def test_acceptance_02(self):
nus = Nussinov('GGAAACCGAAAC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret,([(0,6), (1,5), (7,11)],
[(0,11), (1,5), (6,7)])
)
def test_acceptance_01(self):
nus = Nussinov('GGGAAAUCC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(1, 8), (2, 7),
(3, 6)], [(1, 8), (2, 7),
(4, 6)], [(1, 8), (2, 7), (5, 6)]))
def solve(self, sequence, min_padding=0, tie_break_permute=None, prettify=False):
"""
sequence: string of RNA bases represented as A,U,G,C
min_padding: minimum distance between two paired bases
tie_break_permute: None or order in which to break ties
prettify: True if pretty dot paranthesis is to be returned, otherwise False
return: the number of pairings and the dot parantheses notation
"""
if self.mode == 'greedy':
gr = GreedySolver(sequence)
score = gr.solve()
dot_p = gr.dot_parentheses(prettify)
return score, dot_p
elif self.mode == 'nussinov':
nv = Nussinov(sequence)
score = nv.solve(min_padding, tie_break_permute)
dot_p = nv.dot_parentheses(prettify)
return score, dot_p
elif self.mode == 'zuker':
zk = ZukerFreier(sequence)
score = zk.solve()
dot_p = zk.dot_parentheses()
return score, dot_p
raise ValueError('mode is not set')
def test_fill_matrix():
nussinov = Nussinov()
sequence = "GGUCCAC"
d = [[Cell(i, j) for j in range(len(sequence) + 1)] for i in range(len(sequence) + 1)]
nussinov.fill_matrix(d, sequence)
def test_acceptance_01(self):
nus = Nussinov('GGGAAAUCC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(1,8), (2,7), (3,6)],
[(1,8), (2,7), (4,6)],
[(1,8), (2,7), (5,6)])
)
def RunAlgorithm(self):
i = 0
text = self.RnaCodeTextEdit.toPlainText()
TextList = text.split(QRegExp("\\s+"))
if TextList.count() -1 == 0 :
msgBox = QMessageBox()
msgBox.setText("Can't run algorithm without data!")
msgBox.exec_()
return
self.ResultTabView.setRowCount(TextList.count())
for line in TextList:
nuss = Nussinov(line)
ret = nuss.compute()
item1 = QTableWidgetItem(line)
item2 = QTableWidgetItem(QString(("%s\n" % (ret)) ))
self.ResultTabView.setItem(i,0,item1)
self.ResultTabView.setItem(i,1,item2)
i = i + 1
#self.ResultTabView. .write("%s %s\n" % (len(ret), ret))
self.ResultTabView.resizeColumnsToContents()
def RunAlgorithm(self):
i = 0
text = self.RnaCodeTextEdit.toPlainText()
TextList = text.split(QRegExp("\\s+"))
if TextList.count() - 1 == 0:
msgBox = QMessageBox()
msgBox.setText("Can't run algorithm without data!")
msgBox.exec_()
return
self.ResultTabView.setRowCount(TextList.count())
for line in TextList:
nuss = Nussinov(line)
ret = nuss.compute()
item1 = QTableWidgetItem(line)
item2 = QTableWidgetItem(QString(("%s\n" % (ret))))
self.ResultTabView.setItem(i, 0, item1)
self.ResultTabView.setItem(i, 1, item2)
i = i + 1
#self.ResultTabView. .write("%s %s\n" % (len(ret), ret))
self.ResultTabView.resizeColumnsToContents()
def test_nussinov_guideline():
nussinov = Nussinov()
structures, amount_pairs = nussinov.run("data/nussinov_guideline.fasta", True)
structures_seq1 = structures[0]
amount_pair_seq1 = amount_pairs[0]
assert amount_pair_seq1 == 11
assert '(((((()())(.((()..))..)...))))' in structures_seq1
structures_seq2 = structures[1]
amount_pair_seq2 = amount_pairs[1]
assert amount_pair_seq2 == 24
assert '((((.((((((((((...)))))..)(((()))))()()))((((...)))))...))))' in structures_seq2
structures_seq3 = structures[2]
amount_pair_seq3 = amount_pairs[2]
assert amount_pair_seq3 == 26
assert '(..(((((.())())((.((((()))(((()())))(().))))(.((())))).).))).' in structures_seq3
structures_seq4 = structures[3]
amount_pair_seq4 = amount_pairs[3]
assert amount_pair_seq4 == 27
assert '(((((()(()(((.....(.(((((.()((.)))((()()))).)((().)).)..))))))).))))' in structures_seq4
structures_seq5 = structures[4]
amount_pair_seq5 = amount_pairs[4]
assert amount_pair_seq5 == 35
assert '(()((.))(()(((.)((((.(().).)()))())((()(().).)(((..))(()))))((((((())))))())))).' in structures_seq5
structures_seq6 = structures[5]
amount_pair_seq6 = amount_pairs[5]
assert amount_pair_seq6 == 63
assert '(((()((((((.((()((((((()(((((())(().((())..))).)()((((...).))(()())(())())((.)))()()())))))(.)))))))(()((()(((((.)))))).))(((..))())).)))()..)..))' in structures_seq6
#!/usr/bin/python
from file_reader import *
from nussinov import Nussinov
if __name__ == "__main__":
input_path = 'test_data'
output_path = 'out'
out = open(output_path, 'w')
reader = FileReader(input_path)
