def find_clashes_small(self, mycollider, cursor, par, pepids):
swath_mode = False
mycollider.allpeps = {}
mycollider.non_unique_count = 0
mycollider.total_count = 0
MAX_UIS = 5
for kk, pep in enumerate(pepids):
precursor = Precursor(parent_id=pep['parent_id'], q1=pep['q1'],
ssrcalc=pep['ssrcalc'], modified_sequence = pep['mod_sequence'],
transition_group = pep['transition_group'])
q3_low, q3_high = par.get_q3range_transitions()
transitions = precursor.calculate_transitions(q3_low, q3_high)
nr_transitions = len(transitions)
### if use_db and not swath_mode:
precursors = mycollider._get_all_precursors(par, precursor, cursor)
collisions_per_peptide = collider.get_coll_per_peptide_from_precursors(mycollider,
transitions, precursors, par, precursor, forceNonCpp=False)
collisions_per_peptide_python = collider.get_coll_per_peptide_from_precursors_obj_wrapper(mycollider,
transitions, precursors, par, precursor, forceNonCpp=True)
self.assertEqual(collisions_per_peptide, collisions_per_peptide_python)
non_uis_list = collider.get_nonuis_list(collisions_per_peptide, MAX_UIS)
#
# here we count how many are locally clean, e.g. look at UIS of order 1
mycollider.allpeps[precursor.parent_id] = 1.0 - len(non_uis_list[1]) * 1.0 / nr_transitions
mycollider.non_unique_count += len(non_uis_list[1])
mycollider.total_count += nr_transitions
def test_runuis_nonswath(self):
self.assertEqual(len(self.precursors_to_evaluate), 905)
par = self.par
cursor = self.db.cursor()
prepare = []
for precursor in self.precursors_to_evaluate:
q3_low, q3_high = par.get_q3range_transitions()
transitions = precursor.calculate_transitions(q3_low, q3_high)
nr_transitions = len(transitions)
precursors_obj = self.acollider._get_all_precursors(par, precursor, cursor)
collisions_per_peptide = collider.get_coll_per_peptide_from_precursors(self.acollider,
transitions, precursors_obj, par, precursor)
non_uis_list = collider.get_nonuis_list(collisions_per_peptide, par.max_uis)
for order in range(1,min(par.max_uis+1, nr_transitions+1)):
prepare.append( (len(non_uis_list[order]), collider.choose(nr_transitions,
order), precursor.parent_id , order, -1) )
self.assertEqual(len(prepare), 905*par.max_uis)
self.assertEqual(prepare[0], (0, 17.0, 1, 1, -1))
final_report = self.get_final_report(par, prepare)
self.check_final_report_nonswath(final_report)
def test_runuis_swath(self):
self.assertEqual(len(self.precursors_to_evaluate), 905)
swath_mode = False
par = self.par
R = self.R
cursor = self.db.cursor()
prepare = []
self.min_q1 = 500
self.max_q1 = 525
# Get the precursors (now for 500-525 instead of the full range)
###########################################################################
myprecursors = Precursors()
cursor = self.db.cursor()
myprecursors.getFromDB(par, cursor, self.min_q1 - par.q1_window, self.max_q1 + par.q1_window)
rtree = myprecursors.build_rangetree()
self.precursors_to_evaluate = myprecursors.getPrecursorsToEvaluate(self.min_q1, self.max_q1)
self.assertEqual(len(self.precursors_to_evaluate), 39)
isotope_correction = par.isotopes_up_to * R.mass_diffC13 / min(par.parent_charges)
temp_precursors = Precursors()
temp_precursors.getFromDB(par, self.db.cursor(), self.min_q1 - isotope_correction, self.max_q1)
all_swath_precursors = []
for p in temp_precursors.precursors:
if(p.included_in_isotopic_range(self.min_q1, self.max_q1, par) ):
all_swath_precursors.append(p)
for precursor in self.precursors_to_evaluate:
q3_low, q3_high = par.get_q3range_transitions()
transitions = precursor.calculate_transitions(q3_low, q3_high)
nr_transitions = len(transitions)
if par.ssrcalc_window > 1000:
precursors_obj = [p for p in all_swath_precursors if p.transition_group != precursor.transition_group]
else:
ssrcalc_low = precursor.ssrcalc - par.ssrcalc_window
ssrcalc_high = precursor.ssrcalc + par.ssrcalc_window
precursors_obj = [p for p in all_swath_precursors if p.transition_group != precursor.transition_group
and p.ssrcalc > ssrcalc_low and p.ssrcalc < ssrcalc_high ]
collisions_per_peptide = collider.get_coll_per_peptide_from_precursors(self.acollider,
transitions, precursors_obj, par, precursor)
non_uis_list = collider.get_nonuis_list(collisions_per_peptide, par.max_uis)
for order in range(1,min(par.max_uis+1, nr_transitions+1)):
prepare.append( (len(non_uis_list[order]), collider.choose(nr_transitions,
order), precursor.parent_id , order, -1) )
self.assertEqual(len(prepare), 39*par.max_uis)
self.assertEqual(prepare[0], (5, 8.0, 69, 1, -1) )
final_report = self.get_final_report(par, prepare)
self.check_final_report_swath(final_report)
def test_collisions_per_peptide(self):
""" Test to calculate the collisions per peptide.
