def targetDiseaseCircos(directory, empty, empty2):
print("\n ---------targetDiseaseCircos Protocol ------------ \n")
"""
Create edgelist for network clustered by tissue-miRNA.
"""
if not os.path.exists(directory):
os.makedirs(directory)
allMirnaTargetInteractions = ml.readMirTarBase()
targetMatrix = ml.Matrix(allMirnaTargetInteractions)
tarClustnum = targetMatrix.createClusters()
allMirnaDiseaseInteractions = ml.readMiriadData()
diseaseMatrix = ml.Matrix(allMirnaDiseaseInteractions)
diseaseClustnum = diseaseMatrix.createClusters()
interactionDict = {}
num = 0
mirnaSet = set()
diseaseSet = set()
targetSet = set()
for i in range(tarClustnum):
mirnaTargetInteractions = targetMatrix.getClusterInteractions(i)
for j in range(diseaseClustnum):
mirnaDiseaseInteractions = diseaseMatrix.getClusterInteractions(j)
for disItems, tarItems in [(disItems, tarItems)
for disItems in mirnaDiseaseInteractions
for tarItems in mirnaTargetInteractions
]:
if disItems[0] == ml.simplifyMirnaNames([tarItems[0]])[0][0]:
key = ("targetCluster" + str(i + 1),
"diseaseCluster" + str(j + 1),
len(targetMatrix.getClusterRows(i)) +
len(targetMatrix.getClusterColumns(i)),
len(diseaseMatrix.getClusterRows(j)) +
len(diseaseMatrix.getClusterColumns(j)))
if key not in interactionDict:
interactionDict[key] = 1
else:
interactionDict[key] += 1
num += 1
for mirna in targetMatrix.getClusterRows(i):
mirnaSet.add(mirna)
for mirna in diseaseMatrix.getClusterRows(i):
mirnaSet.add(mirna)
for target in targetMatrix.getClusterColumns(i):
targetSet.add(target)
for disease in diseaseMatrix.getClusterColumns(i):
diseaseSet.add(disease)
print("targetDisease mirna total: ", len(mirnaSet))
print("targetDisease target total: ", len(targetSet))
print("targetDisease disease total: ", len(diseaseSet), "\n")
interactions = []
for key, value in list(interactionDict.items()):
interactions.append(key + (value, ))
#print(key, "\t", value)
edgeList = ml.EdgeList([])
edgeList.addInteractions(interactions)
edgeList.circos(directory + "/targetDisease")
def clusterProtocol(directory, tsi, empty):
print("Cluster lists Protocol")
clusterDirectory = directory + "/clusters"
if not os.path.exists(clusterDirectory):
os.makedirs(clusterDirectory)
allMirnaTargetInteractions = ml.readMirTarBase()
#print(allMirnaTargetInteractions)
targetMatrix = ml.Matrix(allMirnaTargetInteractions)
#print(targetMatrix.getColumns())
tarClustnum = targetMatrix.createClusters()
#print(targetMatrix.getClusterColumns())
allMirnaDiseaseInteractions = ml.readMiriadData()
diseaseMatrix = ml.Matrix(allMirnaDiseaseInteractions)
disClustnum = diseaseMatrix.createClusters()
allMirnaTissueInteractions = ml.readTissueMatrix(ml.readMirnaTSI(tsi))
tissueMatrix = ml.Matrix(allMirnaTissueInteractions)
tisClustnum = tissueMatrix.createClusters()
targetDirectory = clusterDirectory + "/target"
if not os.path.exists(targetDirectory):
os.makedirs(targetDirectory)
allInteractions = []
clusterTxtList = open(clusterDirectory + "/targetClusterList.txt", "w")
for i in range(tarClustnum):
edgeList = ml.EdgeList([])
edgeList.addInteractions(targetMatrix.getClusterInteractions(i))
edgeList.writeEdgeList(targetDirectory + "/targetCluster" +
str(i + 1) + ".txt")
#print(targetMatrix.getClusterInteractions(i))
allInteractions.extend(targetMatrix.getClusterInteractions(i))
clusterTxtList.write("Target Cluster " + str(i + 1) + "\n\n")
targetList = []
for target in targetMatrix.getClusterColumns(i):
targetList.append(target)
#print(target)
targetList.sort()
for target in targetList:
clusterTxtList.write(target + "\n")
clusterTxtList.write("\n")
mirnaList = []
for mirna in targetMatrix.getClusterRows(i):
mirnaList.append(mirna)
mirnaList.sort()
for mirna in mirnaList:
clusterTxtList.write(mirna + "\n")
clusterTxtList.write("\n\n")
clusterTxtList.close()
targetList = ml.EdgeList([])
