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 setUp(self):
self.limit = 100
self.limit_large = 100
self.limit = 300
self.limit_large = 600
try:
import MySQLdb
#db_l = MySQLdb.connect(read_default_file="~/.my.cnf.local")
db = MySQLdb.connect(read_default_file="~/.srm.cnf")
cursor = db.cursor()
self.cursor = cursor
par = test_shared.get_default_setup_parameters()
par.use_sqlite = True
par.q1_window = 1.2 / 2.0
par.q3_window = 2.0 / 2.0
par.ssrcalc_window = 4 / 2.0
par.ssrcalc_window = 9999 / 2.0
par.peptide_tables = ['hroest.srmPeptides_yeast']
par.transition_table = 'hroest.srmTransitions_yeast'
par.isotopes_up_to = 3
self.mycollider = collider.SRMcollider()
par.select_by = "id"
self.par = par
self.min_q1 = 440
self.max_q1 = 450
## For debugging
##self.max_q1 = 440.18
##par.q1_window = 0.009 / 2.0
##par.q3_window = 2.0 / 2.0
##par.isotopes_up_to = 1
import Residues
R = Residues.Residues('mono')
isotope_correction = par.isotopes_up_to * R.mass_diffC13 / min(par.parent_charges)
start = time.time()
query = """
select modified_sequence, transition_group, parent_id, q1_charge, q1, ssrcalc, isotope_nr, 0, 0
from %s where q1 between %s and %s
#and isotope_nr = 0
""" % (par.peptide_tables[0], self.min_q1 - par.q1_window, self.max_q1 + par.q1_window)
cursor.execute(query)
self.alltuples = list(cursor.fetchall() )
#print "len alltuples", len(self.alltuples)
query = """
select modified_sequence, transition_group, parent_id, q1_charge, q1, ssrcalc, isotope_nr, 0, 0
from %s where q1 between %s - %s and %s
and isotope_nr = 0
""" % (par.peptide_tables[0], self.min_q1 - par.q1_window, isotope_correction, self.max_q1 + par.q1_window)
cursor.execute(query)
self.alltuples_isotope_correction = list(cursor.fetchall())
#print "len alltuples zero", len(self.alltuples_isotope_correction)
self.myprecursors = Precursors()
# myprecursors.getFromDB(par, db.cursor(), self.min_q1 - par.q1_window, self.max_q1 + par.q1_window)
##### LEGACY getFromDB -- have isotope_nr = 0 in there!
# Get all precursors from the DB within a window of Q1
lower_q1 = self.min_q1 - par.q1_window
upper_q1 = self.max_q1 + par.q1_window
self.myprecursors.precursors = []
isotope_correction = par.isotopes_up_to * R.mass_diffC13 / min(par.parent_charges)
q = """
select modified_sequence, transition_group, parent_id, q1_charge, q1, ssrcalc, modifications, missed_cleavages, isotopically_modified
from %(peptide_table)s where q1 between %(lowq1)s - %(isotope_correction)s and %(highq1)s
and isotope_nr = 0
""" % {'peptide_table' : par.peptide_tables[0],
'lowq1' : lower_q1, # min_q1 - par.q1_window
'highq1' : upper_q1, # max_q1 + par.q1_window,
'isotope_correction' : isotope_correction
}
cursor.execute(q)
for res in cursor.fetchall():
p = Precursor()
p.initialize(*res)
# Only include those precursors that are actually have isotopes in the specified range
if(p.included_in_isotopic_range(lower_q1, upper_q1, par) ):
self.myprecursors.precursors.append(p)
##### END LEGACY getFromDB
self.precursors_to_evaluate = self.myprecursors.getPrecursorsToEvaluate(self.min_q1, self.max_q1)
except Exception as inst:
print "something went wrong"
print inst
def setUp(self):
self.limit = 100
self.limit_large = 100
self.limit = 300
self.limit_large = 600
try:
import MySQLdb
#db_l = MySQLdb.connect(read_default_file="~/.my.cnf.local")
db = MySQLdb.connect(read_default_file="~/.srm.cnf")
cursor = db.cursor()
self.cursor = cursor
par = test_shared.get_default_setup_parameters()
par.use_sqlite = True
par.q1_window = 1.2 / 2.0
par.q3_window = 2.0 / 2.0
par.ssrcalc_window = 4 / 2.0
par.ssrcalc_window = 9999 / 2.0
par.peptide_tables = ['hroest.srmPeptides_yeast']
par.transition_table = 'hroest.srmTransitions_yeast'
par.isotopes_up_to = 3
self.mycollider = collider.SRMcollider()
par.select_by = "id"
self.par = par
self.min_q1 = 440
self.max_q1 = 450
## For debugging
##self.max_q1 = 440.18
##par.q1_window = 0.009 / 2.0
##par.q3_window = 2.0 / 2.0
##par.isotopes_up_to = 1
import Residues
R = Residues.Residues('mono')
isotope_correction = par.isotopes_up_to * R.mass_diffC13 / min(
par.parent_charges)
start = time.time()
query = """
select modified_sequence, transition_group, parent_id, q1_charge, q1, ssrcalc, isotope_nr, 0, 0
from %s where q1 between %s and %s
#and isotope_nr = 0
""" % (par.peptide_tables[0], self.min_q1 -
par.q1_window, self.max_q1 + par.q1_window)
cursor.execute(query)
self.alltuples = list(cursor.fetchall())
#print "len alltuples", len(self.alltuples)
query = """
select modified_sequence, transition_group, parent_id, q1_charge, q1, ssrcalc, isotope_nr, 0, 0
from %s where q1 between %s - %s and %s
and isotope_nr = 0
""" % (par.peptide_tables[0], self.min_q1 -
par.q1_window, isotope_correction,
self.max_q1 + par.q1_window)
cursor.execute(query)
self.alltuples_isotope_correction = list(cursor.fetchall())
#print "len alltuples zero", len(self.alltuples_isotope_correction)
self.myprecursors = Precursors()
# myprecursors.getFromDB(par, db.cursor(), self.min_q1 - par.q1_window, self.max_q1 + par.q1_window)
##### LEGACY getFromDB -- have isotope_nr = 0 in there!
# Get all precursors from the DB within a window of Q1
lower_q1 = self.min_q1 - par.q1_window
upper_q1 = self.max_q1 + par.q1_window
self.myprecursors.precursors = []
isotope_correction = par.isotopes_up_to * R.mass_diffC13 / min(
par.parent_charges)
q = """
select modified_sequence, transition_group, parent_id, q1_charge, q1, ssrcalc, modifications, missed_cleavages, isotopically_modified
from %(peptide_table)s where q1 between %(lowq1)s - %(isotope_correction)s and %(highq1)s
and isotope_nr = 0
""" % {
'peptide_table': par.peptide_tables[0],
'lowq1': lower_q1, # min_q1 - par.q1_window
'highq1': upper_q1, # max_q1 + par.q1_window,
'isotope_correction': isotope_correction
}
cursor.execute(q)
for res in cursor.fetchall():
p = Precursor()
p.initialize(*res)
# Only include those precursors that are actually have isotopes in the specified range
if (p.included_in_isotopic_range(lower_q1, upper_q1, par)):
self.myprecursors.precursors.append(p)
##### END LEGACY getFromDB
self.precursors_to_evaluate = self.myprecursors.getPrecursorsToEvaluate(
self.min_q1, self.max_q1)
except Exception as inst:
print "something went wrong"
print inst
