def makeClusters(self, tccList): #init self.addedList = [] self.clusters = [] #Create Clusters connectionsDict = compare.makeConnectionsDict(tccList) for tcc in tccList: self.createClusters(connectionsDict, tcc, "top") for cluster in self.clusters: cluster = cg.sortTccList(cluster)
#Start Timer timer = cg.cgTimer() timer.start() #Get list of mature tccs conf = cgConfig.returnConfDict() finalMirFileName = '/u/home8/gxxiao/chrisgre/projects/PipeRuns/LanderHuman/out/LanderHuman-s3k8b17.ALL.FINAL.mirs.tsv' finalMirFileName = conf['resultsRaw'] matureTccs = compare.tccFileToList(finalMirFileName, 1) # list of all mature micro in tcc print 'List getting', timer.split() #make connections dict matureConnections = compare.makeConnectionsDict(matureTccs) print 'Make connections:', timer.split() #Now have to define Clusters... clusters = [] addedList = [] #I don't think python passes by reference? also I think this function is in the middle because it uses a global variable :P def createClusters(item = None, mode = None): if item in addedList: return 0 elif mode == "top": clusters.append([item]) addedList.append(item) ##creates new cluster with the item already stored in it for connectedItem in matureConnections[item]:
def defineClusters(cName = None):
#Start Timer
timer = cg.cgTimer()
timer.start()
#Get list of mature tccs
conf = cgConfig.getConfig(cName) #passed or default
finalMirFileName = conf.conf['resultsRaw']
matureTccs = compare.tccFileToList(finalMirFileName, 1) # list of all mature micro in tcc
print 'List getting', timer.split()
#make connections dict
matureConnections = compare.makeConnectionsDict(matureTccs)
print 'Make connections:', timer.split()
#Now have to define Clusters...
clusters = []
addedList = []
#I don't think python passes by reference? also I think this function is in the middle because it uses a global variable :P
def createClusters(item = None, mode = None):
if item in addedList:
return 0
elif mode == "top":
clusters.append([item])
addedList.append(item) ##creates new cluster with the item already stored in it
for connectedItem in matureConnections[item]:
createClusters(connectedItem, "neighbor")
elif mode == "neighbor":
clusters[-1].append(item) #add this item to the last cluster created
addedList.append(item)
for connectedItem in matureConnections[item]:
createClusters(connectedItem, "neighbor")
for tcc in matureTccs:
createClusters(tcc, "top")
print 'Make Clusters', timer.split()
#Sort Clusters.
sortedClusters = []
for cluster in clusters:
sortedClusters.append(cg.sortTccList(cluster))
print 'Sort Clusters:', timer.split()
#Output sorted cluster file
clusterFileName = conf.conf['sortedClusters']
clusterFile = open(clusterFileName, 'w')
for cluster in sortedClusters:
for hit in cluster:
clusterFile.write('%s,' % hit)
clusterFile.write('\n')
clusterFile.close()
'''
#re-create sortedClusters list:
clusterFileName = 'sortedClusters.data'
clusterFile = open(clusterFileName, 'r')
sortedClusters = []
for line in clusterFile:
sortedClusters.append([])
line = line.strip()[0:-1] #take off last comma ;P
for hit in (line.strip().split(',')):
sortedClusters[-1].append(hit)
'''
print 'Store intermediate data:', timer.split()
#output hitsAround file
outputFile = open(conf.conf['hitsPerFrame'], 'w')
frameLength = 200
frameShift = 1
for cluster in sortedClusters:
#grab first and last coordinate from cluster, for each cluster deduce how many theoretical microRNAs were in hitScope
clusterChrom = cluster[0].split(":")[0]
clusterStrand = cluster[0].split(":")[1]
firstCoord = int(cluster[0].split(":")[2])
#print cluster[-1]
lastCoord = int(cluster[-1].split(":")[3])
startCoord = firstCoord
while startCoord < lastCoord:
#count how many hits there are in this range
rangeStart = startCoord - (frameLength/2)
rangeEnd = startCoord + (frameLength/2)
rangeTcc = '%s:%s:%s:%s' % (clusterChrom, clusterStrand, rangeStart, rangeEnd)
overlappedList = compare.compareTwoTcc([rangeTcc], cluster, 2)
hitCount = len(overlappedList)
#output
outputFile.write('%s\t%s\n' % (rangeTcc, hitCount))
startCoord = startCoord + frameShift #check overlap with range
outputFile.close()
print 'Output Hits per Frame:', timer.split()
print 'Overall Time:', timer.report()
def defineClusters(cName=None):
#Start Timer
timer = cg.cgTimer()
timer.start()
#Get list of mature tccs
conf = cgConfig.getConfig(cName) #passed or default
finalMirFileName = conf.conf['resultsRaw']
matureTccs = compare.tccFileToList(finalMirFileName,
1) # list of all mature micro in tcc
print 'List getting', timer.split()
#make connections dict
matureConnections = compare.makeConnectionsDict(matureTccs)
print 'Make connections:', timer.split()
#Now have to define Clusters...
