def test_mysql_vs_integrated(self):
"""Compare the one table MySQL approach vs the fully integrated Cpp approach
Here we are comparing the old (querying the transitions database as
well as the precursor database) and the new way (only query the
precursor database and calculate the transitions on the fly) way of
calculating the collisions.
"""
print '\n'*1
print "Comparing one table MySQL solution vs integrated solution"
par = self.par
cursor = self.cursor
mypepids = [
{
'mod_sequence' : r[0],
'peptide_key' :r[1],
'transition_group' :r[1],
'parent_id' : r[2],
'q1_charge' : r[3],
'q1' : r[4],
'ssrcalc' : r[5],
}
for r in self.alltuples
if r[3] == 2 #charge is 2
and r[6] == 0 #isotope is 0
and r[4] >= self.min_q1
and r[4] < self.max_q1
]
mycollider = collider.SRMcollider()
#mypepids = _get_unique_pepids(par, cursor)
self.mycollider.pepids = mypepids
self.mycollider.calcinner = 0
shuffle( self.mycollider.pepids )
self.mycollider.pepids = self.mycollider.pepids[:self.limit]
import c_rangetree
r = c_rangetree.ExtendedRangetree_Q1_RT.create()
r.new_rangetree()
r.create_tree(tuple(self.alltuples_isotope_correction))
#c_integrated.create_tree(tuple(self.alltuples_isotope_correction))
MAX_UIS = 5
c_newuistime = 0; oldtime = 0; c_fromprecursortime = 0
oldsql = 0; newsql = 0
newtime = 0
oldcalctime = 0; localsql = 0
self._cursor = False
print "i\toldtime\t\tnewtime\t>>\tspeedup"
for kk, pep in enumerate(self.mycollider.pepids):
ii = kk + 1
p_id = pep['parent_id']
q1 = pep['q1']
q3_low, q3_high = par.get_q3range_transitions()
q1_low = q1 - par.q1_window
q1_high = q1 + par.q1_window
ssrcalc = pep['ssrcalc']
peptide_key = pep['peptide_key']
#correct rounding errors, s.t. we get the same results as before!
ssrcalc_low = ssrcalc - par.ssrcalc_window + 0.001
ssrcalc_high = ssrcalc + par.ssrcalc_window - 0.001
isotope_correction = par.isotopes_up_to * Residues.mass_diffC13 / min(par.parent_charges)
precursor = Precursor(q1=pep['q1'], transition_group=pep['transition_group'], parent_id = pep['parent_id'], modified_sequence=pep['mod_sequence'], ssrcalc=pep['ssrcalc'])
transitions = collider.calculate_transitions_ch(
((q1, pep['mod_sequence'], p_id),), [1], q3_low, q3_high)
#fake some srm_id for the transitions
transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])
##### transitions = self.mycollider._get_all_transitions(par, pep, cursor)
nr_transitions = len( transitions )
if nr_transitions == 0: continue #no transitions in this window
###################################
# Old way to calculate non_uislist
# - get all precursors from the SQL database
# - calculate collisions per peptide in C++
par.query2_add = ' and isotope_nr = 0 ' # due to the new handling of isotopes
mystart = time.time()
self.mycollider.mysqlnewtime= 0
precursors = self.mycollider._get_all_precursors(par, precursor, cursor)
newsql += time.time() - mystart
mystart = time.time()
q3_low, q3_high = par.get_q3range_transitions()
collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series(
transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)
non_uis_list = [ {} for i in range(MAX_UIS+1)]
for order in range(1,MAX_UIS+1):
non_uis_list[order] = c_getnonuis.get_non_uis(
collisions_per_peptide, order)
c_fromprecursortime += time.time() - mystart
newl = [len(n) for n in non_uis_list]
non_uis_list_old_way = [set(kk.keys()) for kk in non_uis_list]
non_uis_list_len = [len(kk) for kk in non_uis_list_old_way[1:]]
###################################
# New way to calculate non_uislist
# - start out from transitions, get non_uislist
mystart = time.time()
newresult = c_integrated.wrap_all_bitwise(transitions, q1_low, ssrcalc_low,
q1_high, ssrcalc_high, peptide_key,
min(MAX_UIS,nr_transitions) , par.q3_window, #q3_low, q3_high,
par.ppm, par.isotopes_up_to, isotope_correction, par, r)
newtime += time.time() - mystart
###################################
# Assert equality, print out result
self.assertEqual( newresult , non_uis_list_len)
mys = "%s\t%0.1fms\t\t%0.2fms\t>>>\t%0.1f" % \
(ii, #i
(c_fromprecursortime + newsql)*1000/ii, # oldtime
(newtime)*1000/ii, # newtime
(c_fromprecursortime + newsql) / (newtime), # speedup
)
self.ESC = chr(27)
sys.stdout.write(self.ESC + '[2K')
if self._cursor:
sys.stdout.write(self.ESC + '[u')
self._cursor = True
sys.stdout.write(self.ESC + '[s')
sys.stdout.write(mys)
sys.stdout.flush()
def test_mysql_vs_integrated(self):
"""Compare the one table MySQL approach vs the fully integrated Cpp approach
Here we are comparing the old (querying the transitions database as
well as the precursor database) and the new way (only query the
precursor database and calculate the transitions on the fly) way of
calculating the collisions.
