def test_get_pair_pos_rev(self):
fold = '((.(.)))'
seq = 'TTGCNGAA'
folder = fn.Fold(fold, seq)
pos = 6
(pos, fold) = folder._reverse(pos)
pair_pos = folder._get_pair(pos)
self.assertEquals(len(fold) - 1 - pair_pos, 1)
def check_hairpin(hairpin_fold, seq):
"""here are the necessary condition for a hairpin:
is_simple
20 <= len <= 80
get_Aprimes() > 1
"""
hairp_fold = fn.Fold(hairpin_fold, seq)
simple = hairp_fold.is_simple()
leng = 19 < hairp_fold.len < 81
aPrimes = hairp_fold.get_Aprimes()
return simple, leng, aPrimes
def test_get_pair1(self):
fold = '.(((...))).'
folder = fn.Fold(fold)
pair = folder._get_pair(1)
self.assertEquals(9, pair)
def test_k10(self):
fold = '.(((((((((((((((((........))))))).))).))))))).'
seq = 'ACTTGATTGTATTTTTAAATTAATTCTTAAAAACTACAAATTAAGA'
folder = fn.Fold(fold, seq)
aPrimes = folder.get_Aprimes()
self.assertEquals(2, len(aPrimes))
def test_osk(self):
fold = '.((((((((((((...((.(((((((((((((((..((....))))))))........)))))..)))))).)))))))))))).'
seq = 'TGCTTTACTTGGAAAATTCGCTTGCACAAAATCAACGCCGCGGCTGATTTATTATTGATGTGCTCAAGCAAATTCAAGTGAAGCA'
folder = fn.Fold(fold, seq)
aPrimes = folder.get_Aprimes()
self.assertEquals(5, len(aPrimes))
def test_hairy(self):
fold = '.(((((((((((.((((.((((....)).)).)))).))...))))))))).'
seq = 'AGACATTTCACATCATTCGCCGGGATTGCGCAAATGTTGCTTTGAAGTGTTG'
folder = fn.Fold(fold, seq)
aPrimes = folder.get_Aprimes()
self.assertEquals(2, len(aPrimes))
def test_fushi2(self):
fold = '.(((((((((((((..(((((((.........))))))).......)))))..)))).)))).'
seq = 'GCGCACTTCTCTCGACCATTTGTAGGTGACACGCAAATGACACAGCCGAGAACGAAGCTGCGA'
folder = fn.Fold(fold, seq)
aPrimes = folder.get_Aprimes()
self.assertEquals(3, len(aPrimes))
def test_count2_Aprimes(self):
fold = '.(((.(((...))).))).'
seq = 'NAAANGGGNNNCCCNTTTN'
folder = fn.Fold(fold, seq)
self.assertEquals(2, len(folder.get_Aprimes()))
def test_get_pair_rev2(self):
fold = '(.((.(...)).))'
folder = fn.Fold(fold)
pair = folder._get_pair(13)
self.assertEquals(0, pair)
def test_orb(self):
fold = '.((((((((((((((((((.....)))))))))))).)))))).'
seq = 'GGAATTTCAATTTTTAAGAAAACATTTTAAAAATTGTAAATTCG'
folder = fn.Fold(fold, seq)
aPrimes = folder.get_Aprimes()
self.assertEquals(4, len(aPrimes))
def test_grk(self):
fold = '.((((.((((.((((((((((.......))).)))))))...))))))))'
seq = 'TTTCGTGCTCTCAACAATTGTCGCCGTCACAGATTGTTGTTCGAGCCGAA'
folder = fn.Fold(fold, seq)
aPrimes = folder.get_Aprimes()
self.assertEquals(2, len(aPrimes))
def test_wg(self):
fold = '.((((((((((((...(((((......)))))..)))))).)))))).'
seq = 'ACTGCTTGCATACTGCTTTGGGCAGGACCAAAACGTATGCGAAGTGGA'
folder = fn.Fold(fold, seq)
aPrimes = folder.get_Aprimes()
self.assertEquals(2, len(aPrimes))
def test_get_pair_pos(self):
fold = '((.(.)))'
seq = 'TTGCNGAA'
folder = fn.Fold(fold, seq)
pair_pos = folder._get_pair(0)
self.assertEquals(pair_pos, 7)
def test_count1_Aprime_porcodio(self):
fold = '((.(.)))'
seq = 'TTGCNGAA'
folder = fn.Fold(fold, seq)
aPrimes = folder.get_Aprimes()
self.assertEquals(0, len(aPrimes))
def test_count1_Aprime_long(self):
fold = '.((((((...)))))).'
seq = 'NAAAGGGNNNCCCTTTN'
folder = fn.Fold(fold, seq)
self.assertEquals(1, len(folder.get_Aprimes()))
def test_get_pair2(self):
fold = '.(..(.(..).)).'
folder = fn.Fold(fold)
pair = folder._get_pair(4)
self.assertEquals(11, pair)
def test_get_pair_rev1(self):
fold = '.((.(...).)).'
folder = fn.Fold(fold)
pair = folder._get_pair(10)
self.assertEquals(2, pair)
def test_bcd(self):
fold = '.((((((((.(((((((.((((((.........)))))))))..))))..)))))))).'
seq = 'AAAATGTTTCTCTTGGGCGTAATCTCATACAATGATTACCCTTAAAGATCGAACATTTA'
folder = fn.Fold(fold, seq)
aPrimes = folder.get_Aprimes()
self.assertEquals(4, len(aPrimes))
def test_corner_case(self):
fold = '(((((.(((...))).)))))......'
seq = 'GTTTTATCATTATGGGAAAATATAAGC'
folder = fn.Fold(fold, seq)
aPrimes = folder.get_Aprimes()
self.assertEquals(2, len(aPrimes))
def test_fushi1(self):
fold = '.(((((((((((...(((((((((....))))))))).)))..)))))))).'
seq = 'GGCGCACTCCCTACGGTGCCCAGGACATTTTGGGCACAAGGACGAGTGCGCA'
folder = fn.Fold(fold, seq)
aPrimes = folder.get_Aprimes()
self.assertEquals(4, len(aPrimes))