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