graph
if optionToRun == "tandem":
newAdjacencyList = adjacencyList
elif optionToRun == "xphase":
newAdjacencyList = abunGraphLib.filterEdge(adjacencyList, folderName,
contigFilename)
# cut here
adjListToRepeatList(newAdjacencyList, folderName, repeatFilename)
def identifyRepeat(folderName, mummerLink, contigFilename, contigReadGraph, repeatFilename, optionToRun):
'''
Input : Graph --- phaseStringGraph1
Output: repeat pairs { [ (1,2), (3,4) ] , [(5,6),(7,8)] }
Algorithm:
a) Reachability test on the graph to find the partners
b) Form Bipartite graph
c) Find connected component in the bipartite and define as repeat pairs
'''
# ## (a) reachability test to find partners
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
# G.reportEdge()
lenDicCC = IORobot.obtainLength(folderName, contigFilename + "_Double.fasta")
adjacencyList = [[] for i in range(len(lenDicCC))]
N1 = len(lenDicCC)
# # Debug
# for i in range(14):
# debugGraphPath(i, 2, G, N1)
# # End Debug
for i in range(len(lenDicCC)):
adjacencyList[i] = abunGraphLib.findAllReachable(i, N1, G)
print "i, adjacencyList[i] : ", i , adjacencyList[i]
# ## (b) formation of bipartite graph
if optionToRun == "tandem" :
newAdjacencyList = adjacencyList
elif optionToRun == "xphase":
newAdjacencyList = abunGraphLib.filterEdge(adjacencyList, folderName, contigFilename)
# cut here
adjListToRepeatList(newAdjacencyList,folderName,repeatFilename )
def identifyRepeat(folderName, mummerLink,contigFilename,contigReadGraph, repeatFilename, optionToRun ):
'''
Input : Graph --- phaseStringGraph1
Output: repeat pairs { [ (1,2), (3,4) ] , [(5,6),(7,8)] }
Algorithm:
a) Reachability test on the graph to find the partners
b) Form Bipartite graph
c) Find connected component in the bipartite and define as repeat pairs
'''
# ## (a) reachability test to find partners
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
# G.reportEdge()
lenDicCC = IORobot.obtainLength(folderName, contigFilename+"_Double.fasta")
adjacencyList = [[] for i in range(len(lenDicCC))]
N1 = len(lenDicCC)
# # Debug
# for i in range(14):
# debugGraphPath(i, 2, G, N1)
# # End Debug
for i in range(len(lenDicCC)):
adjacencyList[i] = abunGraphLib.findAllReachable(i, N1, G)
print "i, adjacencyList[i] : ", i , adjacencyList[i]
# ## (b) formation of bipartite graph
if optionToRun == "tandem" :
newAdjacencyList = adjacencyList
elif optionToRun == "xphase":
newAdjacencyList = abunGraphLib.filterEdge(adjacencyList, folderName, contigFilename)
G2 = abunGraphLib.seqGraphWt(N1 * 2)
for i in range(N1):
for j in newAdjacencyList[i]:
G2.insertEdge(2 * i, 2 * j + 1, 1)
G2.insertEdge(2 * j + 1, 2 * i, 1)
clusters = G2.findConnectedComponents()
repeatList = []
for eachitem in clusters:
leftList, rightList = [], []
for eachsubitem in eachitem:
if eachsubitem % 2 == 0 :
leftList.append(eachsubitem)
else:
rightList.append(eachsubitem)
repeatList.append([abunHouseKeeper.getDistinct(leftList), abunHouseKeeper.getDistinct(rightList)])
with open(folderName + repeatFilename, 'w') as outfile:
json.dump(repeatList, outfile)
json_data = open(folderName + repeatFilename, 'r')
loadData = json.load(json_data)
assert(loadData == repeatList)
def identifyRepeat(folderName, mummerLink, contigFilename, contigReadGraph,
repeatFilename, optionToRun):
'''
Input : Graph --- phaseStringGraph1
Output: repeat pairs { [ (1,2), (3,4) ] , [(5,6),(7,8)] }
Algorithm:
a) Reachability test on the graph to find the partners
b) Form Bipartite graph
c) Find connected component in the bipartite and define as repeat pairs
'''
# ## (a) reachability test to find partners
G = graphLib.seqGraph(0)
G.loadFromFile(folderName, contigReadGraph)
# G.reportEdge()
lenDicCC = IORobot.obtainLength(folderName,
contigFilename + "_Double.fasta")
adjacencyList = [[] for i in range(len(lenDicCC))]
N1 = len(lenDicCC)
# # Debug
# for i in range(14):
# debugGraphPath(i, 2, G, N1)
# # End Debug
for i in range(len(lenDicCC)):
adjacencyList[i] = abunGraphLib.findAllReachable(i, N1, G)
print "i, adjacencyList[i] : ", i, adjacencyList[i]
# ## (b) formation of bipartite graph
if optionToRun == "tandem":
newAdjacencyList = adjacencyList
elif optionToRun == "xphase":
newAdjacencyList = abunGraphLib.filterEdge(adjacencyList, folderName,
contigFilename)
G2 = abunGraphLib.seqGraphWt(N1 * 2)
for i in range(N1):
for j in newAdjacencyList[i]:
G2.insertEdge(2 * i, 2 * j + 1, 1)
G2.insertEdge(2 * j + 1, 2 * i, 1)
clusters = G2.findConnectedComponents()
repeatList = []
for eachitem in clusters:
leftList, rightList = [], []
for eachsubitem in eachitem:
if eachsubitem % 2 == 0:
leftList.append(eachsubitem)
else:
rightList.append(eachsubitem)
repeatList.append([
abunHouseKeeper.getDistinct(leftList),
abunHouseKeeper.getDistinct(rightList)
])
with open(folderName + repeatFilename, 'w') as outfile:
json.dump(repeatList, outfile)
json_data = open(folderName + repeatFilename, 'r')
loadData = json.load(json_data)
assert (loadData == repeatList)