def test_exclude_if_more(self):
"""exclude_if_more should be True if #items in s <= x"""
self.assertRaises(ValueError, exclude_if_more,'lksfj','ksfd') #not int
self.assertRaises(IndexError,exclude_if_more,'ACGU',-3) #negative
f = exclude_if_more('a',0) #zero
self.assertEqual(f(''),1)
self.assertEqual(f('a'),0)
self.assertEqual(f('b'),1)
# works on strings
f = exclude_if_more('ACGU',5) #positive
self.assertEqual(f(''),1)
self.assertEqual(f('ACGUAGCUioooNNNNNA'),0)
self.assertEqual(f('NNNNNNN'),1)
# works on words
f = exclude_if_more(['foo'],1)
self.assertEqual(f(''),1)
self.assertEqual(f(['foo', 'bar','foo']),0)
self.assertEqual(f(['joe']),1)
# works on numbers
f = exclude_if_more([0,1],3)
self.assertEqual(f(''),1)
self.assertEqual(f([0,1,2,3,4,5]),1)
self.assertEqual(f([0,1,0,1]),0)
def test_exclude_if_more(self):
"""exclude_if_more should be True if #items in s <= x"""
self.assertRaises(ValueError, exclude_if_more, 'lksfj',
'ksfd') #not int
self.assertRaises(IndexError, exclude_if_more, 'ACGU', -3) #negative
f = exclude_if_more('a', 0) #zero
self.assertEqual(f(''), 1)
self.assertEqual(f('a'), 0)
self.assertEqual(f('b'), 1)
# works on strings
f = exclude_if_more('ACGU', 5) #positive
self.assertEqual(f(''), 1)
self.assertEqual(f('ACGUAGCUioooNNNNNA'), 0)
self.assertEqual(f('NNNNNNN'), 1)
# works on words
f = exclude_if_more(['foo'], 1)
self.assertEqual(f(''), 1)
self.assertEqual(f(['foo', 'bar', 'foo']), 0)
self.assertEqual(f(['joe']), 1)
# works on numbers
f = exclude_if_more([0, 1], 3)
self.assertEqual(f(''), 1)
self.assertEqual(f([0, 1, 2, 3, 4, 5]), 1)
self.assertEqual(f([0, 1, 0, 1]), 0)
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_exclude_if_more(self):
"""exclude_if_more should be True if #items in s <= x"""
self.assertRaises(ValueError, exclude_if_more, "lksfj", "ksfd") # not int
self.assertRaises(IndexError, exclude_if_more, "ACGU", -3) # negative
f = exclude_if_more("a", 0) # zero
self.assertEqual(f(""), 1)
self.assertEqual(f("a"), 0)
self.assertEqual(f("b"), 1)
# works on strings
f = exclude_if_more("ACGU", 5) # positive
self.assertEqual(f(""), 1)
self.assertEqual(f("ACGUAGCUioooNNNNNA"), 0)
self.assertEqual(f("NNNNNNN"), 1)
# works on words
f = exclude_if_more(["foo"], 1)
self.assertEqual(f(""), 1)
self.assertEqual(f(["foo", "bar", "foo"]), 0)
self.assertEqual(f(["joe"]), 1)
# works on numbers
f = exclude_if_more([0, 1], 3)
self.assertEqual(f(""), 1)
self.assertEqual(f([0, 1, 2, 3, 4, 5]), 1)
self.assertEqual(f([0, 1, 0, 1]), 0)