"""
print '\n' * 1
print "Comparing one table MySQL solution vs integrated solution"
par = self.par
cursor = self.cursor
mypepids = [
{
'mod_sequence': r[0],
'peptide_key': r[1],
'transition_group': r[1],
'parent_id': r[2],
'q1_charge': r[3],
'q1': r[4],
'ssrcalc': r[5],
} for r in self.alltuples if r[3] == 2 #charge is 2
and r[6] == 0 #isotope is 0
and r[4] >= self.min_q1 and r[4] < self.max_q1
]
mycollider = collider.SRMcollider()
#mypepids = _get_unique_pepids(par, cursor)
self.mycollider.pepids = mypepids
self.mycollider.calcinner = 0
shuffle(self.mycollider.pepids)
self.mycollider.pepids = self.mycollider.pepids[:self.limit]
import c_rangetree
r = c_rangetree.ExtendedRangetree_Q1_RT.create()
r.new_rangetree()
r.create_tree(tuple(self.alltuples_isotope_correction))
#c_integrated.create_tree(tuple(self.alltuples_isotope_correction))
MAX_UIS = 5
c_newuistime = 0
oldtime = 0
c_fromprecursortime = 0
oldsql = 0
newsql = 0
newtime = 0
oldcalctime = 0
localsql = 0
self._cursor = False
print "i\toldtime\t\tnewtime\t>>\tspeedup"
for kk, pep in enumerate(self.mycollider.pepids):
ii = kk + 1
p_id = pep['parent_id']
q1 = pep['q1']
q3_low, q3_high = par.get_q3range_transitions()
q1_low = q1 - par.q1_window
q1_high = q1 + par.q1_window
ssrcalc = pep['ssrcalc']
peptide_key = pep['peptide_key']
#correct rounding errors, s.t. we get the same results as before!
ssrcalc_low = ssrcalc - par.ssrcalc_window + 0.001
ssrcalc_high = ssrcalc + par.ssrcalc_window - 0.001
isotope_correction = par.isotopes_up_to * Residues.mass_diffC13 / min(
par.parent_charges)
precursor = Precursor(q1=pep['q1'],
transition_group=pep['transition_group'],
parent_id=pep['parent_id'],
modified_sequence=pep['mod_sequence'],
ssrcalc=pep['ssrcalc'])
transitions = collider.calculate_transitions_ch(
((q1, pep['mod_sequence'], p_id), ), [1], q3_low, q3_high)
#fake some srm_id for the transitions
transitions = tuple([(t[0], i) for i, t in enumerate(transitions)])
##### transitions = self.mycollider._get_all_transitions(par, pep, cursor)
nr_transitions = len(transitions)
if nr_transitions == 0: continue #no transitions in this window
###################################
# Old way to calculate non_uislist
# - get all precursors from the SQL database
# - calculate collisions per peptide in C++
par.query2_add = ' and isotope_nr = 0 ' # due to the new handling of isotopes
mystart = time.time()
self.mycollider.mysqlnewtime = 0
precursors = self.mycollider._get_all_precursors(
par, precursor, cursor)
newsql += time.time() - mystart
mystart = time.time()
q3_low, q3_high = par.get_q3range_transitions()
collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series(
transitions, precursors, par, q3_low, q3_high, par.q3_window,
par.ppm, False)
non_uis_list = [{} for i in range(MAX_UIS + 1)]
for order in range(1, MAX_UIS + 1):
non_uis_list[order] = c_getnonuis.get_non_uis(
collisions_per_peptide, order)
c_fromprecursortime += time.time() - mystart
newl = [len(n) for n in non_uis_list]
