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_all(self):
"""find_all should be True if all words appear in the string"""
f = find_all('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'),0) #one of the elements
self.assertEqual(f('bxxx'),0) #one of the elements
self.assertEqual(f('axxxb'),1) #all elements
self.assertEqual(f('aaaa'),0) #repeated element
# works on any sequence
f = find_all(['foo','bar'])
self.assertEqual(f("joe"),0)
self.assertEqual(f("only foo"),0)
self.assertEqual(f("bar and foo"),1)
def test_find_all(self):
"""find_all should be True if all words appear in the string"""
f = find_all('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'), 0) #one of the elements
self.assertEqual(f('bxxx'), 0) #one of the elements
self.assertEqual(f('axxxb'), 1) #all elements
self.assertEqual(f('aaaa'), 0) #repeated element
# works on any sequence
f = find_all(['foo', 'bar'])
self.assertEqual(f("joe"), 0)
self.assertEqual(f("only foo"), 0)
self.assertEqual(f("bar and foo"), 1)
def test_find_all(self):
"""find_all should be True if all words appear in the string"""
f = find_all("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"), 0) # one of the elements
self.assertEqual(f("bxxx"), 0) # one of the elements
self.assertEqual(f("axxxb"), 1) # all elements
self.assertEqual(f("aaaa"), 0) # repeated element
# works on any sequence
f = find_all(["foo", "bar"])
self.assertEqual(f("joe"), 0)
self.assertEqual(f("only foo"), 0)
self.assertEqual(f("bar and foo"), 1)
def test_init(self):
"""Filter should init as expected"""
empty_filter = Filter('',{})
named_empty_filter = Filter('Archaea',{})
self.assertEqual(empty_filter,{})
self.assertEqual(empty_filter.Name,'')
self.assertEqual(named_empty_filter,{})
self.assertEqual(named_empty_filter.Name,'Archaea')
f = find_all('abcd')
g = keep_if_more_other('ab',7)
fil = Filter('Archaea',{'Arch':[f,g]})
assert fil['Arch'][0] is f
assert fil['Arch'][1] is g
def test_init(self):
"""Filter should init as expected"""
empty_filter = Filter('', {})
named_empty_filter = Filter('Archaea', {})
self.assertEqual(empty_filter, {})
self.assertEqual(empty_filter.Name, '')
self.assertEqual(named_empty_filter, {})
self.assertEqual(named_empty_filter.Name, 'Archaea')
f = find_all('abcd')
g = keep_if_more_other('ab', 7)
fil = Filter('Archaea', {'Arch': [f, g]})
assert fil['Arch'][0] is f
assert fil['Arch'][1] is g
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)