targetList.addInteractions(allInteractions)
targetList.writeLists(targetDirectory + "/targetList", False)
tissueDirectory = clusterDirectory + "/tissue"
allInteractions = []
clusterTxtList = open(clusterDirectory + "/tissueClusterList.txt", "w")
if not os.path.exists(tissueDirectory):
os.makedirs(tissueDirectory)
for i in range(tisClustnum):
edgeList = ml.EdgeList([])
edgeList.addInteractions(tissueMatrix.getClusterInteractions(i))
edgeList.writeEdgeList(tissueDirectory + "/tissueCluster" +
str(i + 1) + ".txt")
allInteractions.extend(tissueMatrix.getClusterInteractions(i))
clusterTxtList.write("Tissue Cluster " + str(i + 1) + "\n\n")
tissueList = []
for tissue in tissueMatrix.getClusterColumns(i):
tissueList.append(tissue)
tissueList.sort()
for tissue in tissueList:
clusterTxtList.write(tissue + "\n")
clusterTxtList.write("\n")
mirnaList = []
for mirna in tissueMatrix.getClusterRows(i):
mirnaList.append(mirna)
mirnaList.sort()
for mirna in mirnaList:
clusterTxtList.write(mirna + "\n")
clusterTxtList.write("\n\n")
clusterTxtList.close()
#print(allInteractions)
tissueList = ml.EdgeList([])
tissueList.addInteractions(allInteractions)
tissueList.writeLists(tissueDirectory + "/tissueList", False)
diseaseDirectory = clusterDirectory + "/disease"
allInteractions = []
clusterTxtList = open(clusterDirectory + "/diseaseClusterList.txt", "w")
if not os.path.exists(diseaseDirectory):
os.makedirs(diseaseDirectory)
for i in range(disClustnum):
edgeList = ml.EdgeList([])
edgeList.addInteractions(diseaseMatrix.getClusterInteractions(i))
edgeList.writeEdgeList(diseaseDirectory + "/diseaseCluster" +
str(i + 1) + ".txt")
allInteractions.extend(diseaseMatrix.getClusterInteractions(i))
clusterTxtList.write("Disease Cluster " + str(i + 1) + "\n\n")
diseaseList = []
for disease in diseaseMatrix.getClusterColumns(i):
diseaseList.append(disease)
diseaseList.sort()
for disease in diseaseList:
clusterTxtList.write(disease + "\n")
clusterTxtList.write("\n")
mirnaList = []
for mirna in diseaseMatrix.getClusterRows(i):
mirnaList.append(mirna)
mirnaList.sort()
for mirna in mirnaList:
clusterTxtList.write(mirna + "\n")
clusterTxtList.write("\n\n")
clusterTxtList.close()
diseaseList = ml.EdgeList([])
diseaseList.addInteractions(allInteractions)
diseaseList.writeLists(diseaseDirectory + "/diseaseList", False)
pathwayDirectory = clusterDirectory + "/pathway"
if not os.path.exists(pathwayDirectory):
os.makedirs(pathwayDirectory)
allInteractions = []
clusterTxtList = open(clusterDirectory + "/pathwayClusterList.txt", "w")
for i in range(tarClustnum):
targetMirnaInteractions = targetMatrix.getClusterInteractions(i)
entrezDict = ml.geneNameEntrezDict()
newTargetMirnaInteractions = []
for interaction in targetMirnaInteractions:
newTargetMirnaInteractions.append([
interaction[0],
ml.Gene(interaction[1], entrezDict[interaction[1]])
])
mirnaPathwayInterations = ml.reactomePA(newTargetMirnaInteractions,
0.05)
edgeList = ml.EdgeList([])
edgeList.addInteractions(mirnaPathwayInterations)
edgeList.writeEdgeList(targetDirectory + "/pathwayCluster" +
str(i + 1) + ".txt")
allInteractions.extend(targetMatrix.getClusterInteractions(i))
clusterTxtList.write("Pathway Cluster " + str(i + 1) + "\n\n")
pathwaySet = set()
mirnaSet = set()
for interaction in mirnaPathwayInterations:
pathwaySet.add(interaction[1])
mirnaSet.add(interaction[0])
pathwayList = sorted(list(pathwaySet))
mirnaList = sorted(list(mirnaSet))
for pathway in pathwayList:
clusterTxtList.write(pathway + "\n")
clusterTxtList.write("\n")
for mirna in mirnaList:
clusterTxtList.write(mirna + "\n")
clusterTxtList.write("\n\n")
clusterTxtList.close()
"""
def tissueTargetCircos(directory, tsi, empty):
print("\n --------- tissueTargetCircos Protocol ------------ \n")
"""
Create edgelist for network clustered by tissue-miRNA.
