def setUp(self): """Define some standard Organizers for testing""" self.Empty = Organizer([]) self.a = Filter('a',{None:[find_any('a')]}) self.b = Filter('b',{None:[find_any('b')]}) self.Ab_org = Organizer([self.a,self.b]) lsu = Filter('LSU',{None:[exclude_if_more('N',5)],\ 'Gene':[find_any(['LSU'])]}) ssu = Filter('SSU',{None:[exclude_if_more('N',5)],\ 'Gene':[find_any(['SSU'])]}) self.Gene_org = Organizer([lsu,ssu]) self.Ab_seq = ['aa','bb','abab','cc',''] self.seq1 = Sequence('ACGU',{'Gene':'LSU'}) self.seq2 = Sequence('ACGUACGU',{'Gene':'SSU'}) self.seq3 = Sequence('ACGUNNNNNN',{'Gene':'LSU'}) self.seq4 = Sequence('ACGUNNNNNN',{'Gene':'SSU'}) self.seq5 = Sequence('ACGU',{}) self.seq6 = Sequence('',{}) self.seq7 = Sequence('ACGU',{'Gene':'unit'}) self.Gene_seq = [self.seq1,self.seq2,self.seq3,self.seq4,\ self.seq5,self.seq6,self.seq7] f = Filter('valid',{None:[find_all('AGCU'),find_no('N')],\ 'Gene':[find_any(['LSU'])]}) self.Mult_func_org = Organizer([f])
def setUp(self): """Define some standard Organizers for testing""" self.Empty = Organizer([]) self.a = Filter('a', {None: [find_any('a')]}) self.b = Filter('b', {None: [find_any('b')]}) self.Ab_org = Organizer([self.a, self.b]) lsu = Filter('LSU',{None:[exclude_if_more('N',5)],\ 'Gene':[find_any(['LSU'])]}) ssu = Filter('SSU',{None:[exclude_if_more('N',5)],\ 'Gene':[find_any(['SSU'])]}) self.Gene_org = Organizer([lsu, ssu]) self.Ab_seq = ['aa', 'bb', 'abab', 'cc', ''] self.seq1 = Sequence('ACGU', {'Gene': 'LSU'}) self.seq2 = Sequence('ACGUACGU', {'Gene': 'SSU'}) self.seq3 = Sequence('ACGUNNNNNN', {'Gene': 'LSU'}) self.seq4 = Sequence('ACGUNNNNNN', {'Gene': 'SSU'}) self.seq5 = Sequence('ACGU', {}) self.seq6 = Sequence('', {}) self.seq7 = Sequence('ACGU', {'Gene': 'unit'}) self.Gene_seq = [self.seq1,self.seq2,self.seq3,self.seq4,\ self.seq5,self.seq6,self.seq7] f = Filter('valid',{None:[find_all('AGCU'),find_no('N')],\ 'Gene':[find_any(['LSU'])]}) self.Mult_func_org = Organizer([f])
def test_find_any(self): """find_any should be True if one of the words is in the string""" f = find_any('ab') self.assertEqual(f(''),0) #empty self.assertRaises(AttributeError,f,None) # none self.assertEqual(f('cde'),0) #none of the elements self.assertEqual(f('axxx'),1) #one of the elements self.assertEqual(f('bxxx'),1) #one of the elements self.assertEqual(f('axxxb'),1) #all elements self.assertEqual(f('aaaa'),1) #repeated element # works on any sequence f = find_any(['foo','bar']) self.assertEqual(f("joe"),0) self.assertEqual(f("only foo"),1) self.assertEqual(f("bar and foo"),1)
def test_find_any(self): """find_any should be True if one of the words is in the string""" f = find_any('ab') self.assertEqual(f(''), 0) #empty self.assertRaises(AttributeError, f, None) # none self.assertEqual(f('cde'), 0) #none of the elements self.assertEqual(f('axxx'), 1) #one of the elements self.assertEqual(f('bxxx'), 1) #one of the elements self.assertEqual(f('axxxb'), 1) #all elements self.assertEqual(f('aaaa'), 1) #repeated element # works on any sequence f = find_any(['foo', 'bar']) self.assertEqual(f("joe"), 0) self.assertEqual(f("only foo"), 1) self.assertEqual(f("bar and foo"), 1)
def test_find_any(self): """find_any should be True if one of the words is in the string""" f = find_any("ab") self.assertEqual(f(""), 0) # empty self.assertRaises(AttributeError, f, None) # none self.assertEqual(f("cde"), 0) # none of the elements self.assertEqual(f("axxx"), 1) # one of the elements self.assertEqual(f("bxxx"), 1) # one of the elements self.assertEqual(f("axxxb"), 1) # all elements self.assertEqual(f("aaaa"), 1) # repeated element # works on any sequence f = find_any(["foo", "bar"]) self.assertEqual(f("joe"), 0) self.assertEqual(f("only foo"), 1) self.assertEqual(f("bar and foo"), 1)
def test_call_full(self): """Filter should return True if the object satisfies all criteria""" seq1 = Sequence('ACGU',{'Gene':'LSU'}) seq2 = Sequence('ACGUACGU',{'Gene':'SSU'}) seq3 = Sequence('ACGUN',{'Gene':'LSU'}) seq4 = Sequence('ACG',{'Gene':'LSU'}) seq5 = Sequence('ACGU',{}) seq6 = Sequence('',{}) f = Filter('valid',{None:[find_all('AGCU'),find_no('N')],\ 'Gene':[find_any(['LSU'])]}) self.assertEqual(f(seq1),True) self.assertEqual(f(seq2),False) self.assertEqual(f(seq3),False) self.assertEqual(f(seq4),False) self.assertEqual(f(seq5),False) self.assertEqual(f(seq6),False)
def test_call_full(self): """Filter should return True if the object satisfies all criteria""" seq1 = Sequence('ACGU', {'Gene': 'LSU'}) seq2 = Sequence('ACGUACGU', {'Gene': 'SSU'}) seq3 = Sequence('ACGUN', {'Gene': 'LSU'}) seq4 = Sequence('ACG', {'Gene': 'LSU'}) seq5 = Sequence('ACGU', {}) seq6 = Sequence('', {}) f = Filter('valid',{None:[find_all('AGCU'),find_no('N')],\ 'Gene':[find_any(['LSU'])]}) self.assertEqual(f(seq1), True) self.assertEqual(f(seq2), False) self.assertEqual(f(seq3), False) self.assertEqual(f(seq4), False) self.assertEqual(f(seq5), False) self.assertEqual(f(seq6), False)