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):
import sys, os, time
self.DDB = DDB
self.R = Residues('mono')
self.pep1 = (500, 'PEPTIDE', 1, 1)
self.pep2 = (400, 'CEPC[160]IDM[147]E', 2, 2)
self.charge = 2
self.q3_low = 300
self.q3_high = 1500
self.transitions_12_between300_1500 = test_shared.transitions_12_between300_1500
self.pep1_yseries = test_shared.pep1_yseries
self.pep1_bseries = test_shared.pep1_bseries
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()
transitions = [(p.peak, i) for i, p in enumerate(peaks)
if p.experimental_height > threshold]
nr_transitions = len(transitions)
if nr_transitions == 0: continue #no transitions in this window
if (nr_transitions > 31):
print "Skipping", spectrum.modified_sequence, "too many transitions (%s)" % nr_transitions
continue
peptide_obj.fix_mprophet_sequence_bug(
) # fix mProphet-bug (modified cysteins are [C160] instead of C[160]
#
# Get all interfering precursors, (w/o the current peptide)
precursors = mycollider._get_all_precursors(par, peptide_obj, cursor)
R = Residues('mono')
q3_low, q3_high = par.get_q3range_collisions()
#
# check for q3_low and q3_high values, if the transitions are outside this
# range, we will not find collisions for those == incorrect results
#
for t in transitions:
if t[0] < q3_low or t[0] > q3_high:
err = "\n"+ "Error: Found transition %s out of range\n" % t[0] + \
"Please adjust the --q3_low and --q3_high parameters to get correct results\n"
print err
sys.stderr.write(err)
sys.exit()
get_precursor_time += time.time() - tmp_time
tmp_time = time.time()
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)