def test_getMinNeededTransitions_2(self):
pep = test_shared.runpep2
transitions = test_shared.runtransitions2
precursors = test_shared.runprecursors2
transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])
par = self.par
q3_high = self.q3_high
q3_low = self.q3_low
R = self.R
par.max_uis = len(transitions) + 1
collisions = list(collider.SRMcollider._get_all_collisions_calculate_sub(
collider.SRMcollider(), precursors, par, R, q3_low, q3_high))
m = self.acollider._getMinNeededTransitions(par, transitions, collisions)
#negative result, the transitions are not sufficient
self.assertEqual(m, -1)
m = c_integrated.getMinNeededTransitions(transitions, tuple(precursors),
par.max_uis, par.q3_window, par.ppm, par)
# TODO fix this
# self.assertEqual(m, 16)
#now also test with lower q3 window
par.q3_window = 1.0
collisions = list(collider.SRMcollider._get_all_collisions_calculate_sub(
collider.SRMcollider(), precursors, par, R, q3_low, q3_high))
m = self.acollider._getMinNeededTransitions(par, transitions, collisions)
self.assertEqual(m, 6)
m = c_integrated.getMinNeededTransitions(transitions, tuple(precursors),
par.max_uis, par.q3_window, par.ppm, par)
self.assertEqual(m, 6)
def test_getMinNeededTransitions_1(self):
pep = test_shared.runpep1
transitions = test_shared.runtransitions1
precursors = test_shared.runprecursors1
transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])
par = self.par
q3_high = self.q3_high
q3_low = self.q3_low
R = self.R
par.max_uis = 15
collisions = list(collider.SRMcollider._get_all_collisions_calculate_sub(
collider.SRMcollider(), precursors, par, R, q3_low, q3_high))
m = self.acollider._getMinNeededTransitions(par, transitions, collisions)
self.assertEqual(m, 8)
m = c_integrated.getMinNeededTransitions(transitions, tuple(precursors),
par.max_uis, par.q3_window, par.ppm, par)
self.assertEqual(m, 8)
#now also test with lower q3 window
par.q3_window = 1.0
collisions = list(collider.SRMcollider._get_all_collisions_calculate_sub(
collider.SRMcollider(), precursors, par, R, q3_low, q3_high))
m = self.acollider._getMinNeededTransitions(par, transitions, collisions)
self.assertEqual(m, 4)
m = c_integrated.getMinNeededTransitions(transitions, tuple(precursors),
par.max_uis, par.q3_window, par.ppm, par)
self.assertEqual(m, 4)
def test_getmintrans1(self):
print '\nTesting _getMinNeededTransitions'
pep = test_shared.runpep1
transitions = test_shared.runtransitions1
precursors = test_shared.runprecursors1
transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])
par = self.par
q3_high = self.q3_high
q3_low = self.q3_low
R = self.R
par.max_uis = 15
collisions = list(collider.SRMcollider._get_all_collisions_calculate_sub(
collider.SRMcollider(), precursors, par, R, q3_low, q3_high))
st = time.time()
m = collider.SRMcollider()._getMinNeededTransitions(par, transitions, collisions)
oldtime = time.time() - st
import c_integrated
st = time.time()
m = c_integrated.getMinNeededTransitions(transitions, tuple(precursors),
par.max_uis, par.q3_window, par.ppm, par)
ctime = time.time() - st
print ctime, oldtime
print "Speedup:", oldtime / ctime
def test_getmintrans1(self):
print '\nTesting _getMinNeededTransitions'
pep = test_shared.runpep1
transitions = test_shared.runtransitions1
precursors = test_shared.runprecursors1
transitions = tuple([(t[0], i) for i, t in enumerate(transitions)])
par = self.par
q3_high = self.q3_high
q3_low = self.q3_low
R = self.R
par.max_uis = 15
collisions = list(
collider.SRMcollider._get_all_collisions_calculate_sub(
collider.SRMcollider(), precursors, par, R, q3_low, q3_high))
st = time.time()
m = collider.SRMcollider()._getMinNeededTransitions(
par, transitions, collisions)
oldtime = time.time() - st
import c_integrated
st = time.time()
m = c_integrated.getMinNeededTransitions(transitions,
tuple(precursors),
par.max_uis, par.q3_window,
par.ppm, par)
ctime = time.time() - st
print ctime, oldtime
print "Speedup:", oldtime / ctime
elif use_randomized_transitions:
import c_getnonuis
transitions = c_getnonuis.calculate_transitions_ch(
((pep['q1'], pep['mod_sequence'], p_id),), [1], 0, 20000)
#get random fragment ions
from random import shuffle
shuffle(transitions)
transitions = [ (t[0], 0) for t in transitions[:10] ]
nr_transitions = len( transitions )
if nr_transitions == 0: continue #no transitions in this window
try:
import c_integrated
if background: precursors = self._get_all_precursors(bgpar, pep, cursor, bysequence=True)
else: precursors = self._get_all_precursors(bgpar, pep, cursor)
min_needed = c_integrated.getMinNeededTransitions(tuple(transitions), tuple(precursors),
par.max_uis, par.q3_window, par.ppm)
except ImportError:
if background: collisions = self._get_all_collisions(bgpar, pep, cursor, bysequence=True, transitions=transitions)
else: collisions = self._get_all_collisions(bgpar, pep, cursor, transitions=transitions)
min_needed = self._getMinNeededTransitions(par, transitions, collisions)
self.min_transitions.append( [p_id, min_needed] )
end = time.time()
if not par.quiet: progressm.update(1)
self.total_time = end - start