non_uis_list_old_way = [set(kk.keys()) for kk in non_uis_list]
non_uis_list_len = [len(kk) for kk in non_uis_list_old_way[1:]]
###################################
# New way to calculate non_uislist
# - start out from transitions, get non_uislist
mystart = time.time()
newresult = c_integrated.wrap_all_bitwise(
transitions,
q1_low,
ssrcalc_low,
q1_high,
ssrcalc_high,
peptide_key,
min(MAX_UIS, nr_transitions),
par.q3_window, #q3_low, q3_high,
par.ppm,
par.isotopes_up_to,
isotope_correction,
par,
r)
newtime += time.time() - mystart
###################################
# Assert equality, print out result
self.assertEqual(newresult, non_uis_list_len)
mys = "%s\t%0.1fms\t\t%0.2fms\t>>>\t%0.1f" % \
(ii, #i
(c_fromprecursortime + newsql)*1000/ii, # oldtime
(newtime)*1000/ii, # newtime
(c_fromprecursortime + newsql) / (newtime), # speedup
)
self.ESC = chr(27)
sys.stdout.write(self.ESC + '[2K')
if self._cursor:
sys.stdout.write(self.ESC + '[u')
self._cursor = True
sys.stdout.write(self.ESC + '[s')
sys.stdout.write(mys)
sys.stdout.flush()
def test_two_table_mysql(self):
"""Compare the two table vs the one table MySQL approach
Here we are comparing the old (querying the transitions database as
well as the precursor database) and the new way (only query the
precursor database and calculate the transitions on the fly) way of
calculating the collisions.
"""
print '\n'*1
print "Comparing one vs two table MySQL solution"
par = self.par
cursor = self.cursor
mycollider = collider.SRMcollider()
mypepids = _get_unique_pepids(par, cursor)
self.mycollider.pepids = mypepids
self.mycollider.calcinner = 0
shuffle( self.mycollider.pepids )
self.mycollider.pepids = self.mycollider.pepids[:self.limit]
MAX_UIS = 5
c_newuistime = 0; oldtime = 0; c_fromprecursortime = 0
oldsql = 0; newsql = 0
oldcalctime = 0; localsql = 0
self._cursor = False
print "oldtime = get UIS from collisions and transitions (getting all collisions from the transitions db)"
print "cuis + oldsql = as oldtime but calculate UIS in C++"
print "py+newsql = only get the precursors from the db and calculate collisions in Python"
print "ctime + newsql = only get the precursors from the db and calculate collisions in C++"
print "new = use fast SQL and C++ code"
print "old = use slow SQL and Python code"
print "i\toldtime\tcuis+oldsql\tpy+newsql\tctime+newsql\t>>>\toldsql\tnewsql\t...\t...\tspeedup"
for kk, pep in enumerate(self.mycollider.pepids):
ii = kk + 1
p_id = pep['parent_id']
q1 = pep['q1']
q3_low, q3_high = par.get_q3range_transitions()
precursor = Precursor(q1=pep['q1'], transition_group=pep['transition_group'], parent_id = pep['parent_id'], modified_sequence=pep['mod_sequence'], ssrcalc=pep['ssrcalc'])
transitions = collider.calculate_transitions_ch(
((q1, pep['mod_sequence'], p_id),), [1], q3_low, q3_high)
#fake some srm_id for the transitions
transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])
##### transitions = self.mycollider._get_all_transitions(par, pep, cursor)
nr_transitions = len( transitions )
