########################################################################### from precursor import Precursors myprecursors = Precursors() myprecursors.getFromDB(par, db.cursor(), min_q1 - par.q1_window, max_q1 + par.q1_window) if not options.query_peptide_table is None and not options.query_peptide_table == "": print "Using a different table for the query peptides than for the background peptides!" print "Will use table %s " % options.query_peptide_table query_precursors = Precursors() query_par = copy(par) query_par.peptide_tables = [options.query_peptide_table] query_precursors.getFromDB(query_par, db.cursor(), min_q1 - par.q1_window, max_q1 + par.q1_window) precursors_to_evaluate = query_precursors.getPrecursorsToEvaluate(min_q1, max_q1) else: precursors_to_evaluate = myprecursors.getPrecursorsToEvaluate(min_q1, max_q1) myprecursors.build_parent_id_lookup() myprecursors.build_transition_group_lookup() # If we dont use the DB, we use the rangetree to query and get our list of # precursors that are interfering. In SWATH we dont include a +/- q1_window # around our range or precursors because the precursor window is fixed to # (min_q1,max_q1) and no other precursors are considered. if not use_db and swath_mode: myprecursors.getFromDB(par, cursor, min_q1, max_q1) rtree = myprecursors.build_rangetree() elif not use_db: #myprecursors.getFromDB(par, cursor, min_q1 - par.q1_window, max_q1 + par.q1_window) rtree = myprecursors.build_rangetree() # In SWATH mode, select all precursors that are relevant for the background at # once. Select all precursors between min_q1 - correction and max_q1 and then # only append those to all_swath_precursors that are actually included in the
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()
