def test_rangetree(self):
c_rangetree.create_tree( self.mytuple1 )
#we get our peptide out again with a large window
res = c_rangetree.query_tree( self.q1 - 1, self.ssrcalc -1,
self.q1 + 1, self.ssrcalc + 1, 1, 0)
self.assertEqual( len(res), 1)
self.assertEqual( res[0][0], 101)
#same result when lower boundary equals the value
res = c_rangetree.query_tree( self.q1 , self.ssrcalc ,
self.q1 + 1, self.ssrcalc + 1, 1, 0)
self.assertEqual( len(res), 1)
self.assertEqual( res[0][0], 101)
#no result when upper boundary equals the value
res = c_rangetree.query_tree( self.q1 - 1, self.ssrcalc -1,
self.q1, self.ssrcalc, 1, 0)
self.assertEqual( len(res), 0)
'peptide_key': r[1],
'parent_id': r[2],
'q1_charge': r[3],
'q1': r[4],
'ssrcalc': r[5],
} for r in alltuples if r[3] == 2 #charge is 2
and r[6] == 0 #isotope is 0
and r[4] >= min_q1 and r[4] < max_q1
]
# we use a rangetree to select the precursors
if not use_db:
parentid_lookup = [[r[2], (r[4], r[0], r[1])] for r in alltuples]
parentid_lookup = dict(parentid_lookup)
print "building tree with %s Nodes" % len(alltuples)
c_rangetree.create_tree(tuple(alltuples))
# in SWATH mode, select all precursors that are relevant for the background at
# once
if swath_mode:
values = "q1, modified_sequence, peptide_key, q1_charge, ssrcalc"
q1_low = min_q1
q1_high = max_q1
query2 = """
select %(values)s
from %(pep)s
where q1 >= %(q1_low)s and q1 <= %(q1_high)s
%(query_add)s
""" % {
'q1_high': q1_high,
'q1_low': q1_low,
'ssrcalc' : r[5],
}
for r in alltuples
if r[3] == 2 #charge is 2
and r[6] == 0 #isotope is 0
and r[4] >= min_q1
and r[4] < max_q1
]
# we use a rangetree to select the precursors
if not use_db:
parentid_lookup = [ [ r[2], (r[4], r[0], r[1]) ]
for r in alltuples ]
parentid_lookup = dict(parentid_lookup)
print "building tree with %s Nodes" % len(alltuples)
c_rangetree.create_tree(tuple(alltuples))
# in SWATH mode, select all precursors that are relevant for the background at
# once
if swath_mode:
values="q1, modified_sequence, peptide_key, q1_charge, ssrcalc"
q1_low = min_q1; q1_high = max_q1
query2 = """
select %(values)s
from %(pep)s
where q1 >= %(q1_low)s and q1 <= %(q1_high)s
%(query_add)s
""" % { 'q1_high' : q1_high, 'q1_low' : q1_low,
'query_add' : par.query2_add,