Esempi in Python per SuffixTree.has_substring

Esempio n. 1

File: test_suffix_tree.py Progetto: jhsrcmh/AlgoRun

 def test_repeated_string(self):
     st = SuffixTree("aaa")
     self.assertEqual(st.find_substring('a'), 0)
     self.assertEqual(st.find_substring('aa'), 0)
     self.assertEqual(st.find_substring('aaa'), 0)
     self.assertEqual(st.find_substring('b'), -1)
     self.assertTrue(st.has_substring('a'))
     self.assertTrue(st.has_substring('aa'))
     self.assertTrue(st.has_substring('aaa'))

Esempio n. 2

File: shortest_nonshared_substring.py Progetto: yzharold/R-Study-Lists

def find_shortest_nonshared_substring(seq_1, seq_2):
    st = SuffixTree(seq_2)
    for k in range(2, len(seq_1) + 1):
        shared = True
        for kmer in generate_kmers(seq_1, k):
            if not st.has_substring(kmer):
                shared = False
                break
        if not shared:
            return kmer

Esempio n. 3

File: test_suffix_tree.py Progetto: yanghongkai/Python-Suffix-Tree

    def test_repeated_string(self):
        st = SuffixTree("aaa")
        self.assertEqual(st.find_substring('a'), 0)
        self.assertEqual(st.find_substring('aa'), 0)
        self.assertEqual(st.find_substring('aaa'), 0)
        self.assertEqual(st.find_substring('b'), -1)
        self.assertTrue(st.has_substring('a'))
        self.assertTrue(st.has_substring('aa'))
        self.assertTrue(st.has_substring('aaa'))

        self.assertFalse(st.has_substring('aaaa'))
        self.assertFalse(st.has_substring('b'))
        #case sensitive by default
        self.assertFalse(st.has_substring('A'))

Esempio n. 4

File: allPythonContent.py Progetto: Mondego/pyreco

 def test_repeated_string(self):
     st = SuffixTree("aaa")
     self.assertEqual(st.find_substring('a'), 0)
     self.assertEqual(st.find_substring('aa'), 0)
     self.assertEqual(st.find_substring('aaa'), 0)
     self.assertEqual(st.find_substring('b'), -1)
     self.assertTrue(st.has_substring('a'))
     self.assertTrue(st.has_substring('aa'))
     self.assertTrue(st.has_substring('aaa'))
     
     self.assertFalse(st.has_substring('aaaa'))
     self.assertFalse(st.has_substring('b'))
     #case sensitive by default
     self.assertFalse(st.has_substring('A'))

Esempio n. 5

File: test_suffix_tree.py Progetto: jhsrcmh/AlgoRun

    def test_chinese_string(self):
	st = SuffixTree(u"才高八斗")
	self.assertTrue(st.has_substring(u'高'))
	self.assertFalse(st.has_substring(u'豆豆'))

Esempio n. 6

File: test_suffix_tree.py Progetto: jhsrcmh/AlgoRun

    def test_text_string(self):
	f = codecs.open("test.txt", encoding='utf-8')
	st = SuffixTree(f.read())
	self.assertTrue(st.has_substring(u'a'))

Esempio n. 7

File: test_suffix_tree.py Progetto: jhsrcmh/AlgoRun

 def test_empty_string(self):
     st = SuffixTree('')
     self.assertEqual(st.find_substring('not there'), -1)
     self.assertEqual(st.find_substring(''), -1)
     self.assertFalse(st.has_substring('not there'))
     self.assertFalse(st.has_substring(''))

Esempio n. 8

File: test_suffix_tree.py Progetto: yanghongkai/Python-Suffix-Tree

 def test_empty_string(self):
     st = SuffixTree('')
     self.assertEqual(st.find_substring('not there'), -1)
     self.assertEqual(st.find_substring(''), -1)
     self.assertFalse(st.has_substring('not there'))
     self.assertFalse(st.has_substring(''))

Esempio n. 9

File: test_suffix_tree.py Progetto: yanghongkai/Python-Suffix-Tree

 def test_long_string(self):
     f = open("test.txt")
     st = SuffixTree(f.read())
     self.assertEqual(st.find_substring('Ukkonen'), 1498)
     self.assertEqual(st.find_substring('Optimal'), 11131)
     self.assertFalse(st.has_substring('ukkonen'))

Esempio n. 10

File: allPythonContent.py Progetto: Mondego/pyreco

 def test_long_string(self):
     f = open("test.txt")
     st = SuffixTree(f.read())
     self.assertEqual(st.find_substring('Ukkonen'), 1498)
     self.assertEqual(st.find_substring('Optimal'), 11131)
     self.assertFalse(st.has_substring('ukkonen'))