def setUp(self):
self.transitions = transitions_def1
self.collisions = collisions_def1
class Minimal: pass
self.par = Minimal()
self.par.q3_window = 4.0
self.par.ppm = False
self.MAX_UIS = 5
self.q3_high = 1500
self.q3_low = 300
self.par.bions = True
self.par.yions = True
self.par.aions = False
self.par.aMinusNH3 = False
self.par.bMinusH2O = False
self.par.bMinusNH3 = False
self.par.bPlusH2O = False
self.par.yMinusH2O = False
self.par.yMinusNH3 = False
self.par.cions = False
self.par.xions = False
self.par.zions = False
self.par.MMinusH2O = False
self.par.MMinusNH3 = False
def returnrange(): return self.q3_high, self.q3_low
self.par.get_q3range_collisions = returnrange
import sys
self.R = Residues('mono')
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase()
def setUp(self):
import sys
self.R = Residues('mono')
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase()
self.real_parameters = test_shared.get_default_setup_parameters()
self.precursor = test_shared.ThreePeptideExample.precursor
self.interfering_precursors = test_shared.ThreePeptideExample.interfering_precursors
def setUp(self):
import sys
self.R = Residues('mono')
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase()
self.real_parameters = test_shared.get_default_setup_parameters()
self.precursor = test_shared.ThreePeptideExample.precursor
self.interfering_precursors = test_shared.ThreePeptideExample.interfering_precursors
def setUp(self):
self.transitions = transitions_def1
self.collisions = collisions_def1
self.MAX_UIS = 5
self.q3_high = 1500
self.q3_low = 300
self.R = Residues('mono')
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase()
self.par = test_shared.get_default_setup_parameters()
self.par.q3_window = 4.0
def setUp(self):
self.transitions = transitions_def1
self.collisions = collisions_def1
self.MAX_UIS = 5
self.q3_high = 1500
self.q3_low = 300
self.R = Residues('mono')
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase()
self.par = test_shared.get_default_setup_parameters()
self.par.q3_window = 4.0
def test_complete_with_isotopes(self):
if not self.database_available: return
#now test with isotopes enabled
par = collider.testcase(testdatabase=test_database)
par.quiet = True
par.isotopes_up_to = 3
par.eval()
par.query2_add = ' and isotope_nr = 0 ' # need to do this because we also have other isotopes in there!
mycollider = collider.SRMcollider()
cursor = self.db.cursor()
#for historic reasons, we only select a subset of peptides
exclude_pepids = [
183, 203, 319, 345, 355, 365, 367, 385, 393, 425, 1227, 1233, 1297,
1299, 1303, 1305, 1307, 1309, 1311, 1509, 1681, 1683
]
mycollider = collider.SRMcollider()
pepids = _get_unique_pepids(par, cursor, ignore_genomeoccurence=True)
pepids = [p for p in pepids if p['parent_id'] not in exclude_pepids]
find_clashes_small(self, mycollider, cursor, par, pepids)
assert abs(mycollider.allpeps[111] - 0.888888888889) < 1e-5
assert abs(mycollider.allpeps[191] - 0.7) < 1e-5
assert abs(mycollider.allpeps[375] - 0.941176470588) < 1e-5
assert abs(mycollider.allpeps[585] - 0.875) < 1e-5
assert abs(mycollider.allpeps[609] - 0.6666666) < 1e-5
assert abs(mycollider.allpeps[929] - 0.857142857143) < 1e-5
assert abs(mycollider.allpeps[1089] - 0.7) < 1e-5
assert abs(mycollider.allpeps[1101] - 0.916666666667) < 1e-5
assert abs(mycollider.allpeps[1177] - 0.928571428571) < 1e-5
assert abs(mycollider.allpeps[1493] - 0.928571428571) < 1e-5
assert abs(mycollider.allpeps[1537] - 0.857142857143) < 1e-5
assert abs(mycollider.allpeps[1585] - 0.933333333333) < 1e-5
assert abs(mycollider.allpeps[1663] - 0.928571428571) < 1e-5
assert abs(mycollider.allpeps[1763] - 0.8125) < 1e-5
assert abs(mycollider.allpeps[1925] - 0.928571428571) < 1e-5
assert abs(mycollider.allpeps[1957] - 0.833333333333) < 1e-5
assert abs(mycollider.allpeps[1967] - 0.857142857143) < 1e-5
assert abs(mycollider.allpeps[1991] - 0.857142857143) < 1e-5
self.assertTrue(
abs(sum(mycollider.allpeps.values()) - 971.215436) < 10**(-3))
self.assertEqual(
len([v for v in mycollider.allpeps.values() if v == 1.0]), 922)
self.assertEqual(mycollider.non_unique_count, 71)
self.assertEqual(mycollider.total_count, 12502)
def test_complete_with_isotopes(self):
if not self.database_available: return
#now test with isotopes enabled
par = collider.testcase(testdatabase=test_database)
par.quiet = True
par.isotopes_up_to = 3
par.eval()
par.query2_add = ' and isotope_nr = 0 ' # need to do this because we also have other isotopes in there!
