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_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_empty(self):
"""Empty Filter should return True when called on anything"""
f = Filter('', {})
data = ['aa', 'bb', 'cc']
self.assertEqual(f(data), True)