def make_ribostructs(): for k, v in rutils.switch_dicts().iteritems(): rfid = 'RF{0:05}'.format(v) savename = 'Riboswitch_list_{1}_{0}'.format(rfid, k) structs, rutils.family_clustered_suboptimals(rfid=rfid, savename=savename, draw=True)
def bsub_riboswitches(run_id): inp_dicts = [] for k,v in rutils.switch_dicts().iteritems(): rfid = 'RF{0:05}'.format(v) inp_dicts.append(dict(family = rfid, inp_run_id = 'RS_{0}'.format(rfid), run_id = 'RS_tree_{0}'.format(rfid))) eyeball = bsub.eyeball(run_id, os.path.abspath(inspect.stack()[0][1]), inp_dicts, func = 'run_treebuilder', mem = 3) eyeball.launch() return dict(cmds=eyeball.cmds)
def bsub_riboswitches(run_id): inp_dicts = [] for k, v in rutils.switch_dicts().iteritems(): rfid = 'RF{0:05}'.format(v) savename = 'Riboswitch_list_{1}_{0}'.format(rfid, k) inp_dicts.append( dict(family=rfid, run_id='RS_{0}'.format(rfid), savename=savename)) eyeball = bsub.eyeball(run_id, os.path.abspath(inspect.stack()[0][1]), inp_dicts, func='run_structmaker', mem=3) eyeball.launch() return dict(cmds=eyeball.cmds)
def bsub_riboswitches(run_id): inp_dicts = [] for k, v in rutils.switch_dicts().iteritems(): rfid = 'RF{0:05}'.format(v) inp_dicts.append( dict(family=rfid, inp_run_id='RS_{0}'.format(rfid), run_id='RS_tree_{0}'.format(rfid))) eyeball = bsub.eyeball(run_id, os.path.abspath(inspect.stack()[0][1]), inp_dicts, func='run_treebuilder', mem=3) eyeball.launch() return dict(cmds=eyeball.cmds)
def bsub_riboswitches(run_id): inp_dicts = [] for k,v in rutils.switch_dicts().iteritems(): rfid = 'RF{0:05}'.format(v) savename = 'Riboswitch_list_{1}_{0}'.format(rfid,k) inp_dicts.append(dict(family = rfid, run_id = 'RS_{0}'.format(rfid), savename = savename)) eyeball = bsub.eyeball(run_id, os.path.abspath(inspect.stack()[0][1]), inp_dicts, func = 'run_structmaker', mem = 3) eyeball.launch() return dict(cmds=eyeball.cmds)
def show_trees(switch_muts, switch_times, switch_structs): for rname,muts, times, structs in zip(switch_times.keys(), switch_muts.values(), switch_times.values(), switch_structs.values(),): if not rname[0:2] == 'RF': rtype = 'switch' rfid = 'RF{0:05}'.format(rutils.switch_dicts()[rname]) else: rfid = rname rtype = 'all' print 'Showing: {0} '.format(rfid) #if rname != 'SAM_alpha':continue show_paired_v_energy(rname,rfid,muts,times,structs,rtype) return
def show_trees(switch_muts, switch_times, switch_structs): for rname, muts, times, structs in zip( switch_times.keys(), switch_muts.values(), switch_times.values(), switch_structs.values(), ): if not rname[0:2] == 'RF': rtype = 'switch' rfid = 'RF{0:05}'.format(rutils.switch_dicts()[rname]) else: rfid = rname rtype = 'all' print 'Showing: {0} '.format(rfid) #if rname != 'SAM_alpha':continue show_paired_v_energy(rname, rfid, muts, times, structs, rtype) return
def check_trees(fam_type = 'riboswitch'): if fam_type == 'riboswitch': sdicts = rutils.switch_dicts() rfids = [ 'RF{0:05}'.format(n) for n in sdicts.values()] names = sdicts.keys() struct_ids = ['RS_{0}'.format(rfid) for rfid in rfids] tree_ids = ['RS_tree_{0}'.format(rfid) for rfid in rfids] elif fam_type == 'all': rfids = [ 'RF{0:05}'.format(n) for n in range(0,1493)] names = rfids struct_ids = ['FA_{0}'.format(rfid) for rfid in rfids] tree_ids = ['FA_tree_{0}'.format(rfid) for rfid in rfids] switch_muts = {} switch_times= {} switch_structs= {} for i, rname in enumerate(names): print 'Loading family for {0}'.format(rname) si, ti = zip(*[struct_ids, tree_ids])[i] try: structs = bsu.load_data(si, 'output') trees = bsu.load_data(ti, 'output') print 'Success! Analyzing tree output' except Exception, e: print 'Failure! Did I make a booboo?' continue str_esrt = argsort(structs['energies'])[::-1] #SORT STRUCTURES IN DECREASING ORDER OF ENERGY (MATCH TREES) structs['structs'] = [structs['structs'][j] for j in str_esrt] structs['energies'] = [structs['energies'][j] for j in str_esrt] mc, tc, sc = {},{},{} sc['energies'] = structs['energies'] sc['structs'] = structs['structs'] sc['seq'] = structs['seq'] for j, t in enumerate(trees): if t == None:continue mc[j] = {} tc[j] = {} for idx in range(len(t['structs'])): t_infos = t['structs'] t_str = t_infos[idx]['pairs'] s_str = structs['structs'][idx] e = structs['energies'][idx] t_times =t_infos[idx]['times'] t_muts =t_infos[idx]['muts'] frac_resolved = t_times['total'] /\ (t_times['total_incl_unresolved']) frac_paired = t_times['paired'] /\ (t_times['unpaired'] + t_times['paired']) n_2cons = t_muts['comp'] n_1cons = t_muts['wob'] n_0cons = t_muts['ucom'] n_pluscons = t_muts['reco'] n_nocons = t_muts['bbad'] frac_silent = (n_2cons+n_1cons+n_pluscons)/\ (n_0cons + n_nocons+\ n_2cons+n_1cons+n_pluscons) frac_double = (n_2cons)/\ (n_2cons+n_1cons) frac_destructive=(n_0cons)/\ (n_2cons+n_1cons+n_0cons) total_muts = (n_0cons + n_nocons+\ n_2cons+n_1cons+n_pluscons) total_silent = (n_2cons+n_1cons) total_pair_mutants = (n_2cons+n_1cons+n_0cons) tc[j][idx] = dict(frac_resolved = frac_resolved, frac_paired = frac_paired, total_time = array([t_times['total_incl_unresolved']]*len(t_times['total'])), total_time_res = t_times['total']) mc[j][idx] = dict(frac_silent = frac_silent, frac_double = frac_double, frac_destructive = frac_destructive, total_muts = total_muts, total_silent = total_silent, total_pair_mutants = total_pair_mutants) print '''Done! Results: {0} subtrees computed. '''.format(len(mc)) switch_muts[rname] = mc switch_times[rname] = tc switch_structs[rname] = sc
def make_ribostructs(): for k,v in rutils.switch_dicts().iteritems(): rfid = 'RF{0:05}'.format(v) savename = 'Riboswitch_list_{1}_{0}'.format(rfid,k) structs, rutils.family_clustered_suboptimals(rfid =rfid,savename = savename, draw = True)
def check_trees(fam_type='riboswitch'): if fam_type == 'riboswitch': sdicts = rutils.switch_dicts() rfids = ['RF{0:05}'.format(n) for n in sdicts.values()] names = sdicts.keys() struct_ids = ['RS_{0}'.format(rfid) for rfid in rfids] tree_ids = ['RS_tree_{0}'.format(rfid) for rfid in rfids] elif fam_type == 'all': rfids = ['RF{0:05}'.format(n) for n in range(0, 1493)] names = rfids struct_ids = ['FA_{0}'.format(rfid) for rfid in rfids] tree_ids = ['FA_tree_{0}'.format(rfid) for rfid in rfids] switch_muts = {} switch_times = {} switch_structs = {} for i, rname in enumerate(names): print 'Loading family for {0}'.format(rname) si, ti = zip(*[struct_ids, tree_ids])[i] try: structs = bsu.load_data(si, 'output') trees = bsu.load_data(ti, 'output') print 'Success! Analyzing tree output' except Exception, e: print 'Failure! Did I make a booboo?' continue str_esrt = argsort(structs['energies'])[::-1] #SORT STRUCTURES IN DECREASING ORDER OF ENERGY (MATCH TREES) structs['structs'] = [structs['structs'][j] for j in str_esrt] structs['energies'] = [structs['energies'][j] for j in str_esrt] mc, tc, sc = {}, {}, {} sc['energies'] = structs['energies'] sc['structs'] = structs['structs'] sc['seq'] = structs['seq'] for j, t in enumerate(trees): if t == None: continue mc[j] = {} tc[j] = {} for idx in range(len(t['structs'])): t_infos = t['structs'] t_str = t_infos[idx]['pairs'] s_str = structs['structs'][idx] e = structs['energies'][idx] t_times = t_infos[idx]['times'] t_muts = t_infos[idx]['muts'] frac_resolved = t_times['total'] /\ (t_times['total_incl_unresolved']) frac_paired = t_times['paired'] /\ (t_times['unpaired'] + t_times['paired']) n_2cons = t_muts['comp'] n_1cons = t_muts['wob'] n_0cons = t_muts['ucom'] n_pluscons = t_muts['reco'] n_nocons = t_muts['bbad'] frac_silent = (n_2cons+n_1cons+n_pluscons)/\ (n_0cons + n_nocons+\ n_2cons+n_1cons+n_pluscons) frac_double = (n_2cons)/\ (n_2cons+n_1cons) frac_destructive=(n_0cons)/\ (n_2cons+n_1cons+n_0cons) total_muts = (n_0cons + n_nocons+\ n_2cons+n_1cons+n_pluscons) total_silent = (n_2cons + n_1cons) total_pair_mutants = (n_2cons + n_1cons + n_0cons) tc[j][idx] = dict( frac_resolved=frac_resolved, frac_paired=frac_paired, total_time=array([t_times['total_incl_unresolved']] * len(t_times['total'])), total_time_res=t_times['total']) mc[j][idx] = dict(frac_silent=frac_silent, frac_double=frac_double, frac_destructive=frac_destructive, total_muts=total_muts, total_silent=total_silent, total_pair_mutants=total_pair_mutants) print '''Done! Results: {0} subtrees computed. '''.format(len(mc)) switch_muts[rname] = mc switch_times[rname] = tc switch_structs[rname] = sc