class Clusters:
def __init__(self, fsClusters, hsClusters):
self.fsClusters = fsClusters
self.hsClusters = hsClusters
self.biGraph = Bipartite(hsClusters)
# In each case, destruction of old cluster must occur first
def join(self, clusterID0, clusterID1, fs=False):
joinHistory = SJGlobals.joinHistory
allowableJoins = SJGlobals.allowableJoins
allowableClusterJoins = SJGlobals.allowableClusterJoins
clusters = self.hsClusters
if fs:
clusters = self.fsClusters
# None of the individuals can be joined again. They're already
# full-sibs
for ind0 in clusters[clusterID0].individuals:
for ind1 in clusters[clusterID1].individuals:
allowableJoins[ind0.index][ind1.index] = False
allowableJoins[ind1.index][ind0.index] = False
else:
self.biGraph.combineNodes(clusterID0, clusterID1)
for i in range(2 * SJGlobals.nIndvs):
allowableClusterJoins[i][clusterID1] = False
if not allowableClusterJoins[clusterID1][i]:
allowableClusterJoins[clusterID0][i] = False
clusters[clusterID1].deleteCluster()
clusters[clusterID0].add(clusters[clusterID1])
del clusters[clusterID1]
def joinFS(self, fsClusterID0, fsClusterID1, hsClusterIDs):
if len(hsClusterIDs) == 2:
hsClusterIDs[0].sort()
hsClusterIDs[1].sort()
self.join(hsClusterIDs[0][0], hsClusterIDs[0][1])
self.join(hsClusterIDs[1][0], hsClusterIDs[1][1])
else:
hsClusterIDs[0].sort()
self.join(hsClusterIDs[0][0], hsClusterIDs[0][1])
def sortMaternalPaternal(self):
clusters = self.hsClusters
"""
Construct the algorithm's half-sibs. We partition the clusters in
to a maternal and paternal side 0 = Maternal, 1 = Paternal. This
part of the algorithm iterates through each cluster and adds the
clusters to the respective 0 or 1 side based on the assumption that
each indiv. will have a mother and a father. Once a cluster has
been added, the members of that cluster are queued up so that their
cluster representing the other parent can be added to the opposite
partition.
"""
aHS = []
addedClusters = dict()
numClusters = len(clusters)
for i in clusters.keys():
# Only process clusters which have not yet been assigned
if i not in addedClusters:
q = Queue.Queue()
tmp = [[], []]
tmp[0].append(copy.deepcopy(clusters[i]))
addedClusters[i] = True
# Stores a list of found individuals
for ind in clusters[i].individuals:
q.put([ind, i, 0])
# Add the other sex parents to the opposite partition
while not q.empty():
cur = q.get()
# Find the cluster which has not just been added
if cur[1] == cur[0].hsClusters[0]:
j = cur[0].hsClusters[1]
else:
j = cur[0].hsClusters[0]
# Add the cluster and mark as added
pMIdx = (cur[2] + 1) % 2
if j not in addedClusters:
tmp[pMIdx].append(copy.deepcopy(clusters[j]))
addedClusters[j] = True
for ind in clusters[j].individuals:
q.put([ind, j, pMIdx])
aHS.append(tmp)
self.aHS = aHS
mHS = []
pHS = []
for s in aHS:
for i in s[0]:
mHS.append(i)
for i in s[1]:
pHS.append(i)
return mHS, pHS
def matchingClusters(self, ind0, ind1):
matchingClusters = []
if ind0.hsClusters[0] == ind0.hsClusters[0]:
matchingClusters.append([0, 0])
if ind0.hsClusters[0] == ind0.hsClusters[1]:
matchingClusters.append([0, 1])
if ind0.hsClusters[1] == ind0.hsClusters[0]:
matchingClusters.append([1, 0])
if ind0.hsClusters[1] == ind0.hsClusters[1]:
matchingClusters.append([1, 1])
return matchingClusters
def findFSInd(self, clusterID0, clusterID1):
c0 = self.hsClusters[clusterID0]
c1 = self.hsClusters[clusterID1]
for ind0 in c0.individuals:
for ind1 in c1.individuals:
if ind0.index == ind1.index:
return ind0
return None
class Clusters:
def __init__(self, fsClusters, hsClusters):
self.fsClusters = fsClusters
self.hsClusters = hsClusters
self.biGraph = Bipartite(hsClusters)
