def test_iteritems(self):
s = set()
l1 = list()
t = SuffixTree()
for x in xrange(100):
k = base64.b64encode(os.urandom(x%10 + 1)).rstrip('=')
if k in s: continue
l1.append((k, x))
t[k] = x
s.add(k)
l1.sort()
self.assertEquals(l1, list(t.iteritems()))
def test_match(self):
t = SuffixTree()
t['what'] = 1
t['where'] = 1
t['when'] = 1
t['widget'] = 1
t['wizard'] = 1
t['wow'] = 1
t['wowo'] = 1
self.assertEquals(dict(t.find('e')), {'where':1,'when':1,'widget':1})
self.assertEquals(dict(t.find('h')), {'where':1,'when':1,'what':1})
self.assertEquals(dict(t.find('a')), {'wizard':1,'what':1})
self.assertEquals(dict(t.find('ow')), {'wow':1,'wowo':1})
def test_find_simple(self):
s = set()
l1 = list()
t = SuffixTree()
for x in xrange(100):
k = base64.b64encode(os.urandom(x%10 + 1)).rstrip('=')
if k in s: continue
l1.append(k)
t[k] = x
s.add(k)
l1.sort()
for x in l1:
assert bool(tuple(t.find(x)))
def test_get_next_iteration(self):
self.tree = SuffixTree("CAG")
self.assertTrue(self.tree._iterator is not None)
self.assertEqual( self.tree.get_next_iteration(), ('G', 3))
self.assertEqual( self.tree.get_next_iteration(), ('AG', 2))
self.assertEqual( self.tree.get_next_iteration(), ('CAG', 1))
# make sure iterator halts when we reach beginning of string
self.assertEqual( self.tree.get_next_iteration(), None)
self.assertEqual( self.tree.get_next_iteration(), None)
class SuffixTreeTest(unittest.TestCase):
def setUp(self):
self.nucleotides = u'CAGTCAGG'
self.tree = SuffixTree(self.nucleotides)
def test_has_root(self):
""" we initialize the tree with a root node """
self.assertTrue(self.tree.rootNode is not None)
self.assertTrue(isinstance(self.tree.rootNode, SuffixRootNode))
def test_get_next_iteration(self):
self.tree = SuffixTree("CAG")
self.assertTrue(self.tree._iterator is not None)
self.assertEqual( self.tree.get_next_iteration(), ('G', 3))
self.assertEqual( self.tree.get_next_iteration(), ('AG', 2))
self.assertEqual( self.tree.get_next_iteration(), ('CAG', 1))
# make sure iterator halts when we reach beginning of string
self.assertEqual( self.tree.get_next_iteration(), None)
self.assertEqual( self.tree.get_next_iteration(), None)
def test_construct_tree(self):
pass
def design(family, param):
result = []
for seq in family:
remain = set(family)
remain.remove(seq)
#build GST s1|s2...|sm
tree = SuffixTree(concat(list(remain)))
n = len(seq)
l_min = param[0]
l_max = param[1]
l_t = param[10]
begin = 0
end = n - (l_t + l_min)
forward = find(l_min, l_max, begin, end, seq, tree)
begin = (l_t + l_min)
end = n
reverse = find(l_min, l_max, begin, end, seq, tree)
result.append(bio.design_primer(seq, param, forward, reverse))
return result
def setUp(self):
self.nucleotides = u'CAGTCAGG'
self.tree = SuffixTree(self.nucleotides)