if nr_transitions == 0: continue #no transitions in this window
#
mystart = time.time()
collisions = list(self.mycollider._get_all_collisions_calculate_new(par, precursor, cursor))
oldcolllen = len(collisions)
oldcalctime += time.time() - mystart
#
mystart = time.time()
collisions = _get_all_collisions(mycollider, par, pep, cursor, transitions = transitions)
oldcsqllen = len(collisions)
oldsql += time.time() - mystart
#
par.query2_add = ' and isotope_nr = 0 ' # due to the new handling of isotopes
mystart = time.time()
self.mycollider.mysqlnewtime= 0
precursors = self.mycollider._get_all_precursors(par, precursor, cursor)
newsql += time.time() - mystart
#
mystart = time.time()
#precursors = self.mycollider._get_all_precursors(par, pep, cursor_l)
localsql += time.time() - mystart
par.query2_add = '' # due to the new handling of isotopes
#
mystart = time.time()
non_uis_list = get_non_UIS_from_transitions(transitions,
tuple(collisions), par, MAX_UIS)
cnewuis = non_uis_list
c_newuistime += time.time() - mystart
#
mystart = time.time()
non_uis_list = get_non_UIS_from_transitions_old(transitions,
collisions, par, MAX_UIS)
oldnonuislist = non_uis_list
oldtime += time.time() - mystart
#
mystart = time.time()
q3_low, q3_high = par.get_q3range_transitions()
collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series(
transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)
non_uis_list = [ {} for i in range(MAX_UIS+1)]
for order in range(1,MAX_UIS+1):
non_uis_list[order] = c_getnonuis.get_non_uis(
collisions_per_peptide, order)
c_fromprecursortime += time.time() - mystart
newl = [len(n) for n in non_uis_list]
self.assertEqual(newl, [len(o) for o in cnewuis])
self.assertEqual(newl, [len(o) for o in oldnonuislist])
non_uis_list = [set(k.keys()) for k in non_uis_list]
cnewuis = [set(k.keys()) for k in cnewuis]
self.assertEqual(non_uis_list, cnewuis)
self.assertEqual(non_uis_list, oldnonuislist)
mys = "%s\t%0.fms\t%0.fms\t\t%0.fms\t\t%0.2fms\t\t>>>\t%0.fms\t%0.2fms\t...\t...\t%0.2f" % \
(ii, #i
(oldtime + oldsql)*1000/ii, #oldtime
(c_newuistime+oldsql)*1000/ii, #cuis + oldsql
(oldcalctime + newsql + oldtime)*1000/ii, #newsql
(c_fromprecursortime + newsql)*1000/ii, #ctime+newsql
#(c_fromprecursortime + localsql)*1000/ii,
oldsql*1000/ii, #newsql
newsql*1000/ii, #oldsql
#localsql*1000/ii,
#oldtime / c_newuistime
(oldtime + oldsql) / (c_fromprecursortime + newsql)
)
self.ESC = chr(27)
sys.stdout.write(self.ESC + '[2K')
if self._cursor:
sys.stdout.write(self.ESC + '[u')
self._cursor = True
sys.stdout.write(self.ESC + '[s')
sys.stdout.write(mys)
sys.stdout.flush()
def test_two_table_mysql(self):
"""Compare the two table vs the one table MySQL approach
Here we are comparing the old (querying the transitions database as
well as the precursor database) and the new way (only query the
precursor database and calculate the transitions on the fly) way of
calculating the collisions.