# In each case, destruction of old cluster must occur first
def join(self, clusterID0, clusterID1, fs=False):
joinHistory = SJGlobals.joinHistory
allowableJoins = SJGlobals.allowableJoins
allowableClusterJoins = SJGlobals.allowableClusterJoins
clusters = self.hsClusters
if fs:
clusters = self.fsClusters
# None of the individuals can be joined again. They're already
# full-sibs
for ind0 in clusters[clusterID0].individuals:
for ind1 in clusters[clusterID1].individuals:
allowableJoins[ind0.index][ind1.index] = False
allowableJoins[ind1.index][ind0.index] = False
else:
self.biGraph.combineNodes(clusterID0, clusterID1)
for i in range(2 * SJGlobals.nIndvs):
allowableClusterJoins[i][clusterID1] = False
if not allowableClusterJoins[clusterID1][i]:
allowableClusterJoins[clusterID0][i] = False
clusters[clusterID1].deleteCluster()
clusters[clusterID0].add(clusters[clusterID1])
del clusters[clusterID1]
def joinFS(self, fsClusterID0, fsClusterID1, hsClusterIDs):
if len(hsClusterIDs) == 2:
hsClusterIDs[0].sort()
hsClusterIDs[1].sort()
self.join(hsClusterIDs[0][0], hsClusterIDs[0][1])
self.join(hsClusterIDs[1][0], hsClusterIDs[1][1])
else:
hsClusterIDs[0].sort()
self.join(hsClusterIDs[0][0], hsClusterIDs[0][1])
def sortMaternalPaternal(self):
clusters = self.hsClusters
'''
Construct the algorithm's half-sibs. We partition the clusters in
to a maternal and paternal side 0 = Maternal, 1 = Paternal. This
part of the algorithm iterates through each cluster and adds the
clusters to the respective 0 or 1 side based on the assumption that
each indiv. will have a mother and a father. Once a cluster has
been added, the members of that cluster are queued up so that their
cluster representing the other parent can be added to the opposite
partition.
'''
aHS = []
addedClusters = dict()
numClusters = len(clusters)
for i in clusters.keys():
# Only process clusters which have not yet been assigned
if i not in addedClusters:
q = Queue.Queue()
tmp = [[], []]
tmp[0].append(copy.deepcopy(clusters[i]))
addedClusters[i] = True
# Stores a list of found individuals
for ind in clusters[i].individuals:
q.put([ind, i, 0])
# Add the other sex parents to the opposite partition
while not q.empty():
cur = q.get()
# Find the cluster which has not just been added
if cur[1] == cur[0].hsClusters[0]:
j = cur[0].hsClusters[1]
else:
j = cur[0].hsClusters[0]
# Add the cluster and mark as added
pMIdx = (cur[2] + 1) % 2
if j not in addedClusters:
tmp[pMIdx].append(copy.deepcopy(clusters[j]))
addedClusters[j] = True
for ind in clusters[j].individuals:
q.put([ind, j, pMIdx])
aHS.append(tmp)
self.aHS = aHS
mHS = []
pHS = []
for s in aHS:
for i in s[0]:
mHS.append(i)
for i in s[1]:
pHS.append(i)
return mHS, pHS
def matchingClusters(self, ind0, ind1):
matchingClusters = []
if ind0.hsClusters[0] == ind0.hsClusters[0]:
matchingClusters.append([0, 0])
if ind0.hsClusters[0] == ind0.hsClusters[1]:
matchingClusters.append([0, 1])
if ind0.hsClusters[1] == ind0.hsClusters[0]:
matchingClusters.append([1, 0])
if ind0.hsClusters[1] == ind0.hsClusters[1]:
matchingClusters.append([1, 1])
return matchingClusters
def findFSInd(self, clusterID0, clusterID1):
c0 = self.hsClusters[clusterID0]
c1 = self.hsClusters[clusterID1]
for ind0 in c0.individuals:
for ind1 in c1.individuals:
if ind0.index == ind1.index:
return ind0
return None
def __init__(self, fsClusters, hsClusters):
self.fsClusters = fsClusters
self.hsClusters = hsClusters
self.biGraph = Bipartite(hsClusters)
def __init__(self, fsClusters, hsClusters):
self.fsClusters = fsClusters
self.hsClusters = hsClusters
self.biGraph = Bipartite(hsClusters)