"""
q3_low, q3_high = self.real_parameters.get_q3range_transitions()
precursor = self.precursor
transitions = precursor.calculate_transitions(q3_low, q3_high)
collisions_per_peptide = collider.get_coll_per_peptide_from_precursors(self.acollider, transitions,
self.interfering_precursors, self.real_parameters, None, False, False)
self.assertEqual(collisions_per_peptide, {665: [4], 618: [0, 2]})
def test_min_needed_transitions(self):
q3_low, q3_high = self.real_parameters.get_q3range_transitions()
precursor = self.precursor
transitions = precursor.calculate_transitions(q3_low, q3_high)
collisions_per_peptide = collider.get_coll_per_peptide_from_precursors(self.acollider, transitions,
self.interfering_precursors, self.real_parameters, None, False, False)
# We need at least 2 transitions to see this peptide because the first transition is interfered with
self.real_parameters.max_uis = 10
min_needed = self.acollider._sub_getMinNeededTransitions(self.real_parameters, transitions, collisions_per_peptide)
self.assertEqual(min_needed, 2)
# Now delete the 2nd element, now we need at least three transtitions because transitions 1 and 2 are interfered with
transitions = list(transitions)
del transitions[1]
min_needed = self.acollider._sub_getMinNeededTransitions(self.real_parameters, tuple(transitions), collisions_per_peptide)
self.assertEqual(min_needed, 3)
def test_collisions_per_peptide_forced_fragment_check(self):
""" Test to calculate the collisions per peptide when enforcing fragment charge checks.
Now the y11++ fragment is not allowed any more because a fragment of
NGTDGGLQVAIDAMR cannot hold 2 charges. Thus we test against 618: [0] without the "2".
"""
q3_low, q3_high = self.real_parameters.get_q3range_transitions()
precursor = self.precursor
transitions = precursor.calculate_transitions(q3_low, q3_high)
collisions_per_peptide = collider.get_coll_per_peptide_from_precursors_obj_wrapper(self.acollider,
transitions, self.interfering_precursors, self.real_parameters, precursor, forceNonCpp=True,
forceFragmentChargeCheck=True)
self.assertEqual(collisions_per_peptide, {665: [4], 618: [0]})
collisions_per_peptide = collider.get_coll_per_peptide_from_precursors(self.acollider,
transitions, self.interfering_precursors, self.real_parameters, precursor, forceNonCpp=False,
forceFragmentChargeCheck=True)
### TODO, forceFragment check will reduce this
self.assertEqual(collisions_per_peptide, {665: [4]})
def find_clashes_small(self, mycollider, cursor, par, pepids):
swath_mode = False
mycollider.allpeps = {}
mycollider.non_unique_count = 0
mycollider.total_count = 0
MAX_UIS = 5
for kk, pep in enumerate(pepids):
precursor = Precursor(parent_id=pep['parent_id'],
q1=pep['q1'],
ssrcalc=pep['ssrcalc'],
modified_sequence=pep['mod_sequence'],
transition_group=pep['transition_group'])
q3_low, q3_high = par.get_q3range_transitions()
transitions = precursor.calculate_transitions(q3_low, q3_high)
nr_transitions = len(transitions)
### if use_db and not swath_mode:
precursors = mycollider._get_all_precursors(par, precursor, cursor)
collisions_per_peptide = collider.get_coll_per_peptide_from_precursors(
mycollider,
transitions,
precursors,
par,
precursor,
forceNonCpp=False)
collisions_per_peptide_python = collider.get_coll_per_peptide_from_precursors_obj_wrapper(
mycollider,
transitions,
precursors,
par,
precursor,
forceNonCpp=True)
self.assertEqual(collisions_per_peptide, collisions_per_peptide_python)
non_uis_list = collider.get_nonuis_list(collisions_per_peptide,
MAX_UIS)
#
# here we count how many are locally clean, e.g. look at UIS of order 1
mycollider.allpeps[precursor.parent_id] = 1.0 - len(
non_uis_list[1]) * 1.0 / nr_transitions
mycollider.non_unique_count += len(non_uis_list[1])
mycollider.total_count += nr_transitions
all_swath_precursors.append(p)
allintertr = []
MAX_UIS = par.max_uis
progressm = progress.ProgressMeter(total=len(precursors_to_evaluate), unit='peptides')
prepare = []
print "analyzing %s peptides" % len(precursors_to_evaluate)
for precursor in precursors_to_evaluate:
transitions = precursor.calculate_transitions_from_param(par)
nr_transitions = len(transitions)
if use_db and not swath_mode:
# Case 1: regular SRMCollider, get transitions from the DB
precursors_obj = mycollider._get_all_precursors(par, precursor, cursor)
collisions_per_peptide = collider.get_coll_per_peptide_from_precursors(mycollider,
transitions, precursors_obj, par, precursor)
elif use_db and swath_mode:
# Case 2: SRMCollider in SWATH mode, get transitions from the DB (e.g. the memory in this case)
if par.ssrcalc_window > 1000:
precursors_obj = [p for p in all_swath_precursors if p.transition_group != precursor.transition_group]
else:
ssrcalc_low = precursor.ssrcalc - par.ssrcalc_window
ssrcalc_high = precursor.ssrcalc + par.ssrcalc_window
precursors_obj = [p for p in all_swath_precursors if p.transition_group != precursor.transition_group
and p.ssrcalc > ssrcalc_low and p.ssrcalc < ssrcalc_high ]
collisions_per_peptide = collider.get_coll_per_peptide_from_precursors(mycollider,
transitions, precursors_obj, par, precursor)
elif not use_db:
if swath_mode:
# Case 3: SRMCollider in SWATH mode, get transitions from the rangetree
collisions_per_peptide = myprecursors.get_collisions_per_peptide_from_rangetree(
