def test_get_non_uis2(self):
print '\nTesting non_uis_list'
pep = test_shared.runpep2
transitions = test_shared.runtransitions2
precursors = test_shared.runprecursors2
transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])
collisions_per_peptide, ctime = runcpp(self, pep, transitions, precursors)
MAX_UIS = self.MAX_UIS
non_uis_list = [set() for i in range(MAX_UIS+1)]
#here we calculate the UIS for this peptide with the given RT-range
st = time.time()
for pepc in collisions_per_peptide.values():
for i in range(1,MAX_UIS+1):
collider.get_non_uis(pepc, non_uis_list[i], i)
oldtime = time.time() - st
st = time.time()
for kk in range(10):
non_uis_list_new = [{} for i in range(MAX_UIS+1)]
for order in range(1,MAX_UIS+1):
non_uis_list_new[order] = c_getnonuis.get_non_uis(
collisions_per_peptide, order)
non_uis_list_new = [set( res.keys() ) for res in non_uis_list_new]
ctime = (time.time() - st)/10
self.assertEqual(non_uis_list_new, non_uis_list)
print ctime, oldtime
print "Speedup:", oldtime / ctime
def test_get_non_uis(self):
test = set()
collider.get_non_uis( [1,2,3], test,2 )
self.assertEqual(test, set([(1, 2), (1, 3), (2, 3)]) )
test = set()
collider.get_non_uis( [1,2,3,4], test,2 )
self.assertEqual(test, set([(1, 2), (1, 3), (1, 4), (2, 3), (3, 4), (2, 4)]))
def test_get_non_uis2(self):
print '\nTesting non_uis_list'
pep = test_shared.runpep2
transitions = test_shared.runtransitions2
precursors = test_shared.runprecursors2
transitions = tuple([(t[0], i) for i, t in enumerate(transitions)])
collisions_per_peptide, ctime = runcpp(self, pep, transitions,
precursors)
MAX_UIS = self.MAX_UIS
non_uis_list = [set() for i in range(MAX_UIS + 1)]
#here we calculate the UIS for this peptide with the given RT-range
st = time.time()
for pepc in collisions_per_peptide.values():
for i in range(1, MAX_UIS + 1):
collider.get_non_uis(pepc, non_uis_list[i], i)
oldtime = time.time() - st
st = time.time()
for kk in range(10):
non_uis_list_new = [{} for i in range(MAX_UIS + 1)]
for order in range(1, MAX_UIS + 1):
non_uis_list_new[order] = c_getnonuis.get_non_uis(
collisions_per_peptide, order)
non_uis_list_new = [set(res.keys()) for res in non_uis_list_new]
ctime = (time.time() - st) / 10
self.assertEqual(non_uis_list_new, non_uis_list)
print ctime, oldtime
print "Speedup:", oldtime / ctime
def get_non_UIS_from_transitions_old(transitions, collisions, par, MAX_UIS, unsorted=False):
""" Get all combinations that are not UIS """
#collisions
#q3, q1, srm_id, peptide_key
#transitions
#q3, srm_id
collisions_per_peptide = {}
non_uis_list = [set() for i in range(MAX_UIS+1)]
q3_window_used = par.q3_window
for t in transitions:
if par.ppm: q3_window_used = par.q3_window * 10**(-6) * t[0]
this_min = q3_window_used
for c in collisions:
if abs( t[0] - c[0] ) <= q3_window_used:
#gets all collisions
if collisions_per_peptide.has_key(c[3]):
if not t[1] in collisions_per_peptide[c[3]]:
collisions_per_peptide[c[3]].append( t[1] )
else: collisions_per_peptide[c[3]] = [ t[1] ]
#here we calculate the UIS for this peptide with the given RT-range
for pepc in collisions_per_peptide.values():
for i in range(1,MAX_UIS+1):
collider.get_non_uis(pepc, non_uis_list[i], i)
return non_uis_list