def make(script_name, input_dicts, mem_req=None):
scr_path = os.path.join(config.root, "scripts")
ls = []
for i in range(len(input_dicts)):
d = input_dicts[i]
inp_file = script_name + str(i)
inp_handle = open(config.scriptInputPath(inp_file), "w")
out_file = script_name + str(i)
pickle.dump(d, inp_handle)
inp_handle.close()
l = "bsub -q compbio-week %s -o %s %s %s" % (
(lambda x: x == None and " " or " -R %s " % (x))(mem_req),
"${HOME}/bsub_logs/" + inp_file,
script_name,
inp_file,
)
ls.append(l)
cmd = "ssh tin '" + "; ".join(ls) + "'"
prc0 = subprocess.Popen(
"rsync -rv ${COMPBIO_PATH}/scripts/scr_inputs/ tin:'${COMPBIO_PATH}/scripts/scr_inputs/'",
shell=True,
stdout=subprocess.PIPE,
)
c0 = prc0.communicate()
print "RSYNCed inputs directory"
prc1 = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
print "Sent batch commands out"
def main(): name= sys.argv[1] print 'getting input dictionary' inp_dic = pickle.load(open(config.scriptInputPath(name))) file_url = inp_dic['file_url'] print 'file_url: %s' % file_url print 'parsing alignment' p = config.dataPath(file_url) gba.fill_from_rfam_stk( p, reset = True)