mycollider = collider.SRMcollider()
cursor = self.db.cursor()
#for historic reasons, we only select a subset of peptides
exclude_pepids = [183, 203, 319, 345, 355, 365, 367, 385, 393, 425, 1227, 1233, 1297, 1299, 1303, 1305, 1307, 1309, 1311, 1509, 1681, 1683]
mycollider = collider.SRMcollider()
pepids = _get_unique_pepids(par, cursor, ignore_genomeoccurence=True)
pepids = [p for p in pepids if p['parent_id'] not in exclude_pepids]
find_clashes_small(self, mycollider, cursor, par, pepids)
assert abs(mycollider.allpeps[111] - 0.888888888889) < 1e-5
assert abs(mycollider.allpeps[191] - 0.7) < 1e-5
assert abs(mycollider.allpeps[375] - 0.941176470588) < 1e-5
assert abs(mycollider.allpeps[585] - 0.875) < 1e-5
assert abs(mycollider.allpeps[609] - 0.6666666) < 1e-5
assert abs(mycollider.allpeps[929] - 0.857142857143) < 1e-5
assert abs(mycollider.allpeps[1089] - 0.7) < 1e-5
assert abs(mycollider.allpeps[1101] - 0.916666666667) < 1e-5
assert abs(mycollider.allpeps[1177] - 0.928571428571) < 1e-5
assert abs(mycollider.allpeps[1493] - 0.928571428571) < 1e-5
assert abs(mycollider.allpeps[1537] - 0.857142857143) < 1e-5
assert abs(mycollider.allpeps[1585] - 0.933333333333) < 1e-5
assert abs(mycollider.allpeps[1663] - 0.928571428571) < 1e-5
assert abs(mycollider.allpeps[1763] - 0.8125) < 1e-5
assert abs(mycollider.allpeps[1925] - 0.928571428571) < 1e-5
assert abs(mycollider.allpeps[1957] - 0.833333333333) < 1e-5
assert abs(mycollider.allpeps[1967] - 0.857142857143) < 1e-5
assert abs(mycollider.allpeps[1991] - 0.857142857143) < 1e-5
self.assertTrue( abs(sum( mycollider.allpeps.values() ) - 971.215436) < 10**(-3) )
self.assertEqual( len([v for v in mycollider.allpeps.values() if v == 1.0 ] ), 922 )
self.assertEqual( mycollider.non_unique_count, 71)
self.assertEqual( mycollider.total_count, 12502 )
def test_complete_without_isotopes(self):
if not self.database_available: return
par = collider.testcase(testdatabase=test_database)
par.query2_add = ' and isotope_nr = 0 ' # still necessary, old style tables
par.quiet = True
mycollider = collider.SRMcollider()
cursor = self.db.cursor()
#for historic reasons, we only select a subset of peptides
exclude_pepids = [183, 203, 319, 345, 355, 365, 367, 385, 393, 425, 1227, 1233, 1297, 1299, 1303, 1305, 1307, 1309, 1311, 1509, 1681, 1683]
mycollider = collider.SRMcollider()
pepids = _get_unique_pepids(par, cursor, ignore_genomeoccurence=True)
pepids = [p for p in pepids if p['parent_id'] not in exclude_pepids]
find_clashes_small(self, mycollider, cursor, par, pepids)
do_check_complete(self, mycollider)
def test_complete_without_isotopes(self):
if not self.database_available: return
par = collider.testcase(testdatabase=test_database)
par.query2_add = ' and isotope_nr = 0 ' # still necessary, old style tables
par.quiet = True
mycollider = collider.SRMcollider()
cursor = self.db.cursor()
#for historic reasons, we only select a subset of peptides
exclude_pepids = [
183, 203, 319, 345, 355, 365, 367, 385, 393, 425, 1227, 1233, 1297,
1299, 1303, 1305, 1307, 1309, 1311, 1509, 1681, 1683
]
mycollider = collider.SRMcollider()
pepids = _get_unique_pepids(par, cursor, ignore_genomeoccurence=True)
pepids = [p for p in pepids if p['parent_id'] not in exclude_pepids]
find_clashes_small(self, mycollider, cursor, par, pepids)
do_check_complete(self, mycollider)
def setUp(self):
import sys
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase()
self.EPSILON = 10**-5
par = collider.SRM_parameters()
par.q1_window = 25 / 2.0
par.q3_window = 1 / 2.0
par.ppm = False
par.q3_low = 400
par.q3_high = 1400
par.q3_range = [par.q3_low, par.q3_high]
par.set_default_vars()
par.eval()
self.real_parameters = par
self.precursor = test_shared.ThreePeptideExample.precursor
self.interfering_precursors = test_shared.ThreePeptideExample.interfering_precursors
self.oldstyle_precursors = tuple([(p.q1, p.modified_sequence, p.transition_group, p.q1_charge, p.isotopically_modified) for p in self.interfering_precursors])
def setUp(self):
