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'))
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'))
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'))
def test_chinese_text(self):
st = SuffixTree(codecs.open("test.txt", encoding="utf-8").read())
self.assertTrue(st.find_substring(u'概括性总结'))
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(''))
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(''))
def test_case_sensitivity(self):
f = open("test.txt")
st = SuffixTree(f.read(), case_insensitive=True)
self.assertEqual(st.find_substring('ukkonen'), 1498)
self.assertEqual(st.find_substring('Optimal'), 1830)
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'))
def test_case_sensitivity(self):
f = open("test.txt")
st = SuffixTree(f.read(), case_insensitive=True)
self.assertEqual(st.find_substring('ukkonen'), 1498)
self.assertEqual(st.find_substring('Optimal'), 1830)
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'))
inputFasta.append(temp)
# print "Input Fasta read"
# print "inputFasta coming up"
# for i in inputFasta:
# print i
outputResultsFile = filename + ".exact"
# if(len(inputFasta)!=len(inputFastaId)):
# print "some problem because total number of reads don't match total number of ids"
# exit()
with open(outputResultsFile, 'w') as f:
for i in range(0, len(inputFasta)):
# outputResults[inputFastaId[i]] = find_substring(stree,inputFasta[i])
# c = inputFastaId[i] + d + str(find_substring(stree,inputFasta[i]))+ "\n"
if (stree.find_substring(inputFasta[i]) >= 0
or stree.find_substring(revc(inputFasta[i])) >= 0):
find = 1
countAlignments += 1
else:
find = 0
c = inputFastaId[i] + d + str(find) + "\n"
f.write(c)
# print "total Alignments - ",countAlignments
if (len(inputFastaId) == 0):
percent = 0
else:
percent = 1.0 * countAlignments / len(inputFastaId)
percent = percent * 100.0
# print "percentage of Alignment - ", percent
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'))
def test_case_sensitivity(self):
f = open("test.txt")
st = SuffixTree(f.read(), case_insensitive=True)
self.assertEqual(st.find_substring('ukkonen'), 1498)
self.assertEqual(st.find_substring('Optimal'), 1830)
def test_repr(self):
st = SuffixTree("t")
output = '\tStart \tEnd \tSuf \tFirst \tLast \tString\n\t0 \t1 \t-1 \t0 \t0 \tt\n'
import pdb;pdb.set_trace()
self.assertEqual(st.__repr__(), output)
"""
if __name__ == '__main__':
# unittest.main()
# f = open("test.txt")
# longstr = f.read()
longstr = "banana"
st = SuffixTree(longstr)
# print(longstr[11074:11081])
st.find_substring('ban')
# print(st.find_substring('Ukkonen'))
# print(st.find_substring('Optimal'))
