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_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