self.transitions = transitions_def1
self.collisions = collisions_def1
class Minimal:
pass
self.par = Minimal()
self.par.q3_window = 4.0
self.par.ppm = False
self.MAX_UIS = 5
self.q3_high = 1500
self.q3_low = 300
self.par.bions = True
self.par.yions = True
self.par.aions = False
self.par.aMinusNH3 = False
self.par.bMinusH2O = False
self.par.bMinusNH3 = False
self.par.bPlusH2O = False
self.par.yMinusH2O = False
self.par.yMinusNH3 = False
self.par.cions = False
self.par.xions = False
self.par.zions = False
self.par.MMinusH2O = False
self.par.MMinusNH3 = False
def returnrange():
return self.q3_high, self.q3_low
self.par.get_q3range_collisions = returnrange
import sys
self.R = Residues('mono')
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase()
def setUp(self):
try:
import MySQLdb
self.database_available = True
except ImportError:
print """Module MySQLdb not available.
Please install it if you want to use it.
Use the following command (on Ubuntu systems):
sudo apt-get install python-mysqldb
"""
self.database_available = False
try:
self.db = MySQLdb.connect(read_default_file=mysql_conf_file)
self.database_available = True
except MySQLdb.OperationalError as e:
print "Could not connect to database: Please check the configuration in test/test_db.py!\n", e
self.database_available = False
class Minimal:
def get_q3_window_transitions(self, q3):
if self.ppm: return [q3 - self.q3_window * 10**(-6) *q3, q3 + self.q3_window * 10**(-6) * q3]
else: return [q3 - self.q3_window, q3 + self.q3_window]
self.par = Minimal()
self.par.q3_window = 4.0
self.par.ppm = False
self.MAX_UIS = 5
self.q3_high = 1500
self.q3_low = 300
self.par.q1_window = 1.2 / 2.0
self.par.ssrcalc_window = 9999
self.par.query2_add = ' and isotope_nr = 0 '
self.par.peptide_tables = [test_database + '.srmPeptides_human']
self.par.transition_table = test_database + '.srmTransitions_human'
self.par.print_query = False
self.par.select_floor = False
self.par.isotopes_up_to = 3
self.par.select_by = "id"
self.par.parent_charges = [2,3]
self.par.bions = True
self.par.yions = True
self.par.aions = False
self.par.aMinusNH3 = False
self.par.bMinusH2O = False
self.par.bMinusNH3 = False
self.par.bPlusH2O = False
self.par.yMinusH2O = False
self.par.yMinusNH3 = False
self.par.cions = False
self.par.xions = False
self.par.zions = False
self.par.MMinusH2O = False
self.par.MMinusNH3 = False
def returntrue(): return True
self.par.do_b_y_only = returntrue
def returnrange(): return self.q3_low, self.q3_high
self.par.get_q3range_collisions = returnrange
#self.par.get_q3_window_transitions = get_q3_window_transitions
#self.par.get_q3_window_transitions = collider.SRM_parameters.get_q3_window_transitions
import sys
self.R = Residues('mono')
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase(testdatabase=test_database)
def setUp(self):
self.transitions = transitions_def1
self.collisions = collisions_def1
self.EPSILON = 10**-5
self.min_q1 = 400
self.max_q1 = 1500
par = collider.SRM_parameters()
par.q1_window = 1 / 2.0
par.q3_window = 1 / 2.0
par.ssrcalc_window = 10 / 2.0
par.ppm = False
par.isotopes_up_to = 3
par.q3_low = 400
par.q3_high = 1400
par.max_uis = 5
par.peptide_tables = [PEPTIDE_TABLE_NAME]
par.mysql_config = '~/.my.cnf'
par.sqlite_database = test_shared.SQLITE_DATABASE_LOCATION
print par.sqlite_database
par.use_sqlite = USE_SQLITE
par.quiet = False
par.bions = True
par.yions = True
par.aions = False
par.aMinusNH3 = False
par.bMinusH2O = False
par.bMinusNH3 = False
par.bPlusH2O = False
par.yMinusH2O = False
par.yMinusNH3 = False
par.cions = False
par.xions = False
par.zions = False
par.MMinusH2O = False
par.MMinusNH3 = False
par.q3_range = [par.q3_low, par.q3_high]
par.set_default_vars()
par.eval()
self.par = par
self.R = Residues('mono')
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase()
self.db = par.get_db()
# Get the precursors
###########################################################################
myprecursors = Precursors()
cursor = self.db.cursor()
