def compute(self, maker, model, release):
mset = self.kb.get_snp_markers_set(maker, model, release)
if not mset:
raise ValueError("SNPMarkersSet[%s,%s,%s] has not been defined." % (maker, model, release))
# projector = (np.arange(0, 100), np.array([101, 109]), np.arange(110,N))
# selector = kb.build_selector(
# s = self.kb.get_gdo_iterator(mset, selector, projector)
s = self.kb.get_gdo_iterator(mset)
# --
start = time.clock()
counts = algo.count_homozygotes(s)
print "counts on %d:" % counts[0], time.clock() - start
start = time.clock()
mafs = algo.maf(None, counts)
print "mafs on %d:" % counts[0], time.clock() - start
start = time.clock()
hwe = algo.hwe(None, counts)
print "hwe on %d:" % counts[0], time.clock() - start
def compute(self, maker, model, release):
mset = self.kb.get_snp_markers_set(maker, model, release)
if not mset:
raise ValueError('SNPMarkersSet[%s,%s,%s] has not been defined.' %
(maker, model, release))
# projector = (np.arange(0, 100), np.array([101, 109]), np.arange(110,N))
# selector = kb.build_selector(
# s = self.kb.get_gdo_iterator(mset, selector, projector)
s = self.kb.get_gdo_iterator(mset)
#--
start = time.clock()
counts = algo.count_homozygotes(s)
print 'counts on %d:' % counts[0], time.clock() - start
start = time.clock()
mafs = algo.maf(None, counts)
print 'mafs on %d:' % counts[0], time.clock() - start
start = time.clock()
hwe = algo.hwe(None, counts)
print 'hwe on %d:' % counts[0], time.clock() - start
def do_check(s): counts = algo.count_homozygotes(s) mafs = algo.maf(None, counts) hwe = algo.hwe(None, counts) return mafs, hwe
def do_check(s):
counts = algo.count_homozygotes(s)
mafs = algo.maf(None, counts)
hwe = algo.hwe(None, counts)
return mafs, hwe