def test_get_uis(self):
non_uis_list = get_non_UIS_from_transitions_old(self.transitions,
self.collisions, self.par, self.MAX_UIS)
srm_ids = [t[1] for t in self.transitions]
rr = collider.get_uis(srm_ids, non_uis_list[2], 2)
self.assertEqual(len(rr), 0)
#
self.transitions = transitions_def2
self.collisions = collisions_def2
non_uis_list = get_non_UIS_from_transitions_old(self.transitions,
self.collisions, self.par, self.MAX_UIS)
srm_ids = [t[1] for t in self.transitions]
rr = collider.get_uis(srm_ids, non_uis_list[2], 2)
self.assertEqual(len(rr), 1)
def write_csv_row(fragments, collisions_per_peptide, current_sequence, uis, wuis):
srm_ids = [f.fragment_count for f in fragments]
srm_lookup = [ (fragment.fragment_count, fragment) for fragment in fragments]
srm_lookup = dict(srm_lookup)
for order in range(1,uis+1):
non_uis = c_getnonuis.get_non_uis(collisions_per_peptide, order)
if False:
# here we just output the non-UIS combinations. Usually
# these are more informative and are preferable to a list
# of UIS combinations.
for comb in non_uis:
tmp = [ srm_lookup[elem] for elem in comb]
myrow = []
for tt in tmp:
myrow.extend( [ tt.q3, tt.annotation ])
wuis.writerow(myrow)
else:
# if you want the real deal, go ahead.
uis_list = collider.get_uis(srm_ids, non_uis, order)
#if(len(uis_list) == 0): wuis.writerow([ 'Sorry, no UIS found for order %s' % order ])
for comb in uis_list:
tmp = [ srm_lookup[elem] for elem in comb]
myrow = [current_sequence, order]
for tt in tmp:
myrow.extend( [ tt.q3, tt.annotation ])
wuis.writerow(myrow)
def test_get_uis_extra1(self):
order = 1
nonuis = set([(1627247L,), (1627240L,), (1627241L,), (1627242L,), (1627248L,), (1627243L,), (1627238L,), (1627249L,), (1627244L,), (1627239L,), (1627250L,), (1627251L,), (1627252L,)])
srm_ids = [1627238L, 1627239L, 1627240L, 1627241L, 1627242L, 1627243L, 1627244L, 1627247L, 1627248L, 1627249L, 1627250L, 1627251L, 1627252L]
uis_list = collider.get_uis(srm_ids, nonuis, order)
self.assertEqual( len(uis_list), 0)
def write_csv_row(fragments, collisions_per_peptide, current_sequence, uis, wuis):
srm_ids = [f.fragment_count for f in fragments]
srm_lookup = [ (fragment.fragment_count, fragment) for fragment in fragments]
srm_lookup = dict(srm_lookup)
for order in range(1,uis+1):
non_uis = c_getnonuis.get_non_uis(collisions_per_peptide, order)
if False:
# here we just output the non-UIS combinations. Usually
# these are more informative and are preferable to a list
# of UIS combinations.
for comb in non_uis:
tmp = [ srm_lookup[elem] for elem in comb]
myrow = []
for tt in tmp:
myrow.extend( [ tt.q3, tt.annotation ])
wuis.writerow(myrow)
else:
# if you want the real deal, go ahead.
uis_list = collider.get_uis(srm_ids, non_uis, order)
#if(len(uis_list) == 0): wuis.writerow([ 'Sorry, no UIS found for order %s' % order ])
for comb in uis_list:
tmp = [ srm_lookup[elem] for elem in comb]
myrow = [current_sequence, order]
for tt in tmp:
myrow.extend( [ tt.q3, tt.annotation ])
wuis.writerow(myrow)