myprecursors.getFromDB(par, cursor, self.min_q1 - par.q1_window,
self.max_q1 + par.q1_window)
testrange = myprecursors.build_rangetree()
self.precursors_to_evaluate = myprecursors.getPrecursorsToEvaluate(
self.min_q1, self.max_q1)
myprecursors.build_parent_id_lookup()
myprecursors.build_transition_group_lookup()
self.myprecursors = myprecursors
cursor.close()
def setUp(self):
self.transitions = transitions_def1
self.collisions = collisions_def1
self.EPSILON = 10**-5
self.min_q1 = 400
self.max_q1 = 1500
par = collider.SRM_parameters()
par.q1_window = 1 / 2.0
par.q3_window = 1 / 2.0
par.ssrcalc_window = 10 / 2.0
par.ppm = False
par.isotopes_up_to = 3
par.q3_low = 400
par.q3_high = 1400
par.max_uis = 5
par.peptide_tables = [ PEPTIDE_TABLE_NAME ]
par.mysql_config = '~/.my.cnf'
par.sqlite_database = test_shared.SQLITE_DATABASE_LOCATION
print par.sqlite_database
par.use_sqlite = USE_SQLITE
par.quiet = False
par.bions = True
par.yions = True
par.aions = False
par.aMinusNH3 = False
par.bMinusH2O = False
par.bMinusNH3 = False
par.bPlusH2O = False
par.yMinusH2O = False
par.yMinusNH3 = False
par.cions = False
par.xions = False
par.zions = False
par.MMinusH2O = False
par.MMinusNH3 = False
par.q3_range = [par.q3_low, par.q3_high]
par.set_default_vars()
par.eval()
self.par = par
self.R = Residues('mono')
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase()
self.db = par.get_db()
# Get the precursors
###########################################################################
myprecursors = Precursors()
cursor = self.db.cursor()
myprecursors.getFromDB(par, cursor, self.min_q1 - par.q1_window, self.max_q1 + par.q1_window)
testrange = myprecursors.build_rangetree()
self.precursors_to_evaluate = myprecursors.getPrecursorsToEvaluate(self.min_q1, self.max_q1)
myprecursors.build_parent_id_lookup()
myprecursors.build_transition_group_lookup()
self.myprecursors = myprecursors
cursor.close()
def setUp(self):
try:
import MySQLdb
self.database_available = True
except ImportError:
print """Module MySQLdb not available.
Please install it if you want to use it.
Use the following command (on Ubuntu systems):
sudo apt-get install python-mysqldb
"""
self.database_available = False
try:
self.db = MySQLdb.connect(read_default_file=mysql_conf_file)
self.database_available = True
except MySQLdb.OperationalError as e:
print "Could not connect to database: Please check the configuration in test/test_db.py!\n", e
self.database_available = False
class Minimal:
def get_q3_window_transitions(self, q3):
if self.ppm:
return [
q3 - self.q3_window * 10**(-6) * q3,
q3 + self.q3_window * 10**(-6) * q3
]
else:
return [q3 - self.q3_window, q3 + self.q3_window]
self.par = Minimal()
self.par.q3_window = 4.0
self.par.ppm = False
self.MAX_UIS = 5
self.q3_high = 1500
self.q3_low = 300
self.par.q1_window = 1.2 / 2.0
self.par.ssrcalc_window = 9999
self.par.query2_add = ' and isotope_nr = 0 '
self.par.peptide_tables = [test_database + '.srmPeptides_human']
self.par.transition_table = test_database + '.srmTransitions_human'
self.par.print_query = False
self.par.select_floor = False
self.par.isotopes_up_to = 3
self.par.select_by = "id"
self.par.parent_charges = [2, 3]
self.par.bions = True
self.par.yions = True
self.par.aions = False
self.par.aMinusNH3 = False
self.par.bMinusH2O = False
self.par.bMinusNH3 = False
self.par.bPlusH2O = False
self.par.yMinusH2O = False
self.par.yMinusNH3 = False
self.par.cions = False
self.par.xions = False
self.par.zions = False
self.par.MMinusH2O = False
self.par.MMinusNH3 = False
def returntrue():
return True
self.par.do_b_y_only = returntrue
def returnrange():
return self.q3_low, self.q3_high
self.par.get_q3range_collisions = returnrange
#self.par.get_q3_window_transitions = get_q3_window_transitions
#self.par.get_q3_window_transitions = collider.SRM_parameters.get_q3_window_transitions
import sys
self.R = Residues('mono')
self.acollider = collider.SRMcollider()
self.aparamset = collider.testcase(testdatabase=test_database)