"""
if not os.path.exists(directory):
os.makedirs(directory)
allMirnaTissueInteractions = ml.readTissueMatrix(ml.readMirnaTSI(tsi))
tissueMatrix = ml.Matrix(allMirnaTissueInteractions)
tisClustnum = tissueMatrix.createClusters()
allMirnaTargetInteractions = ml.readMirTarBase()
targetMatrix = ml.Matrix(allMirnaTargetInteractions)
tarClustnum = targetMatrix.createClusters()
num = 0
interactionDict = {}
mirnaSet = set()
tissueSet = set()
targetSet = set()
for i in range(tisClustnum):
mirnaTissueInteractions = tissueMatrix.getClusterInteractions(i)
tissueClusterName = ""
for name in tissueMatrix.getClusterColumns(i):
tissueClusterName += name
for j in range(tarClustnum):
mirnaTargetInteractions = targetMatrix.getClusterInteractions(j)
#print(mirnaTargetInteractions)
targetClusterName = ""
for name in targetMatrix.getClusterColumns(j):
targetClusterName += name
print("\n")
for tarItems, tisItems in [(tarItems, tisItems)
for tarItems in mirnaTargetInteractions
for tisItems in mirnaTissueInteractions
]:
#print(tisItems)
if tarItems[0] == tisItems[0]:
print(tarItems[0])
#print("+")
#print("\n\nCluster: ", i + 1)
#print("miRNAs: ", + len(tissueMatrix.getClusterRows(i)))
#print("tissues: ", + len(tissueMatrix.getClusterColumns(i)))
tissueClusterSize = (
len(tissueMatrix.getClusterRows(i)) +
len(tissueMatrix.getClusterColumns(i)))
targetClusterSize = (
len(targetMatrix.getClusterRows(j)) +
len(targetMatrix.getClusterColumns(j)))
key = ("tissueCluster" + str(i + 1),
"targetCluster" + str(j + 1), tissueClusterSize,
targetClusterSize)
#print("\n\nCluster: ", i + 1, " Size: ", tissueClusterSize)
if key not in interactionDict:
interactionDict[key] = 1
else:
interactionDict[key] += 1
num += 1
for mirna in targetMatrix.getClusterRows(i):
mirnaSet.add(mirna)
for mirna in tissueMatrix.getClusterRows(i):
mirnaSet.add(mirna)
for target in targetMatrix.getClusterColumns(i):
targetSet.add(target)
for tissue in tissueMatrix.getClusterColumns(i):
tissueSet.add(tissue)
print("tissueTarget mirna total: ", len(mirnaSet))
print("tissueTarget target total: ", len(targetSet))
print("tissueTarget tissue total: ", len(tissueSet), "\n")
interactions = []
for key, value in list(interactionDict.items()):
interactions.append(key + (value, ))
print(key, "\t", value)
edgeList = ml.EdgeList([])
edgeList.addInteractions(interactions)
edgeList.circos(directory + "/tissueTarget")
def diseaseClusterNetwork(directory, tsi, pValue):
"""
A protocol for an individual network by disease clusters
"""
print("\n --------- diseaseclusterNetwork Protocol ------------ \n")
if not os.path.exists(directory):
os.makedirs(directory)
newDir = directory + ("/diseaseClusterNetwork")
if not os.path.exists(newDir):
os.makedirs(newDir)
allDiseaseMirnaInteractions = ml.readMiriadData()
matrix = ml.Matrix(allDiseaseMirnaInteractions)
numberOfClusters = matrix.createClusters()
mirnaTissueInteractions = ml.readTissueMatrix(ml.readMirnaTSI(tsi))
#network for all clusters
print("\n All Clusters \n")
