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