clusters = []
addedList = []
#I don't think python passes by reference? also I think this function is in the middle because it uses a global variable :P
def createClusters(item=None, mode=None):
if item in addedList:
return 0
elif mode == "top":
clusters.append([item])
addedList.append(
item) ##creates new cluster with the item already stored in it
for connectedItem in matureConnections[item]:
createClusters(connectedItem, "neighbor")
elif mode == "neighbor":
clusters[-1].append(
item) #add this item to the last cluster created
addedList.append(item)
for connectedItem in matureConnections[item]:
createClusters(connectedItem, "neighbor")
for tcc in matureTccs:
createClusters(tcc, "top")
print 'Make Clusters', timer.split()
#Sort Clusters.
sortedClusters = []
for cluster in clusters:
sortedClusters.append(cg.sortTccList(cluster))
print 'Sort Clusters:', timer.split()
#Output sorted cluster file
clusterFileName = conf.conf['sortedClusters']
clusterFile = open(clusterFileName, 'w')
for cluster in sortedClusters:
for hit in cluster:
clusterFile.write('%s,' % hit)
clusterFile.write('\n')
clusterFile.close()
'''
#re-create sortedClusters list:
clusterFileName = 'sortedClusters.data'
clusterFile = open(clusterFileName, 'r')
sortedClusters = []
for line in clusterFile:
sortedClusters.append([])
line = line.strip()[0:-1] #take off last comma ;P
for hit in (line.strip().split(',')):
sortedClusters[-1].append(hit)
'''
print 'Store intermediate data:', timer.split()
#output hitsAround file
outputFile = open(conf.conf['hitsPerFrame'], 'w')
frameLength = 200
frameShift = 1
for cluster in sortedClusters:
#grab first and last coordinate from cluster, for each cluster deduce how many theoretical microRNAs were in hitScope
clusterChrom = cluster[0].split(":")[0]
clusterStrand = cluster[0].split(":")[1]
firstCoord = int(cluster[0].split(":")[2])
#print cluster[-1]
lastCoord = int(cluster[-1].split(":")[3])
startCoord = firstCoord
while startCoord < lastCoord:
#count how many hits there are in this range
rangeStart = startCoord - (frameLength / 2)
rangeEnd = startCoord + (frameLength / 2)
rangeTcc = '%s:%s:%s:%s' % (clusterChrom, clusterStrand,
rangeStart, rangeEnd)
overlappedList = compare.compareTwoTcc([rangeTcc], cluster, 2)
hitCount = len(overlappedList)
#output
outputFile.write('%s\t%s\n' % (rangeTcc, hitCount))
startCoord = startCoord + frameShift #check overlap with range
outputFile.close()
print 'Output Hits per Frame:', timer.split()
print 'Overall Time:', timer.report()
