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 mirnaNumber(empty, tsi, empty2):
mirnas = set()
print("cluster mirnaTargets")
allMirnaTargetInteractions = ml.readMirTarBase()
targetMatrix = ml.Matrix(allMirnaTargetInteractions)
tarClustnum = targetMatrix.createClusters()
print("cluster mirnaDiseases")
allMirnaDiseaseInteractions = ml.readMiriadData()
diseaseMatrix = ml.Matrix(allMirnaDiseaseInteractions)
disClustnum = diseaseMatrix.createClusters()
print("cluster mirnaTissues")
allMirnaTissueInteractions = ml.readTissueMatrix(ml.readMirnaTSI(tsi))
tissueMatrix = ml.Matrix(allMirnaTissueInteractions)
tisClustnum = tissueMatrix.createClusters()
print("Calculate")
count = 0
for i in range(tisClustnum):
clusterMirnas = tissueMatrix.getClusterRows(i)
for mirna in clusterMirnas:
mirnas.add(mirna)
count += 1
print("number of miRNAs in tissue clusters: ", count)
tissues = set()
for i in range(tisClustnum):
clusterMirnas = tissueMatrix.getClusterColumns(i)
for tissue in clusterMirnas:
tissues.add(tissue)
print("number of tissues: ", len(tissues))
count = 0
for i in range(tarClustnum):
clusterMirnas = targetMatrix.getClusterRows(i)
for mirna in clusterMirnas:
mirnas.add(mirna)
count += 1
print("number of miRNAs in target clusters: ", count)
targets = set()
for i in range(tarClustnum):
clusterMirnas = targetMatrix.getClusterColumns(i)
for target in clusterMirnas:
targets.add(target)
print("number of targets: ", len(targets))
count = 0
for i in range(disClustnum):
clusterMirnas = diseaseMatrix.getClusterRows(i)
for mirna in clusterMirnas:
count += 1
print("number of miRNAs in disease clusters: ", count)
diseases = set()
for i in range(disClustnum):
clusterMirnas = diseaseMatrix.getClusterColumns(i)
for disease in clusterMirnas:
diseases.add(disease)
print("number of diseases: ", len(diseases))
count = 0
unusedClusters = [
31, 34, 37, 42, 44, 45, 46, 48, 49, 54, 55, 57, 59, 60, 61, 62, 63, 64,
65
]
disMirnas = set()
for i in range(disClustnum):
if i + 1 not in unusedClusters:
clusterMirnas = diseaseMatrix.getClusterRows(i)
for mirna in clusterMirnas:
disMirnas.add(mirna)
count += 1
print("number of miRNAs used in disease clusters: ", count)
simpleMirnas = [m[0] for m in ml.simplifyMirnaNames(mirnas)]
totalMirnas = []
for disMirna in disMirnas:
if disMirna not in simpleMirnas:
totalMirnas.append(disMirna)
totalMirnas.extend(list(mirnas))
print("number total of mirnas used: " + str(len(totalMirnas)))
#check through miRNAs
tarMirnas = targetMatrix.getClusterRows()
tarTisMirnas = []
tarTisDisMirnas = []
for mirna in tarMirnas:
if mirna in tissueMatrix.getClusterRows():
tarTisMirnas.append(mirna)
print(len(tarTisMirnas))
simpleMirnas = [m[0] for m in ml.simplifyMirnaNames(tarTisMirnas)]
print(simpleMirnas)
for m in diseaseMatrix.getClusterRows():
if m in simpleMirnas:
tarTisDisMirnas.append(m)
print("\nNumber of through miRNAs: ", len(tarTisDisMirnas))
print(tarTisDisMirnas)
tisMirnas = []
tissues = set()
for i in range(tisClustnum):
clusterMirnas = tissueMatrix.getClusterRows(i)
for mirna in clusterMirnas:
if mirna in tarTisMirnas:
tisMirnas.extend(clusterMirnas)
print(i + 1)
for tissue in tissueMatrix.getClusterColumns(i):
tissues.add(tissue)
break
print("\nNumber of cluster miRNAs from through miRNAs: ", len(tisMirnas))
print("Number of cluster tissues from through miRNAs: ", len(tissues))
tarMirnas = []
targets = set()
for i in range(tisClustnum):
clusterMirnas = targetMatrix.getClusterRows(i)
for mirna in clusterMirnas:
if mirna in tarTisMirnas:
tarMirnas.extend(clusterMirnas)
print(i + 1)
for target in targetMatrix.getClusterColumns(i):
targets.add(target)
break
print("\nNumber of cluster miRNAs from through miRNAs: ", len(tarMirnas))
print("Number of cluster targets from through miRNAs: ", len(targets))
disMirnas = []
diseases = set()
#simpleMirnas = [m[0] for m in ml.simplifyMirnaNames(tarTisMirnas)]
for i in range(tisClustnum):
clusterMirnas = diseaseMatrix.getClusterRows(i)
for mirna in clusterMirnas:
if mirna in tarTisDisMirnas:
disMirnas.extend(clusterMirnas)
print(i + 1)
for disease in diseaseMatrix.getClusterColumns(i):
diseases.add(disease)
break
print("\nNumber of cluster miRNAs from through miRNAs: ", len(disMirnas))
print("Number of cluster diseases from through miRNAs: ", len(diseases))
totalMirnas = set()
totalMirnas.update(tarMirnas)
print("size1: ", len(totalMirnas))
totalMirnas.update(tisMirnas)
print("size2: ", len(totalMirnas))
final = set()
simpleMirnas = [m[0] for m in ml.simplifyMirnaNames(totalMirnas)]
print(simpleMirnas)
for mirna in disMirnas:
if mirna not in simpleMirnas:
final.add(mirna)
#print(m)
print("size3: ", len(final))
final.update(totalMirnas)
print("\ntotal miRNAs: ", len(final))
#print(final)
#check how prevalent dis/tis/tar are
print("\n\n")
tissueDict = {}
for i in range(tisClustnum):
for tissue in tissueMatrix.getClusterColumns(i):
tissueDict[tissue] = tissueDict.setdefault(tissue, 0) + 1
for key in sorted(tissueDict, key=tissueDict.get):
print(key, ": ", tissueDict[key])
print("\n\n")
diseaseDict = {}
for i in range(disClustnum):
for disease in diseaseMatrix.getClusterColumns(i):
diseaseDict[disease] = diseaseDict.setdefault(disease, 0) + 1
for key in sorted(diseaseDict, key=diseaseDict.get):
print(key, ": ", diseaseDict[key])
print("\n\n")
targetDict = {}
for i in range(tarClustnum):
for target in targetMatrix.getClusterColumns(i):
targetDict[target] = targetDict.setdefault(target, 0) + 1
for key in sorted(targetDict, key=targetDict.get):
print(key, ": ", targetDict[key])
################
for key in sorted(diseaseDict, key=diseaseDict.get):
print("\n\n" + key)
for i in range(disClustnum):
for disease in diseaseMatrix.getClusterColumns(i):
if key == disease:
print("cluster: ", i + 1)
for key in sorted(tissueDict, key=tissueDict.get):
print("\n\n" + key)
for i in range(tisClustnum):
for tissue in tissueMatrix.getClusterColumns(i):
if tissue == key:
print("cluster: ", i + 1)
for key in sorted(targetDict, key=targetDict.get):
print("\n\n" + key)
for i in range(tarClustnum):
for target in targetMatrix.getClusterColumns(i):
if target == key:
print("cluster: ", i + 1)
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 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")