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])
"--allow_contamination",
dest="allow_contamination",
default=3,
type='int',
help="Number of locally contaminated transitions to be allowed")
group.add_option("--GRAVY",
action="store_true",
dest="GRAVY",
default=False,
help="Use GRAVY scores instead of SSRCalc values.")
parser.add_option_group(group)
# Run the collider
###########################################################################
# Parse options
par = collider.SRM_parameters()
par.parse_cmdl_args(parser)
options, args = parser.parse_args(sys.argv[1:])
par.parse_options(options)
forceChargeCheck = False
db = par.get_db()
cursor = db.cursor()
# local arguments
exp_key = sys.argv[1]
min_q1 = float(sys.argv[2])
max_q1 = float(sys.argv[3])
outfile = options.outfile
strike3_ssrcalcwindow = options.ssr3strike
myorder = options.myorder
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()