def remote_batch_1d(run_id): ''' Remote job mothership for a single run that will generate a bunch of bsub commands to run a series of RNAz checks along the gene of interest. inputs: run_id output: the datapath (same for local and remote) of data output each thread ''' #GENERIC SETUP FOR A BSUBBED TASKMGR. #Takes an input in the form of a list of param-dicts. # inp_dicts = butils.load_data(run_id, 'input') #DO EVERYTHING TWIXT --------------------------------[HERE] eyeball = bsub.eyeball(run_id, os.path.abspath(inspect.stack()[0][1]), inp_dicts, func = 'remote_run_1d', name = run_id+'_eye', mem = 2) eyeball.launch() eyeball.await() eyeball.package() eyeball.complete() out = {'result':eyeball.statii()} #AND ------------------------------------------------[HERE] butils.save_data(out, run_id,'output')
def remote_run_1d(run_id): ''' ''' #GENERIC SETUP FOR A SINGLE BSUBBED PROCESS. #Takes an input saved as a single dictionary. # p = butils.load_data(run_id, 'input') #DO EVERYTHING TWIXT --------------------------------[HERE] baserng = p['baserng'] win_len = p['win_len'] win_ofs = p['win_ofs'] spec_count = p['spec_count'] bases = (128693265,129266680) a0 = day0.fetch_num_ali() names = day0.fetch_alinames() ref = a0[0] ali_counts = sum(less(a0,4) * equal(a0, a0[0,:]) ,1) names_all = [names[i] for i in argsort(ali_counts)[::-1]] names = names_all[:spec_count] a0 = a0[argsort(ali_counts)[::-1]][:spec_count] ali_counts = sorted(ali_counts)[::-1][:spec_count] locii, results = day0.run_windows(a0,ref, n_specs = spec_count, win_len = win_len, win_ofs = win_ofs, spec_names = names, baserng = baserng) out = {'locii':locii, 'results':results} #AND ------------------------------------------------[HERE] butils.save_data(out, run_id,'output')