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))