diseaseMirnaInteractions = matrix.getClusterInteractions()
mirnaInteractions = ml.mirnaFullNames(matrix.getClusterRows())
mirnaNames = [interaction[1] for interaction in mirnaInteractions]
mirnaTargetInterations = ml.readMirTarBase(mirnaNames)
#create edgeList
edgeList = ml.EdgeList(mirnaInteractions)
edgeList.addInteractions(diseaseMirnaInteractions)
edgeList.addInteractions(mirnaTargetInterations)
edgeList.addInteractions(mirnaTissueInteractions)
# Lists for node selection in cytoscape
edgeList.writeLists(newDir + "/list")
# reduce network to only through interactions
edgeList.removeIncompleteLinks() ##################################
#edgeList.simplifyMirnaNames()
#All groups
edgeList.writeEdgeList(newDir + "/EdgeListAll.txt")
# No Tissues
tissues = edgeList.popInteractions()
# No Pathways
pathways = edgeList.popInteractions()
edgeList.addInteractions(tissues)
edgeList.writeEdgeList(newDir + "/EdgeListAllNoTargets.txt")
# No Diseases
edgeList.popInteractions()
edgeList.popInteractions()
edgeList.addInteractions(tissues)
edgeList.addInteractions(pathways)
edgeList.writeEdgeList(newDir + "/EdgeListAllNoDiseases.txt")
# network for each cluster
allClusterEdgeList = open(newDir + "/allClusterEdgeList.txt", "w")
allClusterEdgeList.write("Source\tTarget\n")
for i in range(numberOfClusters):
print("\n Cluster " + str(i + 1) + "\n")
diseaseMirnaInteractions = matrix.getClusterInteractions(i)
mirnaInteractions = ml.mirnaFullNames(matrix.getClusterRows(i))
mirnaNames = [interaction[1] for interaction in mirnaInteractions]
mirnaTargetInterations = ml.readMirTarBase(mirnaNames)
#create edgeList
edgeList = ml.EdgeList(mirnaInteractions)
edgeList.addInteractions(mirnaTargetInterations)
edgeList.addInteractions(mirnaTissueInteractions)
edgeList.addInteractions(diseaseMirnaInteractions)
# reduce network to only through interactions
edgeList.removeIncompleteLinks() ################################
#edgeList.simplifyMirnaNames()
#All groups
allClusterEdgeList.write(
edgeList.writeEdgeList(newDir + "/EdgeList" + str(i + 1) + ".txt"))
# No Tissues
tissues = edgeList.popInteractions()
edgeList.writeEdgeList(newDir + "/EdgeListNoTissues" + str(i + 1) +
".txt")
# No Pathways
pathways = edgeList.popInteractions()
edgeList.addInteractions(tissues)
edgeList.writeEdgeList(newDir + "/EdgeListNoTargets" + str(i + 1) +
".txt")
# No Diseases
edgeList.popInteractions()
edgeList.popInteractions()
edgeList.addInteractions(tissues)
edgeList.addInteractions(pathways)
edgeList.writeEdgeList(newDir + "/EdgeListDiseaseNoDiseases" +
str(i + 1) + ".txt")
allClusterEdgeList.close()
def targetClusterNetworkPA(directory, tsi, pValue):
"""
A protocol for an individual network by disease clusters using reacotme
pathways
"""
print("\n --------- targetClusterNetworkPA Protocol ------------ \n")
if not os.path.exists(directory):
os.makedirs(directory)
newDir = directory + ("/targetClusterNetworkPA")
if not os.path.exists(newDir):
os.makedirs(newDir)
allMirnaTargetInteractions = ml.readMirTarBase()