"""
print '\n' * 1
print "Comparing one vs two table MySQL solution"
par = self.par
cursor = self.cursor
mycollider = collider.SRMcollider()
mypepids = _get_unique_pepids(par, cursor)
self.mycollider.pepids = mypepids
self.mycollider.calcinner = 0
shuffle(self.mycollider.pepids)
self.mycollider.pepids = self.mycollider.pepids[:self.limit]
MAX_UIS = 5
c_newuistime = 0
oldtime = 0
c_fromprecursortime = 0
oldsql = 0
newsql = 0
oldcalctime = 0
localsql = 0
self._cursor = False
print "oldtime = get UIS from collisions and transitions (getting all collisions from the transitions db)"
print "cuis + oldsql = as oldtime but calculate UIS in C++"
print "py+newsql = only get the precursors from the db and calculate collisions in Python"
print "ctime + newsql = only get the precursors from the db and calculate collisions in C++"
print "new = use fast SQL and C++ code"
print "old = use slow SQL and Python code"
print "i\toldtime\tcuis+oldsql\tpy+newsql\tctime+newsql\t>>>\toldsql\tnewsql\t...\t...\tspeedup"
for kk, pep in enumerate(self.mycollider.pepids):
ii = kk + 1
p_id = pep['parent_id']
q1 = pep['q1']
q3_low, q3_high = par.get_q3range_transitions()
precursor = Precursor(q1=pep['q1'],
transition_group=pep['transition_group'],
parent_id=pep['parent_id'],
modified_sequence=pep['mod_sequence'],
ssrcalc=pep['ssrcalc'])
transitions = collider.calculate_transitions_ch(
((q1, pep['mod_sequence'], p_id), ), [1], q3_low, q3_high)
#fake some srm_id for the transitions
transitions = tuple([(t[0], i) for i, t in enumerate(transitions)])
##### transitions = self.mycollider._get_all_transitions(par, pep, cursor)
nr_transitions = len(transitions)
if nr_transitions == 0: continue #no transitions in this window
#
mystart = time.time()
collisions = list(
self.mycollider._get_all_collisions_calculate_new(
par, precursor, cursor))
oldcolllen = len(collisions)
oldcalctime += time.time() - mystart
#
mystart = time.time()
collisions = _get_all_collisions(mycollider,
par,
pep,
cursor,
transitions=transitions)
oldcsqllen = len(collisions)
oldsql += time.time() - mystart
#
par.query2_add = ' and isotope_nr = 0 ' # due to the new handling of isotopes
mystart = time.time()
self.mycollider.mysqlnewtime = 0
precursors = self.mycollider._get_all_precursors(
par, precursor, cursor)
newsql += time.time() - mystart
#
mystart = time.time()
#precursors = self.mycollider._get_all_precursors(par, pep, cursor_l)
localsql += time.time() - mystart
par.query2_add = '' # due to the new handling of isotopes
#
mystart = time.time()
non_uis_list = get_non_UIS_from_transitions(
transitions, tuple(collisions), par, MAX_UIS)
cnewuis = non_uis_list
c_newuistime += time.time() - mystart
#
mystart = time.time()
non_uis_list = get_non_UIS_from_transitions_old(
transitions, collisions, par, MAX_UIS)
oldnonuislist = non_uis_list
oldtime += time.time() - mystart
#
mystart = time.time()
q3_low, q3_high = par.get_q3range_transitions()
collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series(
transitions, precursors, par, q3_low, q3_high, par.q3_window,
par.ppm, False)
non_uis_list = [{} for i in range(MAX_UIS + 1)]
for order in range(1, MAX_UIS + 1):
non_uis_list[order] = c_getnonuis.get_non_uis(
collisions_per_peptide, order)
c_fromprecursortime += time.time() - mystart
newl = [len(n) for n in non_uis_list]
self.assertEqual(newl, [len(o) for o in cnewuis])
self.assertEqual(newl, [len(o) for o in oldnonuislist])
non_uis_list = [set(k.keys()) for k in non_uis_list]
cnewuis = [set(k.keys()) for k in cnewuis]
self.assertEqual(non_uis_list, cnewuis)
self.assertEqual(non_uis_list, oldnonuislist)
mys = "%s\t%0.fms\t%0.fms\t\t%0.fms\t\t%0.2fms\t\t>>>\t%0.fms\t%0.2fms\t...\t...\t%0.2f" % \
(ii, #i
(oldtime + oldsql)*1000/ii, #oldtime
(c_newuistime+oldsql)*1000/ii, #cuis + oldsql
(oldcalctime + newsql + oldtime)*1000/ii, #newsql
(c_fromprecursortime + newsql)*1000/ii, #ctime+newsql
#(c_fromprecursortime + localsql)*1000/ii,
oldsql*1000/ii, #newsql
newsql*1000/ii, #oldsql
#localsql*1000/ii,
#oldtime / c_newuistime
(oldtime + oldsql) / (c_fromprecursortime + newsql)
)
self.ESC = chr(27)
sys.stdout.write(self.ESC + '[2K')
if self._cursor:
sys.stdout.write(self.ESC + '[u')
self._cursor = True
sys.stdout.write(self.ESC + '[s')
sys.stdout.write(mys)
sys.stdout.flush()