for line in reader:
nuss = Nussinov(line)
ret = nuss.compute()
out.write("%s %s\n" % (len(ret), ret))
out.close()
#!/usr/bin/python
from file_reader import *
from nussinov import Nussinov
if __name__ == "__main__":
input_path = 'test_data'
output_path = 'out'
out = open(output_path, 'w')
reader = FileReader(input_path)
for line in reader:
nuss = Nussinov(line)
ret = nuss.compute()
out.write("%s %s\n" % (len(ret), ret))
out.close()
def setUp(self):
self.basic_data = 'ACGU'
self.basic = Nussinov(self.basic_data)
def test_acceptance_03(self):
nus = Nussinov('GCGCGCGCGCGCGCGCGCGCGCGC')
ret = nus.compute()
self.assertEqual(len(ret), 12)
class NussinovTest(unittest.TestCase):
def setUp(self):
self.basic_data = 'ACGU'
self.basic = Nussinov(self.basic_data)
def test_compute_return(self):
ret = self.basic.compute()
self.assertIsInstance(ret, list)
def test_init_matrix(self):
self.basic._init_matrix()
self.assertEqual(len(self.basic.matrix), len(self.basic_data))
for i in xrange(len(self.basic_data)):
for j in xrange(len(self.basic_data)):
if i-1 <= j:
self.assertEqual(self.basic.matrix[i][j], 0)
else:
self.assertEqual(self.basic.matrix[i][j], -1)
def test_fill_diagonal(self):
self.basic._fill_diagonal(1)
self.assertEqual(self.basic.matrix[1][2], 1)
self.basic._fill_diagonal(2)
self.basic._fill_diagonal(3)
self.assertEqual(self.basic.matrix[0][3], 2)
def test_build_matrix(self):
self.basic._build_matrix()
self.assertEqual(self.basic.matrix[0][3], 2)
self.assertEqual(self.basic.matrix[1][2], 1)
def test_generate_trace(self):
self.basic._build_matrix()
self.basic._generate_trace()
def test_acceptance_01(self):
nus = Nussinov('GGGAAAUCC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(1,8), (2,7), (3,6)],
[(1,8), (2,7), (4,6)],
[(1,8), (2,7), (5,6)])
)
def test_acceptance_02(self):
nus = Nussinov('GGAAACCGAAAC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret,([(0,6), (1,5), (7,11)],
[(0,11), (1,5), (6,7)])
)
def test_acceptance_03(self):
nus = Nussinov('GCGCGCGCGCGCGCGCGCGCGCGC')
ret = nus.compute()
self.assertEqual(len(ret), 12)
import os
from nussinov import Nussinov
from utils import FastaReader, pairs2parentheses, print_matrix
if __name__ == "__main__":
nus = Nussinov()
#seq = "ACCAGCU"
seq = "GCGCUCUGAUGAGGCCGCAAGGCCGAAACUGCCGCAAGGCAGUCAGCGC"
nus.seq = seq
nus.fill_matrix()
print_matrix(nus.V_matrix, seq=seq)
pairs = nus.get_pairs()
print(pairs)
print(seq)
parentheses = pairs2parentheses(pairs, len(seq))
print(parentheses)
print(parentheses.count("("))
def setUp(self):
self.basic_data = 'ACGU'
self.basic = Nussinov(self.basic_data)
class NussinovTest(unittest.TestCase):
def setUp(self):
self.basic_data = 'ACGU'
self.basic = Nussinov(self.basic_data)
def test_compute_return(self):
ret = self.basic.compute()
self.assertIsInstance(ret, list)
def test_init_matrix(self):
self.basic._init_matrix()
self.assertEqual(len(self.basic.matrix), len(self.basic_data))
for i in xrange(len(self.basic_data)):
for j in xrange(len(self.basic_data)):
if i - 1 <= j:
self.assertEqual(self.basic.matrix[i][j], 0)
else:
self.assertEqual(self.basic.matrix[i][j], -1)
def test_fill_diagonal(self):
self.basic._fill_diagonal(1)
self.assertEqual(self.basic.matrix[1][2], 1)
self.basic._fill_diagonal(2)
self.basic._fill_diagonal(3)
self.assertEqual(self.basic.matrix[0][3], 2)
def test_build_matrix(self):
self.basic._build_matrix()
self.assertEqual(self.basic.matrix[0][3], 2)
self.assertEqual(self.basic.matrix[1][2], 1)
def test_generate_trace(self):
self.basic._build_matrix()
self.basic._generate_trace()
def test_acceptance_01(self):
nus = Nussinov('GGGAAAUCC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(1, 8), (2, 7),
(3, 6)], [(1, 8), (2, 7),
(4, 6)], [(1, 8), (2, 7), (5, 6)]))
def test_acceptance_02(self):
nus = Nussinov('GGAAACCGAAAC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(0, 6), (1, 5), (7, 11)], [(0, 11), (1, 5),
(6, 7)]))
def test_acceptance_03(self):
nus = Nussinov('GCGCGCGCGCGCGCGCGCGCGCGC')
ret = nus.compute()
self.assertEqual(len(ret), 12)
def test_acceptance_03(self):
nus = Nussinov('GCGCGCGCGCGCGCGCGCGCGCGC')
ret = nus.compute()
self.assertEqual(len(ret), 12)
def test_acceptance_02(self):
nus = Nussinov('GGAAACCGAAAC')
ret = nus.compute()
self.assertEqual(len(ret), 3)
self.assertIn(ret, ([(0, 6), (1, 5), (7, 11)], [(0, 11), (1, 5),
(6, 7)]))