matrix = ml.Matrix(allMirnaTargetInteractions)
numberOfClusters = matrix.createClusters()
mirnaTissueInteractions = ml.readTissueMatrix(ml.readMirnaTSI(tsi))
mirnaDiseaseInteractions = ml.readMiriadData()
#network for all clusters
print("\n All Clusters \n")
targetMirnaInteractions = matrix.getClusterInteractions()
entrezDict = ml.geneNameEntrezDict()
newTargetMirnaInteractions = []
for interaction in targetMirnaInteractions:
newTargetMirnaInteractions.append([
interaction[0],
ml.Gene(interaction[1], entrezDict[interaction[1]])
])
mirnaPathwayInterations = ml.reactomePA(newTargetMirnaInteractions, pValue)
mirnaInteractions = ml.simplifyMirnaNames(matrix.getClusterRows())
#create edgeList
edgeList = ml.EdgeList(mirnaInteractions)
edgeList.addInteractions(mirnaPathwayInterations)
edgeList.addInteractions(mirnaDiseaseInteractions)
edgeList.addInteractions(mirnaTissueInteractions)
# Lists for node selection in cytoscape
edgeList.writeLists(newDir + "/list")
# reduce network to only through interactions
edgeList.removeIncompleteLinks()
#edgeList.simplifyMirnaNames()
#All groups
edgeList.writeEdgeList(newDir + "/EdgeListAll.txt")
# No Tissues
tissues = edgeList.popInteractions()
edgeList.writeEdgeList(newDir + "/EdgeListAllNoTissues.txt")
# No Pathways
pathways = edgeList.popInteractions()
edgeList.addInteractions(tissues)
edgeList.writeEdgeList(newDir + "/EdgeAllNoTargets.txt")
# No Diseases
edgeList.popInteractions()
edgeList.popInteractions()
edgeList.addInteractions(tissues)
edgeList.addInteractions(pathways)
edgeList.writeEdgeList(newDir + "/EdgeListAllNoDiseases.txt")
# network for each cluster
for i in range(numberOfClusters):
print("\n Cluster " + str(i + 1) + "\n")
targetMirnaInteractions = matrix.getClusterInteractions(i)
entrezDict = ml.geneNameEntrezDict()
newTargetMirnaInteractions = []
for interaction in targetMirnaInteractions:
newTargetMirnaInteractions.append([
interaction[0],
ml.Gene(interaction[1], entrezDict[interaction[1]])
])
mirnaPathwayInterations = ml.reactomePA(newTargetMirnaInteractions,
pValue)
mirnaInteractions = ml.simplifyMirnaNames(matrix.getClusterRows(i))
#create edgeList
edgeList = ml.EdgeList(mirnaInteractions)
edgeList.addInteractions(mirnaDiseaseInteractions)
edgeList.addInteractions(mirnaTissueInteractions)
edgeList.addInteractions(mirnaPathwayInterations)
# reduce network to only through interactions
edgeList.removeIncompleteLinks()
#edgeList.simplifyMirnaNames()
#All groups
edgeList.writeEdgeList(newDir + "/EdgeList" + str(i + 1) + ".txt")
# No Tissues
tissues = edgeList.popInteractions()
edgeList.writeEdgeList(newDir + "/EdgeListNoTissues" + str(i + 1) +
".txt")
# No Pathways
pathways = edgeList.popInteractions()
edgeList.addInteractions(tissues)
edgeList.writeEdgeList(newDir + "/EdgeListNoTargets" + str(i + 1) +
".txt")
# No Diseases
edgeList.popInteractions()
edgeList.popInteractions()
edgeList.addInteractions(tissues)
edgeList.addInteractions(pathways)
edgeList.writeEdgeList(newDir + "/EdgeListNoDiseases" + str(i + 1) +
".txt")