def rwcd(fName,tx='6',g='/24'): #random walk community detection
print 'Walktrap walk length: '+tx
wDir=os.getcwd()+"/CSV/WalkTrap/"+fName
if not os.path.exists(wDir):
print 'Please prepare files for walktrap using walktrapFile(fName)'
return
else:
for un1,un2,u3 in os.walk(wDir):
wtf=[xx for xx in u3 if ('.w' in xx)]
break
print 'Random walk length parameter: '+tx
if os.path.exists(os.getcwd()+"/Model/"+fName):
print 'Error: ' +fName+' Model already exists, delete to rerun'
return
else:
os.mkdir(os.getcwd()+"/Model/"+fName)
lll=len(wtf)
for j,w in enumerate(wtf):
print '---------------- '+str(j+1) +' / '+str(lll) +' -----------------------'
print 'Prefix: '+w.replace('.w','').replace('s','/')
qq = 'WalkTrap/walktrap '+wDir+'/'+w+ " -t"+tx+" -b -d1 -s |grep community| cut -d'=' -f2 > "+ wDir+'/'+w.replace('.w','.C')
os.system(qq)
#~ communityGraph(fName,w.replace('.w',''))
C = UoSM_input(fName,w.replace('.w',''))
print 'No. of Clusters: '+str(len(C))
print 'Cluster to subnet conversion...'
if len(C)>0:
uos = cluster2sub(C,g)
with open('Model/' + fName + '/'+w.replace('.w','.uos'), 'w') as f:
f.write(str(uos))
print '-------------------------------------------------'
def rwcd(prefix,tx='4',g='/24'): #random walk community detection
w=prefix.replace('/','s')
f=open('Debug/'+w+'.uos','w')
print 'Prefix: '+prefix
fn='Debug/'+w+'.w'
qq = 'WalkTrap/walktrap '+fn+ " -t"+tx+" -b -d1 -s |grep community| cut -d'=' -f2 > Debug/"+w+'.C'
os.system(qq)
#~ communityGraph(fName,w.replace('.w',''))
C = UoSM_input(prefix)
print 'No. of Clusters: '+str(len(C))
print 'Cluster to subnet conversion...'
if len(C)>0:
uos = cluster2sub(C,g)
with open('Debug/'+w+'.uos', 'w') as f:
f.write(str(uos))
print '-------------------------------------------------'
def rwcd(fName, tx="6", g="/24"): # random walk community detection
print "Walktrap walk length: " + tx
wDir = os.getcwd() + "/CSV/WalkTrap/" + fName
if not os.path.exists(wDir):
print "Please prepare files for walktrap using walktrapFile(fName)"
return
else:
for un1, un2, u3 in os.walk(wDir):
wtf = [xx for xx in u3 if (".w" in xx)]
break
print "Random walk length parameter: " + tx
if os.path.exists(os.getcwd() + "/Model/uos-" + fName + ".pk"):
print "Error: " + fName + " Model already exists, delete to rerun"
return
lll = len(wtf)
A = {}
for j, w in enumerate(wtf):
print "---------------- " + str(j + 1) + " / " + str(lll) + " -----------------------"
prefix = w.replace(".w", "").replace("s", "/")
print "Prefix: " + prefix
qq = (
"WalkTrap/walktrap "
+ wDir
+ "/"
+ w
+ " -t"
+ tx
+ " -b -d1 -s |grep community| cut -d'=' -f2 > "
+ wDir
+ "/"
+ w.replace(".w", ".C")
)
os.system(qq)
# ~ communityGraph(fName,w.replace('.w',''))
C = UoSM_input(fName, w.replace(".w", ""))
print "No. of Clusters: " + str(len(C))
print "Cluster to subnet conversion..."
if len(C) > 0:
uos = cluster2sub(C, g)
A[prefix] = uos
with open("Model/uos-" + fName + ".pk", "w") as f:
pk.dump(A, f)
def parse_args():
from optparse import OptionParser
parser = OptionParser(usage=usage())
parser.add_option("-g", "--gap", dest="g", default="/24", help="Optional: threshold to split brackets")
parser.add_option("-f", "--fileName", dest="fName", default=None, help="Required: filename for data")
parser.add_option("-p", "--prefix", dest="prefix", default=None, help="Required: filename for data")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
options, args = parser.parse_args()
if options.fName is None or options.prefix is None:
print "Error: Please provide --filename to read data \n (do not include .G suffix)"
sys.exit(1)
return (options, args)
if __name__ == "__main__":
options, args = parse_args()
fName = options.fName
prefix = options.prefix
g = options.g
walktrapFile(fName)
qq = "WalkTrap/walktrap CSV/" + fName + ".walktrap -b -d1 -s |grep community| cut -d'=' -f2 > CSV/" + fName + ".C"
os.system(qq)
C = UoSM_input(fName)
uos = cluster2sub(C, g)
with open("CSV/" + fName + ".net", "a+b") as f:
f.write(prefix + "," + str(uos) + "\n")