def test_get_charged_mass(self):
pep = test_shared.runpep2
transitions = test_shared.runtransitions2
precursors = test_shared.runprecursors_obj2
par = self.par
q3_high = self.q3_high
q3_low = self.q3_low
precursors = [ (p.q1, p.modified_sequence, p.transition_group) for p in precursors]
colldensity = c_getnonuis.calculate_density(
tuple(transitions), precursors, q3_low, q3_high, par.q3_window, par.ppm)
self.assertEqual(colldensity, [1916, 1800, 2601, 3127, 4525, 4975, 3155, 3091, 2127, 3494, 4519, 5546, 4505, 4429, 5604])
precursors = [
p for p in allprecursors if p[2] != pep['peptide_key']
and p[4] > ssrcalc_low and p[4] < ssrcalc_high
]
elif not use_db:
# Use the rangetree
# correct rounding errors, s.t. we get the same results as before!
# use the rangetree
ssrcalc_low = ssrcalc - par.ssrcalc_window + 0.001
ssrcalc_high = ssrcalc + par.ssrcalc_window - 0.001
precursor_ids = tuple(
c_rangetree.query_tree(q1_low, ssrcalc_low, q1_high, ssrcalc_high))
precursors = [
parentid_lookup[myid[0]] for myid in precursor_ids
#dont select myself
if parentid_lookup[myid[0]][2] != pep['peptide_key']
]
#now calculate collisions in this area of the space
colldensity = c_getnonuis.calculate_density(transitions, precursors,
q3_low, q3_high, par.q3_window,
par.ppm)
assert MAX_UIS == 1
nonuseable = len([c for c in colldensity if c > 0])
prepare.append((nonuseable, nr_transitions, p_id, 1, exp_key))
progressm.update(1)
cursor.executemany(
'insert into %s' % restable + ' (non_useable_UIS, total_UIS, \
parent_key, uisorder, exp_key) values (%s,%s,%s,%s,%s)',
prepare)
precursors = [p for p in allprecursors if p[2] != pep['peptide_key'] ]
else:
ssrcalc_low = ssrcalc - par.ssrcalc_window
ssrcalc_high = ssrcalc + par.ssrcalc_window
precursors = [p for p in allprecursors if p[2] != pep['peptide_key']
and p[4] > ssrcalc_low and p[4] < ssrcalc_high ]
elif not use_db:
# Use the rangetree
# correct rounding errors, s.t. we get the same results as before!
# use the rangetree
ssrcalc_low = ssrcalc - par.ssrcalc_window + 0.001
ssrcalc_high = ssrcalc + par.ssrcalc_window - 0.001
precursor_ids = tuple(c_rangetree.query_tree( q1_low, ssrcalc_low,
q1_high, ssrcalc_high ) )
precursors = [parentid_lookup[myid[0]] for myid in precursor_ids
#dont select myself
if parentid_lookup[myid[0]][2] != pep['peptide_key']]
#now calculate collisions in this area of the space
colldensity = c_getnonuis.calculate_density(
transitions, precursors, q3_low, q3_high, par.q3_window, par.ppm)
assert MAX_UIS == 1
nonuseable = len( [c for c in colldensity if c >0 ] )
prepare.append( (nonuseable, nr_transitions, p_id , 1, exp_key) )
progressm.update(1)
cursor.executemany('insert into %s' % restable + ' (non_useable_UIS, total_UIS, \
parent_key, uisorder, exp_key) values (%s,%s,%s,%s,%s)' , prepare)