def runLDhat(subfile):
#LDhat = '/Users/jinfengchen/biocluster/RecombinationHotspot/tools/LDhat_v2.2'
LDhat = '/rhome/cjinfeng/software/tools/LDhat_v2.2'
cmds = []
for prefix in subfile:
cmdline = LDhat + '/rhomap -seq ' + prefix + '.sites -loc ' + prefix + '.locs -lk lk23.txt -its 1000000 -samp 2000 -burn 100000 -exact -prefix ' + prefix + '.'
print cmdline
cmds.append(cmdline)
#os.system(cmdline)
worker(cmds, 20)
def sequenceLDhot(subfile):
# LDhot = '/Users/jinfengchen/biocluster/RecombinationHotspot/tools/sequenceLDhot'
LDhot = "/rhome/cjinfeng/software/tools/sequenceLDhot"
cmds = []
for prefix in subfile:
sumfile = prefix + ".summary.txt"
infile1 = prefix + ".Infile1"
datafile = prefix + ".Datafile"
rho = getregionrho(sumfile)
Infile(rho, infile1)
cmdline = LDhot + "/sequenceLDhot " + infile1 + " " + datafile
print cmdline
cmds.append(cmdline)
# os.system(cmdline)
worker(cmds, 20)
def sequenceLDhot(subfile):
#LDhot = '/Users/jinfengchen/biocluster/RecombinationHotspot/tools/sequenceLDhot'
LDhot = '/rhome/cjinfeng/software/tools/sequenceLDhot'
cmds = []
for prefix in subfile:
sumfile = prefix + '.summary.txt'
infile1 = prefix + '.Infile1'
datafile = prefix + '.Datafile'
rho = getregionrho(sumfile)
Infile(rho, infile1)
cmdline = LDhot + '/sequenceLDhot ' + infile1 + ' ' + datafile
print cmdline
cmds.append(cmdline)
#os.system(cmdline)
worker(cmds, 20)
def runLDhat(subfile):
# LDhat = '/Users/jinfengchen/biocluster/RecombinationHotspot/tools/LDhat_v2.2'
LDhat = "/rhome/cjinfeng/software/tools/LDhat_v2.2"
cmds = []
for prefix in subfile:
cmdline = (
LDhat
+ "/rhomap -seq "
+ prefix
+ ".sites -loc "
+ prefix
+ ".locs -lk lk23.txt -its 1000000 -samp 2000 -burn 100000 -exact -prefix "
+ prefix
+ "."
)
print cmdline
cmds.append(cmdline)
# os.system(cmdline)
worker(cmds, 20)
def main():
#queue = Queue.Queue()
cmd = [
'python write.py 1', 'python write.py 2', 'python write.py 3',
'python write.py 4', 'python write.py 5', 'python write.py 6',
'python write.py 7'
]
worker(cmd)
'''Create a thread pool with queue'''
#for i in range(5):
# t = Runner(queue)
# t.daemon = True
# t.start()
''''''
#for c in cmd:
#print c
# queue.put(c)
#queue.join()
print 'All job done'
def main():
#queue = Queue.Queue()
cmd = ['python write.py 1',
'python write.py 2',
'python write.py 3',
'python write.py 4',
'python write.py 5',
'python write.py 6',
'python write.py 7']
worker(cmd)
'''Create a thread pool with queue'''
#for i in range(5):
# t = Runner(queue)
# t.daemon = True
# t.start()
''''''
#for c in cmd:
#print c
# queue.put(c)
#queue.join()
print 'All job done'
