def test_get_reduced_alphabet_sequence_predefined_alphabets(self):
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
# checks that a sequence with all 20 amino acids returns a reduced-alphabet sequence
# made up of i-residues which contains exactly i residues!
self.assertEqual(len(set(self.SP_60.get_reduced_alphabet_sequence(i)[0])),i)
random_seqs = testTools.generate_random_sequence(10)
for j in random_seqs:
# build obj
SP = SequenceParameters(j)
# check reduced alphabet sequence length matches
self.assertEqual(len(SP.get_reduced_alphabet_sequence(i)[0]), len(j))
def test_get_reduced_alphabet_sequence_predefined_alphabets(self):
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
# checks that a sequence with all 20 amino acids returns a reduced-alphabet sequence
# made up of i-residues which contains exactly i residues!
self.assertEqual(len(set(self.SP_60.get_reduced_alphabet_sequence(i)[0])),i)
random_seqs = testTools.generate_random_sequence(10)
for j in random_seqs:
# build obj
SP = SequenceParameters(j)
# check reduced alphabet sequence length matches
self.assertEqual(len(SP.get_reduced_alphabet_sequence(i)[0]), len(j))
class TestComplexityFunctions(unittest.TestCase):
def setUp(self):
self.SP_60 = SequenceParameters('QWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNM')
self.SP_10 = SequenceParameters('KDNIKHVPGG')
def test_get_reduced_alphabet_sequence_predefined_alphabets(self):
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
# checks that a sequence with all 20 amino acids returns a reduced-alphabet sequence
# made up of i-residues which contains exactly i residues!
self.assertEqual(len(set(self.SP_60.get_reduced_alphabet_sequence(i)[0])),i)
random_seqs = testTools.generate_random_sequence(10)
for j in random_seqs:
# build obj
SP = SequenceParameters(j)
# check reduced alphabet sequence length matches
self.assertEqual(len(SP.get_reduced_alphabet_sequence(i)[0]), len(j))
def test_get_linear_WF_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',wordSize=i)
def test_get_linear_LC_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',wordSize=i)
def test_get_linear_LZW_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',wordSize=i)
def test_complexity_values(self):
out = {}
# WF alphatbetsize 4
out['WF'] = np.array([ 0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405, 0.86096405, 0.86096405, 0.68048202, 0.68048202,
0.86096405, 0.92321967, 0.92321967, 0.96096405, 0.9854753 ,
0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405, 0.86096405, 0.86096405, 0.68048202, 0.68048202,
0.86096405, 0.92321967, 0.92321967, 0.96096405, 0.9854753 ,
0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405])
# LZW alphabate size=4
out['LZW'] = np.array([ 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8,
0.8, 0.8, 0.8, 0.8, 0.9, 0.9, 0.9, 1. , 1. , 0.9, 0.9,
0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8, 0.8, 0.8,
0.8, 0.8, 0.9, 0.9, 0.9, 1. , 1. , 0.9, 0.9, 0.9, 0.9,
0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8])
# LC alphabet size = 2
out['LC'] = np.array([ 0.625, 0.5 , 0.5 , 0.5 , 0.5 , 0.5 , 0.625, 0.75 ,
0.625, 0.75 , 0.625, 0.75 , 0.875, 0.75 , 0.625, 0.625,
0.625, 0.625, 0.75 , 0.75 , 0.625, 0.5 , 0.5 , 0.5 ,
0.5 , 0.5 , 0.625, 0.75 , 0.625, 0.75 , 0.625, 0.75 ,
0.875, 0.75 , 0.625, 0.625, 0.625, 0.625, 0.75 , 0.75 ,
0.625, 0.5 , 0.5 , 0.5 , 0.5 , 0.5 , 0.625, 0.75 ,
0.625, 0.75 , 0.625])
self.assertEquals((self.SP_60.get_linear_complexity('WF', alphabetSize=4)[1] - out['WF'] < 0.00001).all(), True)
self.assertEquals((self.SP_60.get_linear_complexity('LZW', alphabetSize=4)[1] - out['LZW'] < 0.00001).all(), True)
self.assertEquals((self.SP_60.get_linear_complexity('LC', alphabetSize=2)[1] - out['LC'] < 0.00001).all(), True)
class TestComplexityFunctions(unittest.TestCase):
def setUp(self):
self.SP_60 = SequenceParameters('QWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNMQWERTYIPASDFGHKLCVNM')
self.SP_10 = SequenceParameters('KDNIKHVPGG')
def test_get_reduced_alphabet_sequence_predefined_alphabets(self):
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
# checks that a sequence with all 20 amino acids returns a reduced-alphabet sequence
# made up of i-residues which contains exactly i residues!
self.assertEqual(len(set(self.SP_60.get_reduced_alphabet_sequence(i)[0])),i)
random_seqs = testTools.generate_random_sequence(10)
for j in random_seqs:
# build obj
SP = SequenceParameters(j)
# check reduced alphabet sequence length matches
self.assertEqual(len(SP.get_reduced_alphabet_sequence(i)[0]), len(j))
def test_get_linear_WF_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('WF',wordSize=i)
def test_get_linear_LC_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LC',wordSize=i)
def test_get_linear_LZW_complexity(self):
# general test
random_seqs = testTools.generate_random_sequence_list(10, minLen=15, maxLen=500)
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',alphabetSize=5)
# test all alphabets
for i in [2,3,4,5,6,8,10,11, 12,15,18,20]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',alphabetSize=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',blobLen=i)
# test a range of window sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',blobLen=i)
# test a range of step-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',stepSize=i)
# test a range of word-sizes
for i in [1,2,3,4,5,10]:
for j in random_seqs:
SequenceParameters(j).get_linear_complexity('LZW',wordSize=i)
def test_complexity_values(self):
out = {}
# WF alphatbetsize 4
out['WF'] = np.array([ 0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405, 0.86096405, 0.86096405, 0.68048202, 0.68048202,
0.86096405, 0.92321967, 0.92321967, 0.96096405, 0.9854753 ,
0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405, 0.86096405, 0.86096405, 0.68048202, 0.68048202,
0.86096405, 0.92321967, 0.92321967, 0.96096405, 0.9854753 ,
0.92321967, 0.92321967, 0.92321967, 0.88048202, 0.88048202,
0.92321967, 0.92321967, 0.92321967, 0.94773092, 0.92321967,
0.86096405])
# LZW alphabate size=4
out['LZW'] = np.array([ 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8,
0.8, 0.8, 0.8, 0.8, 0.9, 0.9, 0.9, 1. , 1. , 0.9, 0.9,
0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8, 0.8, 0.8,
0.8, 0.8, 0.9, 0.9, 0.9, 1. , 1. , 0.9, 0.9, 0.9, 0.9,
0.9, 0.9, 0.9, 0.9, 0.8, 0.8, 0.8])
# LC alphabet size = 2
out['LC'] = np.array([ 0.625, 0.5 , 0.5 , 0.5 , 0.5 , 0.5 , 0.625, 0.75 ,
0.625, 0.75 , 0.625, 0.75 , 0.875, 0.75 , 0.625, 0.625,
0.625, 0.625, 0.75 , 0.75 , 0.625, 0.5 , 0.5 , 0.5 ,
0.5 , 0.5 , 0.625, 0.75 , 0.625, 0.75 , 0.625, 0.75 ,
0.875, 0.75 , 0.625, 0.625, 0.625, 0.625, 0.75 , 0.75 ,
0.625, 0.5 , 0.5 , 0.5 , 0.5 , 0.5 , 0.625, 0.75 ,
0.625, 0.75 , 0.625])
self.assertEqual((self.SP_60.get_linear_complexity('WF', alphabetSize=4)[1] - out['WF'] < 0.00001).all(), True)
self.assertEqual((self.SP_60.get_linear_complexity('LZW', alphabetSize=4)[1] - out['LZW'] < 0.00001).all(), True)
self.assertEqual((self.SP_60.get_linear_complexity('LC', alphabetSize=2)[1] - out['LC'] < 0.00001).all(), True)
